configure.ac:20: installing './ar-lib' configure.ac:20: installing './compile' configure.ac:74: installing './config.guess' configure.ac:74: installing './config.sub' configure.ac:8: installing './install-sh' configure.ac:8: installing './missing' src/Makefile.am: installing './depcomp' ack-desc... 0%100%100%100%100%100%Done Fetching tophat.SlackBuild... 0%100%100%100%100%100%Done Fetching tophat.info... 0%100%100%100%100%100%Done tophat-2.1.2/ tophat-2.1.2/.gitignore tophat-2.1.2/AUTHORS tophat-2.1.2/ChangeLog tophat-2.1.2/INSTALL tophat-2.1.2/LICENSE tophat-2.1.2/Makefile.am tophat-2.1.2/NEWS tophat-2.1.2/README tophat-2.1.2/THANKS tophat-2.1.2/TopHat.xcodeproj/ tophat-2.1.2/TopHat.xcodeproj/cole.pbxuser tophat-2.1.2/TopHat.xcodeproj/cole.perspectivev3 tophat-2.1.2/TopHat.xcodeproj/project.pbxproj tophat-2.1.2/autogen.sh tophat-2.1.2/ax_bam.m4 tophat-2.1.2/ax_boost_base.m4 tophat-2.1.2/ax_boost_thread.m4 tophat-2.1.2/ax_check_zlib.m4 tophat-2.1.2/bootstrap tophat-2.1.2/configure.ac tophat-2.1.2/doc/ tophat-2.1.2/doc/html/ tophat-2.1.2/doc/html/add.css tophat-2.1.2/doc/html/css/ tophat-2.1.2/doc/html/css/style.css tophat-2.1.2/doc/html/data/ tophat-2.1.2/doc/html/data/TopHatFusion-poster.pdf tophat-2.1.2/doc/html/data/fusions.out tophat-2.1.2/doc/html/data/mcl tophat-2.1.2/doc/html/data/result.html tophat-2.1.2/doc/html/data/sample_info.txt tophat-2.1.2/doc/html/downloads/ tophat-2.1.2/doc/html/downloads/test_data.zip tophat-2.1.2/doc/html/downloads/tophat-0.7.0.tar.gz tophat-2.1.2/doc/html/faq.html tophat-2.1.2/doc/html/faq.shtml tophat-2.1.2/doc/html/footer.inc.html tophat-2.1.2/doc/html/fusion_index.html tophat-2.1.2/doc/html/fusion_index.shtml tophat-2.1.2/doc/html/fusion_manual.html tophat-2.1.2/doc/html/fusion_manual.shtml tophat-2.1.2/doc/html/fusion_tutorial.html tophat-2.1.2/doc/html/fusion_tutorial.shtml tophat-2.1.2/doc/html/igenome/ tophat-2.1.2/doc/html/igenome/igenome_table.py tophat-2.1.2/doc/html/igenomes.html tophat-2.1.2/doc/html/igenomes.shtml tophat-2.1.2/doc/html/images/ tophat-2.1.2/doc/html/images/IGM_log.png tophat-2.1.2/doc/html/images/IGM_logo.png tophat-2.1.2/doc/html/images/JHU-seal.gif tophat-2.1.2/doc/html/images/UCBerkeley-seal.gif tophat-2.1.2/doc/html/images/UCBerkeley-seal.scaled.gif tophat-2.1.2/doc/html/images/UW_Seal_University_of_Washington.jpg tophat-2.1.2/doc/html/images/bg.jpg tophat-2.1.2/doc/html/images/bluec_l.gif tophat-2.1.2/doc/html/images/bluec_r.gif tophat-2.1.2/doc/html/images/cbcb_logo.gif tophat-2.1.2/doc/html/images/cbcblogo.gif tophat-2.1.2/doc/html/images/cbcblogo.jpg tophat-2.1.2/doc/html/images/cbcblogoandtext.gif tophat-2.1.2/doc/html/images/cbcbstrip.jpg tophat-2.1.2/doc/html/images/ccblogo_ondark.png tophat-2.1.2/doc/html/images/ccblogo_wbg.png tophat-2.1.2/doc/html/images/ccbstrip.jpg tophat-2.1.2/doc/html/images/ccbstrip.png tophat-2.1.2/doc/html/images/ccbtext_wbg.png tophat-2.1.2/doc/html/images/footer.jpg tophat-2.1.2/doc/html/images/greyc.gif tophat-2.1.2/doc/html/images/head.gif tophat-2.1.2/doc/html/images/menu.jpg tophat-2.1.2/doc/html/images/menul.jpg tophat-2.1.2/doc/html/images/menur.jpg tophat-2.1.2/doc/html/images/osi-certified.gif tophat-2.1.2/doc/html/images/sep.gif tophat-2.1.2/doc/html/images/top.jpg tophat-2.1.2/doc/html/images/topl.jpg tophat-2.1.2/doc/html/images/topr.jpg tophat-2.1.2/doc/html/images/ucsc-track.jpg tophat-2.1.2/doc/html/images/ucsc-track.tiff tophat-2.1.2/doc/html/images/univ_washington.png tophat-2.1.2/doc/html/index.html tophat-2.1.2/doc/html/index.shtml tophat-2.1.2/doc/html/manual.html tophat-2.1.2/doc/html/manual.shtml tophat-2.1.2/doc/html/push_ctrapnell.sh tophat-2.1.2/doc/html/push_forephilo.sh tophat-2.1.2/doc/html/sidebar.inc.shtml tophat-2.1.2/doc/html/topbar.inc.shtml tophat-2.1.2/doc/html/tutorial.html tophat-2.1.2/doc/html/tutorial.shtml tophat-2.1.2/fusion_test/ tophat-2.1.2/fusion_test/run_test.sh tophat-2.1.2/fusion_test/test_fusion_inter.fasta tophat-2.1.2/fusion_test/test_fusion_inter2.fasta tophat-2.1.2/fusion_test/test_fusion_intra.fasta tophat-2.1.2/fusion_test/test_fusion_intra2.fasta tophat-2.1.2/fusion_test/test_indel_inter.fasta tophat-2.1.2/fusion_test/test_indel_inter2.fasta tophat-2.1.2/fusion_test/test_indel_intra.fasta tophat-2.1.2/fusion_test/test_indel_intra2.fasta tophat-2.1.2/fusion_test/test_junction_inter.fasta tophat-2.1.2/fusion_test/test_junction_inter2.fasta tophat-2.1.2/fusion_test/test_junction_intra.fasta tophat-2.1.2/fusion_test/test_junction_intra2.fasta tophat-2.1.2/fusion_test/test_total_inter.fasta tophat-2.1.2/fusion_test/test_total_inter2.fasta tophat-2.1.2/fusion_test/test_total_intra.fasta tophat-2.1.2/fusion_test/test_total_intra2.fasta tophat-2.1.2/fusion_test/testcases/ tophat-2.1.2/fusion_test/testcases/generate_fasta tophat-2.1.2/fusion_test/testcases/test.1.ebwt tophat-2.1.2/fusion_test/testcases/test.2.ebwt tophat-2.1.2/fusion_test/testcases/test.3.ebwt tophat-2.1.2/fusion_test/testcases/test.4.ebwt tophat-2.1.2/fusion_test/testcases/test.fa tophat-2.1.2/fusion_test/testcases/test.rev.1.ebwt tophat-2.1.2/fusion_test/testcases/test.rev.2.ebwt tophat-2.1.2/git_revision.sh tophat-2.1.2/make_bin.sh tophat-2.1.2/make_src.sh tophat-2.1.2/src/ tophat-2.1.2/src/FastaTools.cpp tophat-2.1.2/src/FastaTools.h tophat-2.1.2/src/GBase.cpp tophat-2.1.2/src/GBase.h tophat-2.1.2/src/GFaSeqGet.cpp tophat-2.1.2/src/GFaSeqGet.h tophat-2.1.2/src/GHash.hh tophat-2.1.2/src/GList.hh tophat-2.1.2/src/GStr.cpp tophat-2.1.2/src/GStr.h tophat-2.1.2/src/GTFToFasta.cpp tophat-2.1.2/src/GTFToFasta.h tophat-2.1.2/src/GVec.hh tophat-2.1.2/src/Makefile.am tophat-2.1.2/src/Makefile.nolibs tophat-2.1.2/src/SeqAn-1.4.2/ tophat-2.1.2/src/SeqAn-1.4.2/LICENSE tophat-2.1.2/src/SeqAn-1.4.2/README.rst tophat-2.1.2/src/SeqAn-1.4.2/seqan/ tophat-2.1.2/src/SeqAn-1.4.2/seqan/LICENSE tophat-2.1.2/src/SeqAn-1.4.2/seqan/align.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/ tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/INFO tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/align_base.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/align_cols.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/align_config.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/align_iterator_base.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/align_metafunctions.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/align_traceback.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/alignment_algorithm_tags.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/alignment_operations.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/dp_algorithm_impl.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/dp_band.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/dp_cell.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/dp_cell_affine.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/dp_cell_linear.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/dp_formula.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/dp_formula_affine.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/dp_formula_linear.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/dp_matrix.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/dp_matrix_navigator.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/dp_matrix_navigator_score_matrix.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/dp_matrix_navigator_score_matrix_sparse.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/dp_matrix_navigator_trace_matrix.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/dp_matrix_sparse.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/dp_meta_info.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/dp_profile.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/dp_scout.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/dp_setup.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/dp_trace_segment.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/dp_traceback_adaptor.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/dp_traceback_impl.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/evaluate_alignment.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/gap_anchor.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/gapped_value_type.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/gaps_anchor.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/gaps_array.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/gaps_base.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/gaps_iterator_anchor.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/gaps_iterator_array.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/gaps_iterator_base.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/global_alignment_banded.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/global_alignment_hirschberg_impl.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/global_alignment_myers_hirschberg_impl.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/global_alignment_myers_impl.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/global_alignment_specialized.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/global_alignment_unbanded.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/local_alignment_banded.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/local_alignment_banded_waterman_eggert_impl.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/local_alignment_enumeration.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/local_alignment_enumeration_banded.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/local_alignment_enumeration_unbanded.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/local_alignment_unbanded.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/local_alignment_waterman_eggert_impl.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/align/matrix_base.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/arg_parse.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/arg_parse/ tophat-2.1.2/src/SeqAn-1.4.2/seqan/arg_parse/INFO tophat-2.1.2/src/SeqAn-1.4.2/seqan/arg_parse/arg_parse_argument.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/arg_parse/arg_parse_ctd_support.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/arg_parse/arg_parse_doc.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/arg_parse/arg_parse_exceptions.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/arg_parse/arg_parse_option.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/arg_parse/arg_parse_parse.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/arg_parse/arg_parse_type_support.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/arg_parse/argument_parser.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/arg_parse/tool_doc.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/arg_parse/xml_support.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/bam_io.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/bam_io/ tophat-2.1.2/src/SeqAn-1.4.2/seqan/bam_io/INFO tophat-2.1.2/src/SeqAn-1.4.2/seqan/bam_io/bam_alignment_record.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/bam_io/bam_alignment_record_util.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/bam_io/bam_header_record.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/bam_io/bam_index_bai.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/bam_io/bam_index_base.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/bam_io/bam_io_context.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/bam_io/bam_reader.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/bam_io/bam_sam_conversion.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/bam_io/bam_stream.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/bam_io/bam_tags_dict.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/bam_io/bam_writer.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/bam_io/cigar.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/bam_io/read_bam.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/bam_io/read_sam.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/bam_io/sam_reader.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/bam_io/sam_writer.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/bam_io/write_bam.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/bam_io/write_sam.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/bam_io/xam_reader.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/bam_io/xam_writer.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/ tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/INFO tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/aggregate_concept.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/allocator_chunkpool.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/allocator_interface.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/allocator_multipool.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/allocator_simple.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/allocator_singlepool.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/allocator_to_std.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/alphabet_adapt_builtins.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/alphabet_bio.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/alphabet_concept.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/alphabet_math.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/alphabet_profile.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/alphabet_qualities.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/alphabet_residue.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/alphabet_residue_funcs.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/alphabet_residue_tabs.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/alphabet_simple_type.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/alphabet_storage.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/array_construct_destruct.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/basic_aggregate.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/basic_allocator.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/basic_alphabet.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/basic_concept.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/basic_container.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/basic_debug.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/basic_exception.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/basic_fundamental.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/basic_iterator.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/basic_math.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/basic_metaprogramming.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/basic_parallelism.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/basic_proxy.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/basic_smart_pointer.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/basic_tangle.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/basic_type.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/boost_preprocessor_subset.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/builtin_functions.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/concept_checking.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/container_concept.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/debug_helper.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/debug_test_system.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/fundamental_comparison.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/fundamental_concepts.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/fundamental_conversion.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/fundamental_metafunctions.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/fundamental_tags.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/fundamental_transport.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/holder_base.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/holder_simple.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/holder_tristate.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/hosted_type_interface.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/iterator_adapt_pointer.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/iterator_adapt_std.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/iterator_adaptor.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/iterator_base.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/iterator_concept.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/iterator_interface.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/iterator_position.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/macro_deprecated.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/math_functions.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/math_log_space_value.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/metaprogramming_control.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/metaprogramming_enable_if.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/metaprogramming_logic.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/metaprogramming_math.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/metaprogramming_type.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/pair_base.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/pair_bit_compressed.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/pair_packed.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/profiling.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/proxy_base.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/proxy_iterator.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/test_system.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/triple_base.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/triple_packed.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/tuple_base.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/tuple_bit_compressed.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/basic/volatile_ptr.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/consensus.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/consensus/ tophat-2.1.2/src/SeqAn-1.4.2/seqan/consensus/INFO tophat-2.1.2/src/SeqAn-1.4.2/seqan/consensus/consensus_base.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/consensus/consensus_library.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/consensus/consensus_realign.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/consensus/consensus_score.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/file.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/file/ tophat-2.1.2/src/SeqAn-1.4.2/seqan/file/INFO tophat-2.1.2/src/SeqAn-1.4.2/seqan/file/chunk_collector.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/file/cstream.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/file/file_base.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/file/file_cstyle.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/file/file_filereader.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/file/file_filereaderiterator.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/file/file_format.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/file/file_format_cgviz.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/file/file_format_embl.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/file/file_format_fasta.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/file/file_format_fasta_align.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/file/file_format_genbank.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/file/file_format_guess.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/file/file_format_mmap.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/file/file_format_raw.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/file/file_forwards.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/file/file_interface.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/file/file_mapping.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/file/file_page.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/file/meta.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/file/stream.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/file/stream_algorithms.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/file/string_external.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/file/string_mmap.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/find.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/find/ tophat-2.1.2/src/SeqAn-1.4.2/seqan/find/INFO tophat-2.1.2/src/SeqAn-1.4.2/seqan/find/find_abndm.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/find/find_ahocorasick.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/find/find_base.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/find/find_begin.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/find/find_bndm.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/find/find_bom.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/find/find_hamming_simple.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/find/find_horspool.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/find/find_multi.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/find/find_multiple_bfam.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/find/find_multiple_shiftand.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/find/find_myers_ukkonen.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/find/find_pattern_base.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/find/find_pex.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/find/find_score.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/find/find_set_horspool.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/find/find_shiftand.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/find/find_shiftor.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/find/find_simple.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/find/find_wild_shiftand.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/find/find_wumanber.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/gff_io.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/gff_io/ tophat-2.1.2/src/SeqAn-1.4.2/seqan/gff_io/INFO tophat-2.1.2/src/SeqAn-1.4.2/seqan/gff_io/gff_io_base.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/gff_io/gff_io_context.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/gff_io/gff_stream.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_algorithms.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_algorithms/ tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_algorithms/INFO tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_algorithms/graph_algorithm.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_algorithms/graph_algorithm_heap_tree.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_algorithms/graph_algorithm_hmm.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_algorithms/graph_algorithm_lis_his.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_align.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_align/ tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_align/INFO tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_align/graph_algorithm_refine_align.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_align/graph_algorithm_refine_aligngraph.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_align/graph_algorithm_refine_annotation.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_align/graph_algorithm_refine_exact.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_align/graph_algorithm_refine_exact_iterative.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_align/graph_algorithm_refine_fragment.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_align/graph_algorithm_refine_inexact.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_align/graph_algorithm_refine_scoring.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_align/graph_impl_align.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_align/graph_impl_align_adapt.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_msa.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_msa/ tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_msa/INFO tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_msa/graph_align_tcoffee_base.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_msa/graph_align_tcoffee_distance.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_msa/graph_align_tcoffee_guidetree.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_msa/graph_align_tcoffee_io.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_msa/graph_align_tcoffee_kmer.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_msa/graph_align_tcoffee_library.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_msa/graph_align_tcoffee_msa.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_msa/graph_align_tcoffee_progressive.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_msa/graph_align_tcoffee_refinement.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_types.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_types/ tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_types/INFO tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_types/graph_base.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_types/graph_drawing.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_types/graph_edgestump.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_types/graph_idmanager.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_types/graph_impl_automaton.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_types/graph_impl_directed.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_types/graph_impl_fragment.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_types/graph_impl_hmm.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_types/graph_impl_oracle.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_types/graph_impl_tree.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_types/graph_impl_trie.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_types/graph_impl_undirected.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_types/graph_impl_wordgraph.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_types/graph_interface.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_types/graph_iterator.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_types/graph_iterator_adjacency.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_types/graph_iterator_bfs.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_types/graph_iterator_dfs.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_types/graph_iterator_edge.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_types/graph_iterator_outedge.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_types/graph_iterator_vertex.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_types/graph_property.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/graph_types/graph_utility_parsing.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/ tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/INFO tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/find_index.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/find_index_approx.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/find_index_esa.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/find_index_qgram.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/find_pigeonhole.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/find_quasar.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/find_swift.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_base.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_bwt.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_childtab.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_dfi.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_esa_algs.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_esa_algs_multi.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_esa_base.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_esa_drawing.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_esa_stree.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_fm.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_fm_compressed_sa.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_fm_compressed_sa_iterator.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_fm_doc.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_fm_dox.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_fm_lf_table.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_fm_prefix_sum_table.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_fm_rank_dictionary_bms.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_fm_rank_dictionary_wt.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_fm_rank_support_bit_string.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_fm_rank_support_bit_string_iterator.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_fm_right_array_binary_tree.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_fm_right_array_binary_tree_iterator.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_fm_sentinel_rank_dictionary.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_fm_sparse_string.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_fm_stree.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_forwards.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_lcp.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_lcp_tree.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_pizzachili.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_pizzachili_find.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_pizzachili_string.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_qgram.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_qgram_openaddressing.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_sa_btree.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_sa_bwtwalk.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_sa_lss.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_sa_mm.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_sa_qsort.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_shawarma.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_shims.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_skew3.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_skew7.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_skew7_multi.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/index_wotd.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/pipe_merger3.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/pipe_merger7.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/pizzachili_api.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/pump_extender3.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/pump_extender7.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/pump_lcp_core.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/pump_separator7.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/radix.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/repeat_base.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/shape_base.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/shape_gapped.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/shape_onegapped.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/shape_predefined.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/index/shape_threshold.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/map.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/map/ tophat-2.1.2/src/SeqAn-1.4.2/seqan/map/INFO tophat-2.1.2/src/SeqAn-1.4.2/seqan/map/map_adapter_stl.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/map/map_base.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/map/map_chooser.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/map/map_skiplist.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/map/map_vector.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/map/sumlist.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/map/sumlist_mini.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/map/sumlist_skip.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/misc/ tophat-2.1.2/src/SeqAn-1.4.2/seqan/misc/INFO tophat-2.1.2/src/SeqAn-1.4.2/seqan/misc/cmdparser/ tophat-2.1.2/src/SeqAn-1.4.2/seqan/misc/cmdparser/INFO tophat-2.1.2/src/SeqAn-1.4.2/seqan/misc/cmdparser/cmdoption.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/misc/cmdparser/cmdparser.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/misc/cmdparser/cmdparser_ctd_support.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/misc/cmdparser/cmdparser_parse.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/misc/cmdparser/cmdparser_type_support.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/misc/edit_environment.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/misc/misc_accumulators.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/misc/misc_base.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/misc/misc_bit_twiddling.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/misc/misc_cmdparser.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/misc/misc_dequeue.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/misc/misc_interval_tree.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/misc/misc_map.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/misc/misc_memset.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/misc/misc_name_store_cache.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/misc/misc_parsing.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/misc/misc_set.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/misc/misc_sse2.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/misc/misc_svg.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/misc/misc_terminal.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/misc/misc_union_find.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/misc/priority_type_base.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/misc/priority_type_heap.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/modifier.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/modifier/ tophat-2.1.2/src/SeqAn-1.4.2/seqan/modifier/INFO tophat-2.1.2/src/SeqAn-1.4.2/seqan/modifier/modifier_alphabet.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/modifier/modifier_alphabet_expansion.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/modifier/modifier_functors.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/modifier/modifier_iterator.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/modifier/modifier_reverse.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/modifier/modifier_shortcuts.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/modifier/modifier_string.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/modifier/modifier_view.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/parallel.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/parallel/ tophat-2.1.2/src/SeqAn-1.4.2/seqan/parallel/INFO tophat-2.1.2/src/SeqAn-1.4.2/seqan/parallel/parallel_algorithms.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/parallel/parallel_atomic_misc.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/parallel/parallel_atomic_primitives.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/parallel/parallel_macros.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/parallel/parallel_splitting.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/parallel/parallel_tags.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/pipe.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/pipe/ tophat-2.1.2/src/SeqAn-1.4.2/seqan/pipe/INFO tophat-2.1.2/src/SeqAn-1.4.2/seqan/pipe/pipe_base.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/pipe/pipe_caster.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/pipe/pipe_counter.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/pipe/pipe_echoer.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/pipe/pipe_edit_environment.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/pipe/pipe_filter.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/pipe/pipe_iterator.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/pipe/pipe_joiner.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/pipe/pipe_namer.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/pipe/pipe_sampler.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/pipe/pipe_shifter.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/pipe/pipe_source.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/pipe/pipe_tupler.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/pipe/pool_base.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/pipe/pool_mapper.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/pipe/pool_sorter.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/platform.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/platform/ tophat-2.1.2/src/SeqAn-1.4.2/seqan/platform/INFO tophat-2.1.2/src/SeqAn-1.4.2/seqan/platform/platform_gcc.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/platform/platform_icc.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/platform/platform_mingw.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/platform/platform_nvcc.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/platform/platform_pgi.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/platform/platform_solaris.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/platform/platform_windows.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/platform/windows_stdint.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/random.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/random/ tophat-2.1.2/src/SeqAn-1.4.2/seqan/random/INFO tophat-2.1.2/src/SeqAn-1.4.2/seqan/random/ext_MersenneTwister.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/random/random_base.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/random/random_beta.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/random/random_beta_kfunc.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/random/random_geometric.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/random/random_lognormal.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/random/random_mt19937.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/random/random_normal.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/random/random_rng_functor.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/random/random_shuffle.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/random/random_uniform.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/score.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/score/ tophat-2.1.2/src/SeqAn-1.4.2/seqan/score/INFO tophat-2.1.2/src/SeqAn-1.4.2/seqan/score/score_base.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/score/score_edit.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/score/score_matrix.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/score/score_matrix_data.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/score/score_matrix_io.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/score/score_simple.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/seeds.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/seeds/ tophat-2.1.2/src/SeqAn-1.4.2/seqan/seeds/INFO tophat-2.1.2/src/SeqAn-1.4.2/seqan/seeds/banded_chain_alignment.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/seeds/banded_chain_alignment_impl.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/seeds/banded_chain_alignment_profile.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/seeds/banded_chain_alignment_scout.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/seeds/banded_chain_alignment_traceback.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/seeds/basic_iter_indirect.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/seeds/seeds_base.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/seeds/seeds_combination.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/seeds/seeds_extension.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/seeds/seeds_global_chaining.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/seeds/seeds_global_chaining_base.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/seeds/seeds_global_chaining_gusfield.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/seeds/seeds_seed_base.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/seeds/seeds_seed_chained.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/seeds/seeds_seed_diagonal.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/seeds/seeds_seed_set_base.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/seeds/seeds_seed_set_non_scored.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/seeds/seeds_seed_set_scored.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/seeds/seeds_seed_set_unordered.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/seeds/seeds_seed_simple.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/seq_io.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/seq_io/ tophat-2.1.2/src/SeqAn-1.4.2/seqan/seq_io/INFO tophat-2.1.2/src/SeqAn-1.4.2/seqan/seq_io/fai_index.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/seq_io/genomic_region.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/seq_io/guess_stream_format.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/seq_io/read_embl.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/seq_io/read_fasta_fastq.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/seq_io/read_genbank.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/seq_io/sequence_stream.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/seq_io/sequence_stream_impl.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/seq_io/simple_read_fasta.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/seq_io/write_fasta_fastq.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/sequence.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/sequence/ tophat-2.1.2/src/SeqAn-1.4.2/seqan/sequence/INFO tophat-2.1.2/src/SeqAn-1.4.2/seqan/sequence/adapt_array_pointer.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/sequence/adapt_std_list.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/sequence/adapt_std_string.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/sequence/adapt_std_vector.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/sequence/iter_concat_virtual.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/sequence/segment_base.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/sequence/segment_infix.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/sequence/segment_prefix.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/sequence/segment_suffix.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/sequence/segment_utils.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/sequence/sequence_concatenator.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/sequence/sequence_forwards.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/sequence/sequence_interface.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/sequence/sequence_lexical.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/sequence/sequence_shortcuts.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/sequence/string_alloc.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/sequence/string_array.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/sequence/string_base.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/sequence/string_block.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/sequence/string_cstyle.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/sequence/string_packed.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/sequence/string_packed_old.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/sequence/string_set_base.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/sequence/string_set_concat_direct.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/sequence/string_set_dependent_generous.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/sequence/string_set_dependent_tight.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/sequence/string_set_owner.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/sequence_journaled.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/sequence_journaled/ tophat-2.1.2/src/SeqAn-1.4.2/seqan/sequence_journaled/INFO tophat-2.1.2/src/SeqAn-1.4.2/seqan/sequence_journaled/journal_entries_sorted_array.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/sequence_journaled/journal_entries_unbalanced_tree.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/sequence_journaled/journal_entries_unbalanced_tree_iterator.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/sequence_journaled/journal_entries_unbalanced_tree_node.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/sequence_journaled/journal_entry.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/sequence_journaled/sequence_journaled.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/sequence_journaled/sequence_journaled_iterator.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/store.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/store/ tophat-2.1.2/src/SeqAn-1.4.2/seqan/store/INFO tophat-2.1.2/src/SeqAn-1.4.2/seqan/store/store_align.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/store/store_align_intervals.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/store/store_all.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/store/store_annotation.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/store/store_base.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/store/store_contig.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/store/store_intervaltree.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/store/store_io.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/store/store_io_gff.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/store/store_io_sam.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/store/store_io_ucsc.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/store/store_library.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/store/store_matepair.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/store/store_read.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/stream.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/stream/ tophat-2.1.2/src/SeqAn-1.4.2/seqan/stream/INFO tophat-2.1.2/src/SeqAn-1.4.2/seqan/stream/adapt_cstdio.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/stream/adapt_fstream.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/stream/adapt_iostream.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/stream/adapt_mmap.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/stream/adapt_sstream.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/stream/concept_stream.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/stream/file_stream.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/stream/is.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/stream/lexical_cast.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/stream/read.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/stream/read_auto_format.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/stream/read_sam.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/stream/record_reader_base.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/stream/record_reader_double.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/stream/record_reader_double_mmap.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/stream/record_reader_single.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/stream/record_reader_single_mmap.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/stream/stream_base.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/stream/stream_bgzf.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/stream/stream_bz2_file.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/stream/stream_char_array.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/stream/stream_gz_file.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/stream/stream_put.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/stream/tokenize.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/stream/write.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/system.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/system/ tophat-2.1.2/src/SeqAn-1.4.2/seqan/system/INFO tophat-2.1.2/src/SeqAn-1.4.2/seqan/system/file_async.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/system/file_directory.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/system/file_forwards.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/system/file_sync.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/system/system_base.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/system/system_event.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/system/system_forwards.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/system/system_mutex.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/system/system_sema.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/system/system_thread.h tophat-2.1.2/src/SeqAn-1.4.2/seqan/version.h tophat-2.1.2/src/align_status.cpp tophat-2.1.2/src/align_status.h tophat-2.1.2/src/alphabet.c tophat-2.1.2/src/alphabet.h tophat-2.1.2/src/assert_helpers.h tophat-2.1.2/src/bam2fastx.cpp tophat-2.1.2/src/bam_merge.cpp tophat-2.1.2/src/bam_merge.h tophat-2.1.2/src/bam_merge_impl.cpp tophat-2.1.2/src/bed_to_juncs tophat-2.1.2/src/bwt_map.cpp tophat-2.1.2/src/bwt_map.h tophat-2.1.2/src/closures.cpp tophat-2.1.2/src/closures.h tophat-2.1.2/src/codons.cpp tophat-2.1.2/src/codons.h tophat-2.1.2/src/common.cpp tophat-2.1.2/src/common.h tophat-2.1.2/src/contig_to_chr_coords tophat-2.1.2/src/coverage.cpp tophat-2.1.2/src/coverage.h tophat-2.1.2/src/deletions.cpp tophat-2.1.2/src/deletions.h tophat-2.1.2/src/extract_reads.cpp tophat-2.1.2/src/fix_map_ordering.cpp tophat-2.1.2/src/fragments.cpp tophat-2.1.2/src/fragments.h tophat-2.1.2/src/fusions.cpp tophat-2.1.2/src/fusions.h tophat-2.1.2/src/gdna.cpp tophat-2.1.2/src/gdna.h tophat-2.1.2/src/generate_chromosome.py tophat-2.1.2/src/gff.cpp tophat-2.1.2/src/gff.h tophat-2.1.2/src/gtf_juncs.cpp tophat-2.1.2/src/insertions.cpp tophat-2.1.2/src/insertions.h tophat-2.1.2/src/inserts.cpp tophat-2.1.2/src/inserts.h tophat-2.1.2/src/intervaltree/ tophat-2.1.2/src/intervaltree/__init__.py tophat-2.1.2/src/intervaltree/interval.py tophat-2.1.2/src/intervaltree/intervaltree.py tophat-2.1.2/src/intervaltree/node.py tophat-2.1.2/src/juncs_db.cpp tophat-2.1.2/src/junctions.cpp tophat-2.1.2/src/junctions.h tophat-2.1.2/src/library_stats.cpp tophat-2.1.2/src/long_spanning_reads.cpp tophat-2.1.2/src/map2gtf.cpp tophat-2.1.2/src/map2gtf.h tophat-2.1.2/src/mask_sam.cpp tophat-2.1.2/src/prep_reads.cpp tophat-2.1.2/src/qual.cpp tophat-2.1.2/src/qual.h tophat-2.1.2/src/reads.cpp tophat-2.1.2/src/reads.h tophat-2.1.2/src/sam_juncs.cpp tophat-2.1.2/src/samtools-0.1.18/ tophat-2.1.2/src/samtools-0.1.18/AUTHORS tophat-2.1.2/src/samtools-0.1.18/COPYING tophat-2.1.2/src/samtools-0.1.18/ChangeLog tophat-2.1.2/src/samtools-0.1.18/INSTALL tophat-2.1.2/src/samtools-0.1.18/Makefile tophat-2.1.2/src/samtools-0.1.18/Makefile.mingw tophat-2.1.2/src/samtools-0.1.18/NEWS tophat-2.1.2/src/samtools-0.1.18/bam.c tophat-2.1.2/src/samtools-0.1.18/bam.h tophat-2.1.2/src/samtools-0.1.18/bam2bcf.c tophat-2.1.2/src/samtools-0.1.18/bam2bcf.h tophat-2.1.2/src/samtools-0.1.18/bam2bcf_indel.c tophat-2.1.2/src/samtools-0.1.18/bam2depth.c tophat-2.1.2/src/samtools-0.1.18/bam_aux.c tophat-2.1.2/src/samtools-0.1.18/bam_cat.c tophat-2.1.2/src/samtools-0.1.18/bam_color.c tophat-2.1.2/src/samtools-0.1.18/bam_endian.h tophat-2.1.2/src/samtools-0.1.18/bam_import.c tophat-2.1.2/src/samtools-0.1.18/bam_index.c tophat-2.1.2/src/samtools-0.1.18/bam_lpileup.c tophat-2.1.2/src/samtools-0.1.18/bam_mate.c tophat-2.1.2/src/samtools-0.1.18/bam_md.c tophat-2.1.2/src/samtools-0.1.18/bam_pileup.c tophat-2.1.2/src/samtools-0.1.18/bam_plcmd.c tophat-2.1.2/src/samtools-0.1.18/bam_reheader.c tophat-2.1.2/src/samtools-0.1.18/bam_rmdup.c tophat-2.1.2/src/samtools-0.1.18/bam_rmdupse.c tophat-2.1.2/src/samtools-0.1.18/bam_sort.c tophat-2.1.2/src/samtools-0.1.18/bam_stat.c tophat-2.1.2/src/samtools-0.1.18/bam_tview.c tophat-2.1.2/src/samtools-0.1.18/bamtk.c tophat-2.1.2/src/samtools-0.1.18/bcftools/ tophat-2.1.2/src/samtools-0.1.18/bcftools/Makefile tophat-2.1.2/src/samtools-0.1.18/bcftools/README tophat-2.1.2/src/samtools-0.1.18/bcftools/bcf.c tophat-2.1.2/src/samtools-0.1.18/bcftools/bcf.h tophat-2.1.2/src/samtools-0.1.18/bcftools/bcf.tex tophat-2.1.2/src/samtools-0.1.18/bcftools/bcf2qcall.c tophat-2.1.2/src/samtools-0.1.18/bcftools/bcfutils.c tophat-2.1.2/src/samtools-0.1.18/bcftools/call1.c tophat-2.1.2/src/samtools-0.1.18/bcftools/em.c tophat-2.1.2/src/samtools-0.1.18/bcftools/fet.c tophat-2.1.2/src/samtools-0.1.18/bcftools/index.c tophat-2.1.2/src/samtools-0.1.18/bcftools/kfunc.c tophat-2.1.2/src/samtools-0.1.18/bcftools/kmin.c tophat-2.1.2/src/samtools-0.1.18/bcftools/kmin.h tophat-2.1.2/src/samtools-0.1.18/bcftools/main.c tophat-2.1.2/src/samtools-0.1.18/bcftools/mut.c tophat-2.1.2/src/samtools-0.1.18/bcftools/prob1.c tophat-2.1.2/src/samtools-0.1.18/bcftools/prob1.h tophat-2.1.2/src/samtools-0.1.18/bcftools/vcf.c tophat-2.1.2/src/samtools-0.1.18/bcftools/vcfutils.pl tophat-2.1.2/src/samtools-0.1.18/bedidx.c tophat-2.1.2/src/samtools-0.1.18/bgzf.c tophat-2.1.2/src/samtools-0.1.18/bgzf.h tophat-2.1.2/src/samtools-0.1.18/bgzip.c tophat-2.1.2/src/samtools-0.1.18/cut_target.c tophat-2.1.2/src/samtools-0.1.18/errmod.c tophat-2.1.2/src/samtools-0.1.18/errmod.h tophat-2.1.2/src/samtools-0.1.18/examples/ tophat-2.1.2/src/samtools-0.1.18/examples/00README.txt tophat-2.1.2/src/samtools-0.1.18/examples/Makefile tophat-2.1.2/src/samtools-0.1.18/examples/bam2bed.c tophat-2.1.2/src/samtools-0.1.18/examples/calDepth.c tophat-2.1.2/src/samtools-0.1.18/examples/ex1.fa tophat-2.1.2/src/samtools-0.1.18/examples/ex1.sam.gz tophat-2.1.2/src/samtools-0.1.18/examples/toy.fa tophat-2.1.2/src/samtools-0.1.18/examples/toy.sam tophat-2.1.2/src/samtools-0.1.18/faidx.c tophat-2.1.2/src/samtools-0.1.18/faidx.h tophat-2.1.2/src/samtools-0.1.18/kaln.c tophat-2.1.2/src/samtools-0.1.18/kaln.h tophat-2.1.2/src/samtools-0.1.18/khash.h tophat-2.1.2/src/samtools-0.1.18/klist.h tophat-2.1.2/src/samtools-0.1.18/knetfile.c tophat-2.1.2/src/samtools-0.1.18/knetfile.h tophat-2.1.2/src/samtools-0.1.18/kprobaln.c tophat-2.1.2/src/samtools-0.1.18/kprobaln.h tophat-2.1.2/src/samtools-0.1.18/kseq.h tophat-2.1.2/src/samtools-0.1.18/ksort.h tophat-2.1.2/src/samtools-0.1.18/kstring.c tophat-2.1.2/src/samtools-0.1.18/kstring.h tophat-2.1.2/src/samtools-0.1.18/misc/ tophat-2.1.2/src/samtools-0.1.18/misc/HmmGlocal.java tophat-2.1.2/src/samtools-0.1.18/misc/Makefile tophat-2.1.2/src/samtools-0.1.18/misc/blast2sam.pl tophat-2.1.2/src/samtools-0.1.18/misc/bowtie2sam.pl tophat-2.1.2/src/samtools-0.1.18/misc/export2sam.pl tophat-2.1.2/src/samtools-0.1.18/misc/interpolate_sam.pl tophat-2.1.2/src/samtools-0.1.18/misc/maq2sam.c tophat-2.1.2/src/samtools-0.1.18/misc/md5.c tophat-2.1.2/src/samtools-0.1.18/misc/md5.h tophat-2.1.2/src/samtools-0.1.18/misc/md5fa.c tophat-2.1.2/src/samtools-0.1.18/misc/novo2sam.pl tophat-2.1.2/src/samtools-0.1.18/misc/psl2sam.pl tophat-2.1.2/src/samtools-0.1.18/misc/sam2vcf.pl tophat-2.1.2/src/samtools-0.1.18/misc/samtools.pl tophat-2.1.2/src/samtools-0.1.18/misc/seqtk.c tophat-2.1.2/src/samtools-0.1.18/misc/soap2sam.pl tophat-2.1.2/src/samtools-0.1.18/misc/varfilter.py tophat-2.1.2/src/samtools-0.1.18/misc/wgsim.c tophat-2.1.2/src/samtools-0.1.18/misc/wgsim_eval.pl tophat-2.1.2/src/samtools-0.1.18/misc/zoom2sam.pl tophat-2.1.2/src/samtools-0.1.18/phase.c tophat-2.1.2/src/samtools-0.1.18/razf.c tophat-2.1.2/src/samtools-0.1.18/razf.h tophat-2.1.2/src/samtools-0.1.18/razip.c tophat-2.1.2/src/samtools-0.1.18/sam.c tophat-2.1.2/src/samtools-0.1.18/sam.h tophat-2.1.2/src/samtools-0.1.18/sam_header.c tophat-2.1.2/src/samtools-0.1.18/sam_header.h tophat-2.1.2/src/samtools-0.1.18/sam_view.c tophat-2.1.2/src/samtools-0.1.18/sample.c tophat-2.1.2/src/samtools-0.1.18/sample.h tophat-2.1.2/src/samtools-0.1.18/samtools.1 tophat-2.1.2/src/samtools-0.1.18/win32/ tophat-2.1.2/src/samtools-0.1.18/win32/xcurses.h tophat-2.1.2/src/samtools-0.1.18/win32/zconf.h tophat-2.1.2/src/samtools-0.1.18/win32/zlib.h tophat-2.1.2/src/segment_juncs.cpp tophat-2.1.2/src/segments.h tophat-2.1.2/src/sortedcontainers/ tophat-2.1.2/src/sortedcontainers/__init__.py tophat-2.1.2/src/sortedcontainers/sorteddict.py tophat-2.1.2/src/sortedcontainers/sortedlist.py tophat-2.1.2/src/sortedcontainers/sortedlistwithkey.py tophat-2.1.2/src/sortedcontainers/sortedset.py tophat-2.1.2/src/sra_to_solid tophat-2.1.2/src/timer.h tophat-2.1.2/src/tokenize.cpp tophat-2.1.2/src/tokenize.h tophat-2.1.2/src/tophat-fusion-post tophat-2.1.2/src/tophat.py tophat-2.1.2/src/tophat2.sh tophat-2.1.2/src/tophat_reports.cpp tophat-2.1.2/src/utils.cpp tophat-2.1.2/src/utils.h tophat-2.1.2/src/wiggles.cpp tophat-2.1.2/src/wiggles.h tophat-2.1.2/tests/ tophat-2.1.2/tests/regression_tests/ tophat-2.1.2/tests/regression_tests/README.txt tophat-2.1.2/tests/regression_tests/regression_test.py tophat-2.1.2/tests/regression_tests/test_cases/ tophat-2.1.2/tests/regression_tests/test_cases/common_genomes/ tophat-2.1.2/tests/regression_tests/test_cases/common_genomes/fake.1.ebwt tophat-2.1.2/tests/regression_tests/test_cases/common_genomes/fake.2.ebwt tophat-2.1.2/tests/regression_tests/test_cases/common_genomes/fake.3.ebwt tophat-2.1.2/tests/regression_tests/test_cases/common_genomes/fake.4.ebwt tophat-2.1.2/tests/regression_tests/test_cases/common_genomes/fake.fa tophat-2.1.2/tests/regression_tests/test_cases/common_genomes/fake.fa.fai tophat-2.1.2/tests/regression_tests/test_cases/common_genomes/fake.rev.1.ebwt tophat-2.1.2/tests/regression_tests/test_cases/common_genomes/fake.rev.2.ebwt tophat-2.1.2/tests/regression_tests/test_cases/test_3Segment/ tophat-2.1.2/tests/regression_tests/test_cases/test_3Segment/command.txt tophat-2.1.2/tests/regression_tests/test_cases/test_3Segment/input/ tophat-2.1.2/tests/regression_tests/test_cases/test_3Segment/input/readOne.fq tophat-2.1.2/tests/regression_tests/test_cases/test_3Segment/input/readTwo.fq tophat-2.1.2/tests/regression_tests/test_cases/test_3Segment/tophat_out/ tophat-2.1.2/tests/regression_tests/test_cases/test_3Segment/tophat_out/accepted_hits.bam tophat-2.1.2/tests/regression_tests/test_cases/test_3Segment/tophat_out/accepted_hits.sam tophat-2.1.2/tests/regression_tests/test_cases/test_3Segment/tophat_out/deletions.bed tophat-2.1.2/tests/regression_tests/test_cases/test_3Segment/tophat_out/insertions.bed tophat-2.1.2/tests/regression_tests/test_cases/test_3Segment/tophat_out/junctions.bed tophat-2.1.2/tests/regression_tests/test_cases/test_3Segment/tophat_out/logs/ tophat-2.1.2/tests/regression_tests/test_cases/test_3Segment/tophat_out/logs/accepted_hits_bam_sort.log tophat-2.1.2/tests/regression_tests/test_cases/test_3Segment/tophat_out/logs/accepted_hits_sam_to_bam.log tophat-2.1.2/tests/regression_tests/test_cases/test_3Segment/tophat_out/logs/bowtie_build.log tophat-2.1.2/tests/regression_tests/test_cases/test_3Segment/tophat_out/logs/file2Ymfao.log tophat-2.1.2/tests/regression_tests/test_cases/test_3Segment/tophat_out/logs/file3r5aUS.log tophat-2.1.2/tests/regression_tests/test_cases/test_3Segment/tophat_out/logs/file8Oqtbf.log tophat-2.1.2/tests/regression_tests/test_cases/test_3Segment/tophat_out/logs/fileAZ9INz.log tophat-2.1.2/tests/regression_tests/test_cases/test_3Segment/tophat_out/logs/fileBZLdYU.log tophat-2.1.2/tests/regression_tests/test_cases/test_3Segment/tophat_out/logs/fileBi8MNU.log tophat-2.1.2/tests/regression_tests/test_cases/test_3Segment/tophat_out/logs/fileCB0d38.log tophat-2.1.2/tests/regression_tests/test_cases/test_3Segment/tophat_out/logs/fileDs7BpD.log tophat-2.1.2/tests/regression_tests/test_cases/test_3Segment/tophat_out/logs/fileELiTuC.log tophat-2.1.2/tests/regression_tests/test_cases/test_3Segment/tophat_out/logs/fileHuqgkl.log tophat-2.1.2/tests/regression_tests/test_cases/test_3Segment/tophat_out/logs/fileX6DUKF.log tophat-2.1.2/tests/regression_tests/test_cases/test_3Segment/tophat_out/logs/filebybGBo.log tophat-2.1.2/tests/regression_tests/test_cases/test_3Segment/tophat_out/logs/filemwiFIE.log tophat-2.1.2/tests/regression_tests/test_cases/test_3Segment/tophat_out/logs/filewmfFLY.log tophat-2.1.2/tests/regression_tests/test_cases/test_3Segment/tophat_out/logs/juncs_db.log tophat-2.1.2/tests/regression_tests/test_cases/test_3Segment/tophat_out/logs/long_spanning_reads.log tophat-2.1.2/tests/regression_tests/test_cases/test_3Segment/tophat_out/logs/prep_reads.log tophat-2.1.2/tests/regression_tests/test_cases/test_3Segment/tophat_out/logs/reports.log tophat-2.1.2/tests/regression_tests/test_cases/test_3Segment/tophat_out/logs/run.log tophat-2.1.2/tests/regression_tests/test_cases/test_3Segment/tophat_out/logs/segment_juncs.log tophat-2.1.2/tests/regression_tests/test_cases/test_IndelLowerCase/ tophat-2.1.2/tests/regression_tests/test_cases/test_IndelLowerCase/command.txt tophat-2.1.2/tests/regression_tests/test_cases/test_IndelLowerCase/input/ tophat-2.1.2/tests/regression_tests/test_cases/test_IndelLowerCase/input/fakeReads.fq tophat-2.1.2/tests/regression_tests/test_cases/test_IndelLowerCase/tophat_out/ tophat-2.1.2/tests/regression_tests/test_cases/test_IndelLowerCase/tophat_out/accepted_hits.bam tophat-2.1.2/tests/regression_tests/test_cases/test_IndelLowerCase/tophat_out/accepted_hits.sam tophat-2.1.2/tests/regression_tests/test_cases/test_IndelLowerCase/tophat_out/deletions.bed tophat-2.1.2/tests/regression_tests/test_cases/test_IndelLowerCase/tophat_out/insertions.bed tophat-2.1.2/tests/regression_tests/test_cases/test_IndelLowerCase/tophat_out/junctions.bed tophat-2.1.2/tests/regression_tests/test_cases/test_IndelLowerCase/tophat_out/logs/ tophat-2.1.2/tests/regression_tests/test_cases/test_IndelLowerCase/tophat_out/logs/accepted_hits_bam_sort.log tophat-2.1.2/tests/regression_tests/test_cases/test_IndelLowerCase/tophat_out/logs/accepted_hits_sam_to_bam.log tophat-2.1.2/tests/regression_tests/test_cases/test_IndelLowerCase/tophat_out/logs/bowtie_build.log tophat-2.1.2/tests/regression_tests/test_cases/test_IndelLowerCase/tophat_out/logs/fileFY1IyM.log tophat-2.1.2/tests/regression_tests/test_cases/test_IndelLowerCase/tophat_out/logs/fileGwBAwE.log tophat-2.1.2/tests/regression_tests/test_cases/test_IndelLowerCase/tophat_out/logs/fileQNmFjm.log tophat-2.1.2/tests/regression_tests/test_cases/test_IndelLowerCase/tophat_out/logs/filed9PQx2.log tophat-2.1.2/tests/regression_tests/test_cases/test_IndelLowerCase/tophat_out/logs/filenwquIq.log tophat-2.1.2/tests/regression_tests/test_cases/test_IndelLowerCase/tophat_out/logs/juncs_db.log tophat-2.1.2/tests/regression_tests/test_cases/test_IndelLowerCase/tophat_out/logs/long_spanning_reads.log tophat-2.1.2/tests/regression_tests/test_cases/test_IndelLowerCase/tophat_out/logs/prep_reads.log tophat-2.1.2/tests/regression_tests/test_cases/test_IndelLowerCase/tophat_out/logs/reports.log tophat-2.1.2/tests/regression_tests/test_cases/test_IndelLowerCase/tophat_out/logs/run.log tophat-2.1.2/tests/regression_tests/test_cases/test_IndelLowerCase/tophat_out/logs/segment_juncs.log tophat-2.1.2/tests/regression_tests/test_cases/test_IndelWithErrors/ tophat-2.1.2/tests/regression_tests/test_cases/test_IndelWithErrors/command.txt tophat-2.1.2/tests/regression_tests/test_cases/test_IndelWithErrors/input/ tophat-2.1.2/tests/regression_tests/test_cases/test_IndelWithErrors/input/fakeReads_errors.fq tophat-2.1.2/tests/regression_tests/test_cases/test_IndelWithErrors/tophat_out/ tophat-2.1.2/tests/regression_tests/test_cases/test_IndelWithErrors/tophat_out/accepted_hits.bam tophat-2.1.2/tests/regression_tests/test_cases/test_IndelWithErrors/tophat_out/accepted_hits.sam tophat-2.1.2/tests/regression_tests/test_cases/test_IndelWithErrors/tophat_out/deletions.bed tophat-2.1.2/tests/regression_tests/test_cases/test_IndelWithErrors/tophat_out/insertions.bed tophat-2.1.2/tests/regression_tests/test_cases/test_IndelWithErrors/tophat_out/junctions.bed tophat-2.1.2/tests/regression_tests/test_cases/test_IndelWithErrors/tophat_out/logs/ tophat-2.1.2/tests/regression_tests/test_cases/test_IndelWithErrors/tophat_out/logs/accepted_hits_bam_sort.log tophat-2.1.2/tests/regression_tests/test_cases/test_IndelWithErrors/tophat_out/logs/accepted_hits_sam_to_bam.log tophat-2.1.2/tests/regression_tests/test_cases/test_IndelWithErrors/tophat_out/logs/bowtie_build.log tophat-2.1.2/tests/regression_tests/test_cases/test_IndelWithErrors/tophat_out/logs/file0r5XKH.log tophat-2.1.2/tests/regression_tests/test_cases/test_IndelWithErrors/tophat_out/logs/fileISlgU4.log tophat-2.1.2/tests/regression_tests/test_cases/test_IndelWithErrors/tophat_out/logs/fileaRAfnk.log tophat-2.1.2/tests/regression_tests/test_cases/test_IndelWithErrors/tophat_out/logs/filesfXFTC.log tophat-2.1.2/tests/regression_tests/test_cases/test_IndelWithErrors/tophat_out/logs/filetDhGo5.log tophat-2.1.2/tests/regression_tests/test_cases/test_IndelWithErrors/tophat_out/logs/juncs_db.log tophat-2.1.2/tests/regression_tests/test_cases/test_IndelWithErrors/tophat_out/logs/long_spanning_reads.log tophat-2.1.2/tests/regression_tests/test_cases/test_IndelWithErrors/tophat_out/logs/prep_reads.log tophat-2.1.2/tests/regression_tests/test_cases/test_IndelWithErrors/tophat_out/logs/reports.log tophat-2.1.2/tests/regression_tests/test_cases/test_IndelWithErrors/tophat_out/logs/run.log tophat-2.1.2/tests/regression_tests/test_cases/test_IndelWithErrors/tophat_out/logs/segment_juncs.log tophat-2.1.2/tests/regression_tests/test_cases/test_Indel_1/ tophat-2.1.2/tests/regression_tests/test_cases/test_Indel_1/command.txt tophat-2.1.2/tests/regression_tests/test_cases/test_Indel_1/input/ tophat-2.1.2/tests/regression_tests/test_cases/test_Indel_1/input/fakeReads_read28.fq tophat-2.1.2/tests/regression_tests/test_cases/test_Indel_1/input/insertions.bed tophat-2.1.2/tests/regression_tests/test_cases/test_Indel_1/tophat_out/ tophat-2.1.2/tests/regression_tests/test_cases/test_Indel_1/tophat_out/accepted_hits.bam tophat-2.1.2/tests/regression_tests/test_cases/test_Indel_1/tophat_out/accepted_hits.sam tophat-2.1.2/tests/regression_tests/test_cases/test_Indel_1/tophat_out/deletions.bed tophat-2.1.2/tests/regression_tests/test_cases/test_Indel_1/tophat_out/insertions.bed tophat-2.1.2/tests/regression_tests/test_cases/test_Indel_1/tophat_out/junctions.bed tophat-2.1.2/tests/regression_tests/test_cases/test_Indel_1/tophat_out/logs/ tophat-2.1.2/tests/regression_tests/test_cases/test_Indel_1/tophat_out/logs/accepted_hits_bam_sort.log tophat-2.1.2/tests/regression_tests/test_cases/test_Indel_1/tophat_out/logs/accepted_hits_sam_to_bam.log tophat-2.1.2/tests/regression_tests/test_cases/test_Indel_1/tophat_out/logs/bowtie_build.log tophat-2.1.2/tests/regression_tests/test_cases/test_Indel_1/tophat_out/logs/file4j45mU.log tophat-2.1.2/tests/regression_tests/test_cases/test_Indel_1/tophat_out/logs/fileKCkgBq.log tophat-2.1.2/tests/regression_tests/test_cases/test_Indel_1/tophat_out/logs/fileV5MmJx.log tophat-2.1.2/tests/regression_tests/test_cases/test_Indel_1/tophat_out/logs/filefiPUuS.log tophat-2.1.2/tests/regression_tests/test_cases/test_Indel_1/tophat_out/logs/filelqUo6Y.log tophat-2.1.2/tests/regression_tests/test_cases/test_Indel_1/tophat_out/logs/juncs_db.log tophat-2.1.2/tests/regression_tests/test_cases/test_Indel_1/tophat_out/logs/long_spanning_reads.log tophat-2.1.2/tests/regression_tests/test_cases/test_Indel_1/tophat_out/logs/prep_reads.log tophat-2.1.2/tests/regression_tests/test_cases/test_Indel_1/tophat_out/logs/reports.log tophat-2.1.2/tests/regression_tests/test_cases/test_Indel_1/tophat_out/logs/run.log tophat-2.1.2/tests/regression_tests/test_cases/test_Indel_1/tophat_out/logs/segment_juncs.log tophat-2.1.2/tests/regression_tests/test_cases/test_Paired/ tophat-2.1.2/tests/regression_tests/test_cases/test_Paired/command.txt tophat-2.1.2/tests/regression_tests/test_cases/test_Paired/input/ tophat-2.1.2/tests/regression_tests/test_cases/test_Paired/input/readOne.fq tophat-2.1.2/tests/regression_tests/test_cases/test_Paired/input/readTwo.fq tophat-2.1.2/tests/regression_tests/test_cases/test_Paired/tophat_out/ tophat-2.1.2/tests/regression_tests/test_cases/test_Paired/tophat_out/accepted_hits.bam tophat-2.1.2/tests/regression_tests/test_cases/test_Paired/tophat_out/accepted_hits.sam tophat-2.1.2/tests/regression_tests/test_cases/test_Paired/tophat_out/deletions.bed tophat-2.1.2/tests/regression_tests/test_cases/test_Paired/tophat_out/insertions.bed tophat-2.1.2/tests/regression_tests/test_cases/test_Paired/tophat_out/junctions.bed tophat-2.1.2/tests/regression_tests/test_cases/test_Paired/tophat_out/logs/ tophat-2.1.2/tests/regression_tests/test_cases/test_Paired/tophat_out/logs/accepted_hits_bam_sort.log tophat-2.1.2/tests/regression_tests/test_cases/test_Paired/tophat_out/logs/accepted_hits_sam_to_bam.log tophat-2.1.2/tests/regression_tests/test_cases/test_Paired/tophat_out/logs/bowtie_build.log tophat-2.1.2/tests/regression_tests/test_cases/test_Paired/tophat_out/logs/file1obaLt.log tophat-2.1.2/tests/regression_tests/test_cases/test_Paired/tophat_out/logs/fileA5pHZh.log tophat-2.1.2/tests/regression_tests/test_cases/test_Paired/tophat_out/logs/fileC5MXPT.log tophat-2.1.2/tests/regression_tests/test_cases/test_Paired/tophat_out/logs/fileL66CzG.log tophat-2.1.2/tests/regression_tests/test_cases/test_Paired/tophat_out/logs/fileSlcgoq.log tophat-2.1.2/tests/regression_tests/test_cases/test_Paired/tophat_out/logs/fileXTZYq8.log tophat-2.1.2/tests/regression_tests/test_cases/test_Paired/tophat_out/logs/filebJ5Vjd.log tophat-2.1.2/tests/regression_tests/test_cases/test_Paired/tophat_out/logs/filegStX7K.log tophat-2.1.2/tests/regression_tests/test_cases/test_Paired/tophat_out/logs/filekgzR9t.log tophat-2.1.2/tests/regression_tests/test_cases/test_Paired/tophat_out/logs/filel0a7lG.log tophat-2.1.2/tests/regression_tests/test_cases/test_Paired/tophat_out/logs/juncs_db.log tophat-2.1.2/tests/regression_tests/test_cases/test_Paired/tophat_out/logs/long_spanning_reads.log tophat-2.1.2/tests/regression_tests/test_cases/test_Paired/tophat_out/logs/prep_reads.log tophat-2.1.2/tests/regression_tests/test_cases/test_Paired/tophat_out/logs/reports.log tophat-2.1.2/tests/regression_tests/test_cases/test_Paired/tophat_out/logs/run.log tophat-2.1.2/tests/regression_tests/test_cases/test_Paired/tophat_out/logs/segment_juncs.log tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementIndel/ tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementIndel/command.txt tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementIndel/input/ tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementIndel/input/fakeReads_rc.fq tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementIndel/tophat_out/ tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementIndel/tophat_out/accepted_hits.bam tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementIndel/tophat_out/accepted_hits.sam tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementIndel/tophat_out/deletions.bed tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementIndel/tophat_out/insertions.bed tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementIndel/tophat_out/junctions.bed tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementIndel/tophat_out/logs/ tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementIndel/tophat_out/logs/accepted_hits_bam_sort.log tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementIndel/tophat_out/logs/accepted_hits_sam_to_bam.log tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementIndel/tophat_out/logs/bowtie_build.log tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementIndel/tophat_out/logs/file0qFtaO.log tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementIndel/tophat_out/logs/file4gDPVV.log tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementIndel/tophat_out/logs/file64cZ5O.log tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementIndel/tophat_out/logs/fileAKazrl.log tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementIndel/tophat_out/logs/fileeZBaYg.log tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementIndel/tophat_out/logs/juncs_db.log tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementIndel/tophat_out/logs/long_spanning_reads.log tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementIndel/tophat_out/logs/prep_reads.log tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementIndel/tophat_out/logs/reports.log tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementIndel/tophat_out/logs/run.log tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementIndel/tophat_out/logs/segment_juncs.log tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementSplicing/ tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementSplicing/command.txt tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementSplicing/input/ tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementSplicing/input/fakeReads_rc.fq tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementSplicing/tophat_out/ tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementSplicing/tophat_out/accepted_hits.bam tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementSplicing/tophat_out/accepted_hits.sam tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementSplicing/tophat_out/deletions.bed tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementSplicing/tophat_out/insertions.bed tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementSplicing/tophat_out/junctions.bed tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementSplicing/tophat_out/logs/ tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementSplicing/tophat_out/logs/accepted_hits_bam_sort.log tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementSplicing/tophat_out/logs/accepted_hits_sam_to_bam.log tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementSplicing/tophat_out/logs/bowtie_build.log tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementSplicing/tophat_out/logs/file5dkWI7.log tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementSplicing/tophat_out/logs/file6jhGKc.log tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementSplicing/tophat_out/logs/fileIZFMp4.log tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementSplicing/tophat_out/logs/filegYGrS2.log tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementSplicing/tophat_out/logs/filezlwQw8.log tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementSplicing/tophat_out/logs/juncs_db.log tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementSplicing/tophat_out/logs/long_spanning_reads.log tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementSplicing/tophat_out/logs/prep_reads.log tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementSplicing/tophat_out/logs/reports.log tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementSplicing/tophat_out/logs/run.log tophat-2.1.2/tests/regression_tests/test_cases/test_ReverseComplementSplicing/tophat_out/logs/segment_juncs.log tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleIndel/ tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleIndel/command.txt tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleIndel/input/ tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleIndel/input/fakeReads.fq tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleIndel/tophat_out/ tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleIndel/tophat_out/accepted_hits.bam tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleIndel/tophat_out/accepted_hits.sam tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleIndel/tophat_out/deletions.bed tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleIndel/tophat_out/insertions.bed tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleIndel/tophat_out/junctions.bed tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleIndel/tophat_out/logs/ tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleIndel/tophat_out/logs/accepted_hits_bam_sort.log tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleIndel/tophat_out/logs/accepted_hits_sam_to_bam.log tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleIndel/tophat_out/logs/bowtie_build.log tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleIndel/tophat_out/logs/fileAclpaI.log tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleIndel/tophat_out/logs/fileI3q4Mq.log tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleIndel/tophat_out/logs/fileYWyJSm.log tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleIndel/tophat_out/logs/filesGjGO7.log tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleIndel/tophat_out/logs/fileuiIhIZ.log tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleIndel/tophat_out/logs/juncs_db.log tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleIndel/tophat_out/logs/long_spanning_reads.log tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleIndel/tophat_out/logs/prep_reads.log tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleIndel/tophat_out/logs/reports.log tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleIndel/tophat_out/logs/run.log tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleIndel/tophat_out/logs/segment_juncs.log tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleSplicing/ tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleSplicing/command.txt tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleSplicing/input/ tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleSplicing/input/fakeReads.fq tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleSplicing/tophat_out/ tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleSplicing/tophat_out/accepted_hits.bam tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleSplicing/tophat_out/accepted_hits.sam tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleSplicing/tophat_out/deletions.bed tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleSplicing/tophat_out/insertions.bed tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleSplicing/tophat_out/junctions.bed tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleSplicing/tophat_out/logs/ tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleSplicing/tophat_out/logs/accepted_hits_bam_sort.log tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleSplicing/tophat_out/logs/accepted_hits_sam_to_bam.log tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleSplicing/tophat_out/logs/bowtie_build.log tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleSplicing/tophat_out/logs/file1DrDbe.log tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleSplicing/tophat_out/logs/file9CGtmu.log tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleSplicing/tophat_out/logs/fileC9Pt7y.log tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleSplicing/tophat_out/logs/fileLCntBB.log tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleSplicing/tophat_out/logs/fileuFqHi5.log tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleSplicing/tophat_out/logs/juncs_db.log tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleSplicing/tophat_out/logs/long_spanning_reads.log tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleSplicing/tophat_out/logs/prep_reads.log tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleSplicing/tophat_out/logs/reports.log tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleSplicing/tophat_out/logs/run.log tophat-2.1.2/tests/regression_tests/test_cases/test_SimpleSplicing/tophat_out/logs/segment_juncs.log tophat-2.1.2/tests/simulation/ tophat-2.1.2/tests/simulation/tiny_multihit/ tophat-2.1.2/tests/simulation/tiny_multihit/ref_genes.gtf tophat-2.1.2/tests/simulation/tiny_multihit/reference.1.ebwt tophat-2.1.2/tests/simulation/tiny_multihit/reference.2.ebwt tophat-2.1.2/tests/simulation/tiny_multihit/reference.3.ebwt tophat-2.1.2/tests/simulation/tiny_multihit/reference.4.ebwt tophat-2.1.2/tests/simulation/tiny_multihit/reference.fa tophat-2.1.2/tests/simulation/tiny_multihit/reference.rev.1.ebwt tophat-2.1.2/tests/simulation/tiny_multihit/reference.rev.2.ebwt tophat-2.1.2/tests/simulation/tiny_multihit/reference_1.fa tophat-2.1.2/tests/simulation/tiny_multihit/reference_2.fa tophat-2.1.2/tests/simulation/tiny_multihit/tiny_sim.sam tophat-2.1.2/tests/simulation/tiny_multihit/tiny_sim.simexpr tophat-2.1.2/tests/simulation/tiny_multihit/tiny_sim_1.fq tophat-2.1.2/tests/simulation/tiny_multihit/tiny_sim_2.fq tophat-2.1.2/tests/simulation/tiny_multihit/tiny_test.cfg tophat-2.1.2/tests/unit_tests/ tophat-2.1.2/tests/unit_tests/testjunctions.cpp tophat-2.1.2/unbootstrap patching file src/juncs_db.cpp patching file src/tophat_reports.cpp checking for a BSD-compatible install... /usr/bin/ginstall -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... gcc3 checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking for ar... ar checking the archiver (ar) interface... ar checking for gawk... (cached) gawk checking whether we are using the GNU C++ compiler... (cached) yes checking whether g++ accepts -g... (cached) yes checking dependency style of g++... (cached) gcc3 checking for gcc... (cached) gcc checking whether we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ISO C89... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking dependency style of gcc... (cached) gcc3 checking whether make sets $(MAKE)... (cached) yes checking for ranlib... ranlib checking for a Python interpreter with version >= 2.4... python checking for python... /usr/bin/python checking for python version... 2.7 checking for python platform... linux2 checking for python script directory... ${prefix}/lib/python2.7/site-packages checking for python extension module directory... ${exec_prefix}/lib/python2.7/site-packages checking for boostlib >= 1.38.0... yes checking whether the compiler implements namespaces... yes checking whether the Boost::Thread library is available... yes checking for main in -lboost_thread... yes checking whether Boost::Thread needs Boost::System library... no checking how to run the C++ preprocessor... g++ -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for ANSI C header files... (cached) yes checking for stdbool.h that conforms to C99... no checking for _Bool... no checking for inline... inline checking for pid_t... yes checking for size_t... yes checking for ptrdiff_t... yes checking for an ANSI C-conforming const... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... 64 checking for gzread in -lz... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for memset... yes checking for strdup... yes checking for strrchr... yes checking for strtol... yes checking for strsep... yes checking build system type... i586-slackware-linux-gnu checking host system type... i586-slackware-linux-gnu checking how to create a pax tar archive... gnutar checking dependency style of gcc... (cached) gcc3 checking dependency style of g++... (cached) gcc3 checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating config.h config.status: executing depfiles commands -- tophat 2.1.2 Configuration Results -- C++ compiler: g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 Linker flags: -L./samtools-0.1.18 -L/usr/lib BOOST libraries: -lboost_thread GCC version: gcc (GCC) 11.2.0 Host System type: i586-slackware-linux-gnu Install prefix: /usr Install eprefix: ${prefix} See config.h for further configuration information. Email bug reports to . make all-recursive make[1]: Entering directory '/usr/src/slapt-src/academic/tophat/tophat-2.1.2' Making all in src make[2]: Entering directory '/usr/src/slapt-src/academic/tophat/tophat-2.1.2/src' Makefile:1880: warning: overriding recipe for target 'samtools_0.1.18' Makefile:1427: warning: ignoring old recipe for target 'samtools_0.1.18' Makefile:1883: warning: overriding recipe for target 'libbam.a' Makefile:1372: warning: ignoring old recipe for target 'libbam.a' echo "ZORG!" ZORG! cd ./samtools-0.1.18 && make samtools_0.1.18 && cp libbam.a samtools_0.1.18 .. make[3]: Entering directory '/usr/src/slapt-src/academic/tophat/tophat-2.1.2/src/samtools-0.1.18' make[4]: Entering directory '/usr/src/slapt-src/academic/tophat/tophat-2.1.2/src/samtools-0.1.18' gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bgzf.c -o bgzf.o bgzf.c: In function ‘bgzf_close’: bgzf.c:630:29: warning: variable ‘count’ set but not used [-Wunused-but-set-variable] 630 | int count, block_length = deflate_block(fp, 0); | ^~~~~ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. kstring.c -o kstring.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_aux.c -o bam_aux.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam.c -o bam.o bam.c: In function ‘bam_header_write’: bam.c:116:9: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation] 116 | strncpy(buf, "BAM\001", 4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_import.c -o bam_import.o bam_import.c: In function ‘append_text’: bam_import.c:179:55: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 179 | fprintf(stderr,"realloc failed to alloc %ld bytes\n", y); | ~~^ ~ | | | | long int size_t {aka unsigned int} | %d bam_import.c:186:46: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 186 | fprintf(stderr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n", header->l_text+str->l+1,header->n_text,x,y); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %d bam_import.c:186:51: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 186 | fprintf(stderr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n", header->l_text+str->l+1,header->n_text,x,y); | ~~^ ~~~~~~~~~~~~~~ | | | | long int size_t {aka unsigned int} | %d bam_import.c:186:58: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 186 | fprintf(stderr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n", header->l_text+str->l+1,header->n_text,x,y); | ~~^ ~ | | | | long int size_t {aka unsigned int} | %d bam_import.c:186:64: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 6 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 186 | fprintf(stderr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n", header->l_text+str->l+1,header->n_text,x,y); | ~~^ ~ | | | | long int size_t {aka unsigned int} | %d gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. sam.c -o sam.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_index.c -o bam_index.o bam_index.c: In function ‘bam_index_core’: bam_index.c:173:42: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int32_t’ {aka ‘int’} changes value from ‘last_bin = 4294967295’ to ‘-1’ [-Woverflow] 173 | save_bin = save_tid = last_tid = last_bin = 0xffffffffu; | ^~~~~~~~ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_pileup.c -o bam_pileup.o bam_pileup.c: In function ‘resolve_cigar2’: bam_pileup.c:75:16: warning: variable ‘is_head’ set but not used [-Wunused-but-set-variable] 75 | int k, is_head = 0; | ^~~~~~~ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_lpileup.c -o bam_lpileup.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_md.c -o bam_md.o bam_md.c: In function ‘bam_prob_realn_core’: bam_md.c:209:35: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 209 | *(bq - 3) = 'Z'; | ~~~~~~~~~~^~~~~ bam_md.c:198:19: note: at offset -2 into destination object of size [0, 2147483647] allocated by ‘bam_aux_get’ 198 | if ((bq = bam_aux_get(b, "BQ")) != 0) ++bq; | ^~~~~~~~~~~~~~~~~~~~ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. razf.c -o razf.o razf.c: In function ‘razf_open_w’: razf.c:178:9: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation] 178 | strncpy((char*)rz->header->extra, "RAZF", 4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. faidx.c -o faidx.o faidx.c: In function ‘fai_load’: faidx.c:277:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 277 | else | ^~~~ faidx.c:280:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 280 | if (fp == 0) { | ^~ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bedidx.c -o bedidx.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. knetfile.c -o knetfile.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_sort.c -o bam_sort.o In file included from bam_sort.c:9: bam_sort.c:309:26: warning: ‘bam1_lt’ is static but used in inline function ‘__ks_insertsort_sort’ which is not static 309 | KSORT_INIT(sort, bam1_p, bam1_lt) | ^~~~~~~ ksort.h:148:46: note: in definition of macro ‘KSORT_INIT’ 148 | for (j = i; j > s && __sort_lt(*j, *(j-1)); --j) { \ | ^~~~~~~~~ bam_sort.c:53:27: warning: ‘heap_lt’ is static but used in inline function ‘__ks_insertsort_heap’ which is not static 53 | KSORT_INIT(heap, heap1_t, heap_lt) | ^~~~~~~ ksort.h:148:46: note: in definition of macro ‘KSORT_INIT’ 148 | for (j = i; j > s && __sort_lt(*j, *(j-1)); --j) { \ | ^~~~~~~~~ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. sam_header.c -o sam_header.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_reheader.c -o bam_reheader.o bam_reheader.c: In function ‘bam_reheader’: bam_reheader.c:11:23: warning: variable ‘old’ set but not used [-Wunused-but-set-variable] 11 | bam_header_t *old; | ^~~ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. kprobaln.c -o kprobaln.o kprobaln.c: In function ‘kpa_glocal’: kprobaln.c:78:28: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable] 78 | int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr; | ^~~~~~~ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_cat.c -o bam_cat.o ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o make[4]: Leaving directory '/usr/src/slapt-src/academic/tophat/tophat-2.1.2/src/samtools-0.1.18' make[4]: Entering directory '/usr/src/slapt-src/academic/tophat/tophat-2.1.2/src/samtools-0.1.18/bcftools' gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. bcf.c -o bcf.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. vcf.c -o vcf.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. bcfutils.c -o bcfutils.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. prob1.c -o prob1.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. em.c -o em.o em.c: In function ‘bcf_em1’: em.c:174:19: warning: variable ‘n2’ set but not used [-Wunused-but-set-variable] 174 | int i, n, n2; | ^~ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. kfunc.c -o kfunc.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. kmin.c -o kmin.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. index.c -o index.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. fet.c -o fet.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. mut.c -o mut.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. bcf2qcall.c -o bcf2qcall.o ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o make[4]: Leaving directory '/usr/src/slapt-src/academic/tophat/tophat-2.1.2/src/samtools-0.1.18/bcftools' gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_tview.c -o bam_tview.o bam_tview.c:434:2: warning: #warning "No curses library is available; tview is disabled." [-Wcpp] 434 | #warning "No curses library is available; tview is disabled." | ^~~~~~~ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_plcmd.c -o bam_plcmd.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. sam_view.c -o sam_view.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_rmdup.c -o bam_rmdup.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_rmdupse.c -o bam_rmdupse.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_mate.c -o bam_mate.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_stat.c -o bam_stat.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_color.c -o bam_color.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bamtk.c -o bamtk.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. kaln.c -o kaln.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam2bcf.c -o bam2bcf.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam2bcf_indel.c -o bam2bcf_indel.o bam2bcf_indel.c: In function ‘bcf_call_add_rg’: bam2bcf_indel.c:32:25: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 32 | for (r = p; *r && *r != '\t' && *r != '\n'; ++r); lp = r - p; | ^~~ bam2bcf_indel.c:32:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 32 | for (r = p; *r && *r != '\t' && *r != '\n'; ++r); lp = r - p; | ^~ bam2bcf_indel.c:33:25: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 33 | for (r = q; *r && *r != '\t' && *r != '\n'; ++r); lq = r - q; | ^~~ bam2bcf_indel.c:33:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 33 | for (r = q; *r && *r != '\t' && *r != '\n'; ++r); lq = r - q; | ^~ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. errmod.c -o errmod.o errmod.c: In function ‘errmod_cal’: errmod.c:79:15: warning: self-comparison always evaluates to false [-Wtautological-compare] 79 | if (m > m) return -1; | ^ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. sample.c -o sample.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. cut_target.c -o cut_target.o cut_target.c: In function ‘main_cut_target’: cut_target.c:137:43: warning: variable ‘lastpos’ set but not used [-Wunused-but-set-variable] 137 | int c, tid, pos, n, lasttid = -1, lastpos = -1, l, max_l; | ^~~~~~~ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. phase.c -o phase.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam2depth.c -o bam2depth.o gcc -g -Wall -O2 -o samtools_0.1.18 bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lm -lz #-lcurses make[3]: Leaving directory '/usr/src/slapt-src/academic/tophat/tophat-2.1.2/src/samtools-0.1.18' true g++ -DHAVE_CONFIG_H -I. -I.. -O2 -march=i586 -mtune=i686 -std=c++14 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -MT prep_reads.o -MD -MP -MF .deps/prep_reads.Tpo -c -o prep_reads.o prep_reads.cpp mv -f .deps/prep_reads.Tpo .deps/prep_reads.Po g++ -DHAVE_CONFIG_H -I. -I.. -O2 -march=i586 -mtune=i686 -std=c++14 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -MT reads.o -MD -MP -MF .deps/reads.Tpo -c -o reads.o reads.cpp mv -f .deps/reads.Tpo .deps/reads.Po gcc -DHAVE_CONFIG_H -I. -I.. -O2 -march=i586 -mtune=i686 -std=c++14 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -MT alphabet.o -MD -MP -MF .deps/alphabet.Tpo -c -o alphabet.o alphabet.c cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C mv -f .deps/alphabet.Tpo .deps/alphabet.Po g++ -DHAVE_CONFIG_H -I. -I.. -O2 -march=i586 -mtune=i686 -std=c++14 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -MT bwt_map.o -MD -MP -MF .deps/bwt_map.Tpo -c -o bwt_map.o bwt_map.cpp bwt_map.cpp: In function ‘bool spliceCigar(std::vector&, const std::vector&, std::vector, int&, int, int, CigarOpCode, int&)’: bwt_map.cpp:705:9: warning: variable ‘prev_opcode’ set but not used [-Wunused-but-set-variable] 705 | int prev_opcode=0; | ^~~~~~~~~~~ bwt_map.cpp:706:9: warning: variable ‘prev_oplen’ set but not used [-Wunused-but-set-variable] 706 | int prev_oplen=0; | ^~~~~~~~~~ bwt_map.cpp: In member function ‘virtual bool BAMHitFactory::get_hit_from_buf(const char*, BowtieHit&, bool, char*, char*, char*, char*)’: bwt_map.cpp:1112:7: warning: variable ‘text_mate_pos’ set but not used [-Wunused-but-set-variable] 1112 | int text_mate_pos = hit_buf->core.mpos; | ^~~~~~~~~~~~~ bwt_map.cpp:1118:7: warning: variable ‘num_hits’ set but not used [-Wunused-but-set-variable] 1118 | int num_hits = 1; | ^~~~~~~~ bwt_map.cpp: In member function ‘virtual bool SplicedBAMHitFactory::get_hit_from_buf(const char*, BowtieHit&, bool, char*, char*, char*, char*)’: bwt_map.cpp:1481:7: warning: variable ‘text_mate_pos’ set but not used [-Wunused-but-set-variable] 1481 | int text_mate_pos = hit_buf->core.mpos; | ^~~~~~~~~~~~~ bwt_map.cpp:1486:8: warning: variable ‘spliced_alignment’ set but not used [-Wunused-but-set-variable] 1486 | bool spliced_alignment = false; | ^~~~~~~~~~~~~~~~~ In file included from ./SeqAn-1.4.2/seqan/basic/basic_fundamental.h:79, from ./SeqAn-1.4.2/seqan/basic.h:58, from ./SeqAn-1.4.2/seqan/sequence.h:51, from bwt_map.cpp:21: ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]’: ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]’ ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, seqan::True) [with TValueSource = seqan::SimpleType; TValueTarget = seqan::SimpleType]’ ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = seqan::SimpleType; TValueTarget = seqan::SimpleType]’ ./SeqAn-1.4.2/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::SimpleType; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagExact_]’ ./SeqAn-1.4.2/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::SimpleType; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagExact_; typename seqan::Size >::Type = unsigned int]’ ./SeqAn-1.4.2/seqan/sequence/string_alloc.h:131:16: required from ‘seqan::String >::String(const seqan::String >&) [with TValue = seqan::SimpleType; TSpec = void]’ bwt_map.cpp:2377:88: required from here ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./SeqAn-1.4.2/seqan/basic/basic_alphabet.h:84, from ./SeqAn-1.4.2/seqan/basic.h:68, from ./SeqAn-1.4.2/seqan/sequence.h:51, from bwt_map.cpp:21: ./SeqAn-1.4.2/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ mv -f .deps/bwt_map.Tpo .deps/bwt_map.Po g++ -DHAVE_CONFIG_H -I. -I.. -O2 -march=i586 -mtune=i686 -std=c++14 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -MT common.o -MD -MP -MF .deps/common.Tpo -c -o common.o common.cpp common.cpp: In function ‘void str_appendInt(std::string&, int64_t)’: common.cpp:441:23: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘int64_t’ {aka ‘long long int’} [-Wformat=] 441 | sprintf(int_str, "%ld", v); | ~~^ ~ | | | | | int64_t {aka long long int} | long int | %lld common.cpp: In function ‘void str_appendUInt(std::string&, uint64_t)’: common.cpp:447:24: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘uint64_t’ {aka ‘long long unsigned int’} [-Wformat=] 447 | sprintf(uint_str, "%lu", v); | ~~^ ~ | | | | | uint64_t {aka long long unsigned int} | long unsigned int | %llu common.cpp: In member function ‘std::string GBamRecord::seqData(std::string*)’: common.cpp:1259:8: warning: variable ‘mate_num’ set but not used [-Wunused-but-set-variable] 1259 | int mate_num=0; | ^~~~~~~~ mv -f .deps/common.Tpo .deps/common.Po g++ -DHAVE_CONFIG_H -I. -I.. -O2 -march=i586 -mtune=i686 -std=c++14 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -MT junctions.o -MD -MP -MF .deps/junctions.Tpo -c -o junctions.o junctions.cpp mv -f .deps/junctions.Tpo .deps/junctions.Po g++ -DHAVE_CONFIG_H -I. -I.. -O2 -march=i586 -mtune=i686 -std=c++14 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -MT insertions.o -MD -MP -MF .deps/insertions.Tpo -c -o insertions.o insertions.cpp mv -f .deps/insertions.Tpo .deps/insertions.Po g++ -DHAVE_CONFIG_H -I. -I.. -O2 -march=i586 -mtune=i686 -std=c++14 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -MT deletions.o -MD -MP -MF .deps/deletions.Tpo -c -o deletions.o deletions.cpp mv -f .deps/deletions.Tpo .deps/deletions.Po g++ -DHAVE_CONFIG_H -I. -I.. -O2 -march=i586 -mtune=i686 -std=c++14 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -MT fusions.o -MD -MP -MF .deps/fusions.Tpo -c -o fusions.o fusions.cpp In file included from ./SeqAn-1.4.2/seqan/align.h:166, from fusions.cpp:29: ./SeqAn-1.4.2/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const seqan::String&, const seqan::String&, const MyersBitVector&)’: ./SeqAn-1.4.2/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ ./SeqAn-1.4.2/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from ./SeqAn-1.4.2/seqan/align.h:174, from fusions.cpp:29: ./SeqAn-1.4.2/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(seqan::LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: ./SeqAn-1.4.2/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ ./SeqAn-1.4.2/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ mv -f .deps/fusions.Tpo .deps/fusions.Po g++ -DHAVE_CONFIG_H -I. -I.. -O2 -march=i586 -mtune=i686 -std=c++14 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -MT align_status.o -MD -MP -MF .deps/align_status.Tpo -c -o align_status.o align_status.cpp mv -f .deps/align_status.Tpo .deps/align_status.Po g++ -DHAVE_CONFIG_H -I. -I.. -O2 -march=i586 -mtune=i686 -std=c++14 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -MT fragments.o -MD -MP -MF .deps/fragments.Tpo -c -o fragments.o fragments.cpp mv -f .deps/fragments.Tpo .deps/fragments.Po g++ -DHAVE_CONFIG_H -I. -I.. -O2 -march=i586 -mtune=i686 -std=c++14 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -MT tokenize.o -MD -MP -MF .deps/tokenize.Tpo -c -o tokenize.o tokenize.cpp mv -f .deps/tokenize.Tpo .deps/tokenize.Po g++ -DHAVE_CONFIG_H -I. -I.. -O2 -march=i586 -mtune=i686 -std=c++14 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -MT inserts.o -MD -MP -MF .deps/inserts.Tpo -c -o inserts.o inserts.cpp mv -f .deps/inserts.Tpo .deps/inserts.Po g++ -DHAVE_CONFIG_H -I. -I.. -O2 -march=i586 -mtune=i686 -std=c++14 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -MT qual.o -MD -MP -MF .deps/qual.Tpo -c -o qual.o qual.cpp mv -f .deps/qual.Tpo .deps/qual.Po g++ -DHAVE_CONFIG_H -I. -I.. -O2 -march=i586 -mtune=i686 -std=c++14 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -MT bam_merge_impl.o -MD -MP -MF .deps/bam_merge_impl.Tpo -c -o bam_merge_impl.o bam_merge_impl.cpp mv -f .deps/bam_merge_impl.Tpo .deps/bam_merge_impl.Po g++ -DHAVE_CONFIG_H -I. -I.. -O2 -march=i586 -mtune=i686 -std=c++14 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -MT utils.o -MD -MP -MF .deps/utils.Tpo -c -o utils.o utils.cpp utils.cpp: In function ‘bool calculate_offsets(const std::vector >&, std::vector&, std::vector >&)’: utils.cpp:42:34: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 42 | sprintf(suffix, "%lu.bam", j); | ~~^ ~ | | | | | size_t {aka unsigned int} | long unsigned int | %u mv -f .deps/utils.Tpo .deps/utils.Po g++ -DHAVE_CONFIG_H -I. -I.. -O2 -march=i586 -mtune=i686 -std=c++14 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -MT coverage.o -MD -MP -MF .deps/coverage.Tpo -c -o coverage.o coverage.cpp coverage.cpp: In member function ‘void Coverage::print_info() const’: coverage.cpp:226:40: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘std::map >::size_type’ {aka ‘unsigned int’} [-Wformat=] 226 | fprintf(stderr, "# of islands: %lu, # of bases covered: %lu\n", itr->second.size(), bases); | ~~^ ~~~~~~~~~~~~~~~~~~ | | | | long unsigned int std::map >::size_type {aka unsigned int} | %u coverage.cpp:226:65: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 226 | fprintf(stderr, "# of islands: %lu, # of bases covered: %lu\n", itr->second.size(), bases); | ~~^ ~~~~~ | | | | long unsigned int size_t {aka unsigned int} | %u coverage.cpp:230:40: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 230 | fprintf(stderr, "# of total bases: %lu\n", total_bases); | ~~^ ~~~~~~~~~~~ | | | | | size_t {aka unsigned int} | long unsigned int | %u coverage.cpp: In member function ‘void Coverage::print_info(int, const std::vector&) const’: coverage.cpp:250:39: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wformat=] 250 | fprintf(stderr, "\tPos: %d, size: %lu\n", pos, cov.size()); | ~~^ ~~~~~~~~~~ | | | | long unsigned int std::vector::size_type {aka unsigned int} | %u mv -f .deps/coverage.Tpo .deps/coverage.Po rm -f libtophat.a ar cru libtophat.a reads.o alphabet.o bwt_map.o common.o junctions.o insertions.o deletions.o fusions.o align_status.o fragments.o tokenize.o inserts.o qual.o bam_merge_impl.o utils.o coverage.o ranlib libtophat.a g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -L./samtools-0.1.18 -L./samtools-0.1.18 -L/usr/lib -L./samtools-0.1.18 -L/usr/lib -o prep_reads prep_reads.o libtophat.a -lbam -lz g++ -DHAVE_CONFIG_H -I. -I.. -O2 -march=i586 -mtune=i686 -std=c++14 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -MT GTFToFasta.o -MD -MP -MF .deps/GTFToFasta.Tpo -c -o GTFToFasta.o GTFToFasta.cpp mv -f .deps/GTFToFasta.Tpo .deps/GTFToFasta.Po g++ -DHAVE_CONFIG_H -I. -I.. -O2 -march=i586 -mtune=i686 -std=c++14 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -MT FastaTools.o -MD -MP -MF .deps/FastaTools.Tpo -c -o FastaTools.o FastaTools.cpp mv -f .deps/FastaTools.Tpo .deps/FastaTools.Po g++ -DHAVE_CONFIG_H -I. -I.. -O2 -march=i586 -mtune=i686 -std=c++14 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -MT GBase.o -MD -MP -MF .deps/GBase.Tpo -c -o GBase.o GBase.cpp mv -f .deps/GBase.Tpo .deps/GBase.Po g++ -DHAVE_CONFIG_H -I. -I.. -O2 -march=i586 -mtune=i686 -std=c++14 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -MT codons.o -MD -MP -MF .deps/codons.Tpo -c -o codons.o codons.cpp mv -f .deps/codons.Tpo .deps/codons.Po g++ -DHAVE_CONFIG_H -I. -I.. -O2 -march=i586 -mtune=i686 -std=c++14 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -MT gdna.o -MD -MP -MF .deps/gdna.Tpo -c -o gdna.o gdna.cpp mv -f .deps/gdna.Tpo .deps/gdna.Po g++ -DHAVE_CONFIG_H -I. -I.. -O2 -march=i586 -mtune=i686 -std=c++14 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -MT GStr.o -MD -MP -MF .deps/GStr.Tpo -c -o GStr.o GStr.cpp mv -f .deps/GStr.Tpo .deps/GStr.Po g++ -DHAVE_CONFIG_H -I. -I.. -O2 -march=i586 -mtune=i686 -std=c++14 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -MT GFaSeqGet.o -MD -MP -MF .deps/GFaSeqGet.Tpo -c -o GFaSeqGet.o GFaSeqGet.cpp mv -f .deps/GFaSeqGet.Tpo .deps/GFaSeqGet.Po g++ -DHAVE_CONFIG_H -I. -I.. -O2 -march=i586 -mtune=i686 -std=c++14 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -MT gff.o -MD -MP -MF .deps/gff.Tpo -c -o gff.o gff.cpp In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gff.cpp:1: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GffCDSeg]’: GVec.hh:436:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GffCDSeg]’ GVec.hh:81:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GffCDSeg]’ GList.hh:231:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GffCDSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GffCDSeg]’ gff.cpp:2117:16: required from here GVec.hh:364:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GffCDSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 364 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.cpp:1: gff.h:427:7: note: ‘class GffCDSeg’ declared here 427 | class GffCDSeg:public GSeg { | ^~~~~~~~ mv -f .deps/gff.Tpo .deps/gff.Po rm -f libgc.a ar cru libgc.a GBase.o codons.o gdna.o GStr.o GFaSeqGet.o gff.o ranlib libgc.a g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -L./samtools-0.1.18 -L./samtools-0.1.18 -L/usr/lib -L./samtools-0.1.18 -L/usr/lib -o gtf_to_fasta GTFToFasta.o FastaTools.o libtophat.a libgc.a -lbam -lz g++ -DHAVE_CONFIG_H -I. -I.. -O2 -march=i586 -mtune=i686 -std=c++14 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -MT fix_map_ordering.o -MD -MP -MF .deps/fix_map_ordering.Tpo -c -o fix_map_ordering.o fix_map_ordering.cpp mv -f .deps/fix_map_ordering.Tpo .deps/fix_map_ordering.Po g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -L./samtools-0.1.18 -L./samtools-0.1.18 -L/usr/lib -L./samtools-0.1.18 -L/usr/lib -o fix_map_ordering fix_map_ordering.o libtophat.a -lbam -lz g++ -DHAVE_CONFIG_H -I. -I.. -O2 -march=i586 -mtune=i686 -std=c++14 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -MT bam2fastx.o -MD -MP -MF .deps/bam2fastx.Tpo -c -o bam2fastx.o bam2fastx.cpp mv -f .deps/bam2fastx.Tpo .deps/bam2fastx.Po g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -L./samtools-0.1.18 -L./samtools-0.1.18 -L/usr/lib -L./samtools-0.1.18 -L/usr/lib -o bam2fastx bam2fastx.o libgc.a -lbam -lz g++ -DHAVE_CONFIG_H -I. -I.. -O2 -march=i586 -mtune=i686 -std=c++14 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -MT segment_juncs.o -MD -MP -MF .deps/segment_juncs.Tpo -c -o segment_juncs.o segment_juncs.cpp segment_juncs.cpp: In function ‘void get_seqs(std::istream&, RefSequenceTable&, bool)’: segment_juncs.cpp:84:33: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘seqan::Size, seqan::Packed > > >::Type’ {aka ‘unsigned int’} [-Wformat=] 84 | fprintf(stderr, " done (%ld bases).\n", seqan::length(*ref_str)); | ~~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | long int seqan::Size, seqan::Packed > > >::Type {aka unsigned int} | %d segment_juncs.cpp: In member function ‘void SegmentSearchWorker::operator()()’: segment_juncs.cpp:4625:27: warning: variable ‘last_read_id’ set but not used [-Wunused-but-set-variable] 4625 | uint64_t read_id = 0, last_read_id = 0; | ^~~~~~~~~~~~ segment_juncs.cpp: In function ‘void driver(std::istream&, FILE*, FILE*, FILE*, FILE*, std::string&, std::string&, std::vector >&, std::string&, std::string&, std::vector >&)’: segment_juncs.cpp:5063:32: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘std::set::size_type’ {aka ‘unsigned int’} [-Wformat=] 5063 | fprintf(stderr, "Reporting %lu potential deletions...\n", deletions.size()); | ~~^ ~~~~~~~~~~~~~~~~ | | | | long unsigned int std::set::size_type {aka unsigned int} | %u segment_juncs.cpp:5081:32: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘std::set::size_type’ {aka ‘unsigned int’} [-Wformat=] 5081 | fprintf(stderr, "Reporting %lu potential insertions...\n", insertions.size()); | ~~^ ~~~~~~~~~~~~~~~~~ | | | | long unsigned int std::set::size_type {aka unsigned int} | %u In file included from ./SeqAn-1.4.2/seqan/basic/basic_aggregate.h:60, from ./SeqAn-1.4.2/seqan/basic.h:71, from segment_juncs.cpp:27: ./SeqAn-1.4.2/seqan/basic/tuple_bit_compressed.h: In instantiation of ‘seqan::Tuple >::TBitVector* seqan::Tuple >::operator&() [with TValue = seqan::SimpleType; unsigned int SIZE = 21; seqan::Tuple >::TBitVector = long long unsigned int]’: ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h:406:19: required from ‘static void seqan::ValueDestructor_::destruct(TIterator) [with TIterator = seqan::Tuple, 21, seqan::BitPacked<> >*]’ ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h:461:26: required from ‘void seqan::valueDestruct(TIterator) [with TIterator = seqan::Tuple, 21, seqan::BitPacked<> >*]’ ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h:732:22: required from ‘void seqan::_arrayDestructDefault(TIterator1, TIterator2) [with TIterator1 = seqan::Tuple, 21, seqan::BitPacked<> >*; TIterator2 = seqan::Tuple, 21, seqan::BitPacked<> >*]’ ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h:1489:26: required from ‘void seqan::_arrayDestructPointer(TValue*, TValue*, seqan::False) [with TValue = seqan::Tuple, 21, seqan::BitPacked<> >]’ ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h:1498:26: required from ‘void seqan::arrayDestruct(TValue*, TValue*) [with TValue = seqan::Tuple, 21, seqan::BitPacked<> >]’ ./SeqAn-1.4.2/seqan/sequence/string_alloc.h:188:22: required from ‘seqan::String >::~String() [with TValue = seqan::Tuple, 21, seqan::BitPacked<> >; TSpec = void]’ ./SeqAn-1.4.2/seqan/sequence/string_packed.h:145:7: required from here ./SeqAn-1.4.2/seqan/basic/tuple_bit_compressed.h:185:17: warning: taking address of packed member of ‘seqan::Tuple, 21, seqan::BitPacked<> >’ may result in an unaligned pointer value [-Waddress-of-packed-member] 185 | return &i; | ^ In file included from ./SeqAn-1.4.2/seqan/basic/basic_fundamental.h:79, from ./SeqAn-1.4.2/seqan/basic.h:58, from segment_juncs.cpp:27: ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]’: ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]’ ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, seqan::True) [with TValueSource = seqan::SimpleType; TValueTarget = seqan::SimpleType]’ ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = seqan::SimpleType; TValueTarget = seqan::SimpleType]’ ./SeqAn-1.4.2/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::SimpleType; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagExact_]’ ./SeqAn-1.4.2/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::SimpleType; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagExact_; typename seqan::Size >::Type = unsigned int]’ ./SeqAn-1.4.2/seqan/sequence/string_alloc.h:131:16: required from ‘seqan::String >::String(const seqan::String >&) [with TValue = seqan::SimpleType; TSpec = void]’ segment_juncs.cpp:749:31: required from here ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./SeqAn-1.4.2/seqan/basic/basic_alphabet.h:84, from ./SeqAn-1.4.2/seqan/basic.h:68, from segment_juncs.cpp:27: ./SeqAn-1.4.2/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from ./SeqAn-1.4.2/seqan/basic/basic_fundamental.h:79, from ./SeqAn-1.4.2/seqan/basic.h:58, from segment_juncs.cpp:27: ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]’: ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]’ ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, seqan::True) [with TValueSource = seqan::SimpleType; TValueTarget = seqan::SimpleType]’ ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = seqan::SimpleType; TValueTarget = seqan::SimpleType]’ ./SeqAn-1.4.2/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::SimpleType; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagExact_]’ ./SeqAn-1.4.2/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::SimpleType; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagExact_; typename seqan::Size >::Type = unsigned int]’ ./SeqAn-1.4.2/seqan/sequence/string_alloc.h:131:16: required from ‘seqan::String >::String(const seqan::String >&) [with TValue = seqan::SimpleType; TSpec = void]’ segment_juncs.cpp:2499:122: required from here ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./SeqAn-1.4.2/seqan/basic/basic_alphabet.h:84, from ./SeqAn-1.4.2/seqan/basic.h:68, from segment_juncs.cpp:27: ./SeqAn-1.4.2/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ mv -f .deps/segment_juncs.Tpo .deps/segment_juncs.Po g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -L./samtools-0.1.18 -L./samtools-0.1.18 -L/usr/lib -L/usr/lib -L./samtools-0.1.18 -L/usr/lib -o segment_juncs segment_juncs.o libtophat.a -lboost_thread -lbam -lz g++ -DHAVE_CONFIG_H -I. -I.. -O2 -march=i586 -mtune=i686 -std=c++14 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -MT gtf_juncs.o -MD -MP -MF .deps/gtf_juncs.Tpo -c -o gtf_juncs.o gtf_juncs.cpp mv -f .deps/gtf_juncs.Tpo .deps/gtf_juncs.Po g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -L./samtools-0.1.18 -L./samtools-0.1.18 -L/usr/lib -L./samtools-0.1.18 -L/usr/lib -o gtf_juncs gtf_juncs.o libtophat.a libgc.a -lbam -lz g++ -DHAVE_CONFIG_H -I. -I.. -O2 -march=i586 -mtune=i686 -std=c++14 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -MT juncs_db.o -MD -MP -MF .deps/juncs_db.Tpo -c -o juncs_db.o juncs_db.cpp In file included from ./SeqAn-1.4.2/seqan/basic/basic_aggregate.h:60, from ./SeqAn-1.4.2/seqan/basic.h:71, from ./SeqAn-1.4.2/seqan/sequence.h:51, from juncs_db.cpp:26: ./SeqAn-1.4.2/seqan/basic/tuple_bit_compressed.h: In instantiation of ‘seqan::Tuple >::TBitVector* seqan::Tuple >::operator&() [with TValue = seqan::SimpleType; unsigned int SIZE = 21; seqan::Tuple >::TBitVector = long long unsigned int]’: ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h:406:19: required from ‘static void seqan::ValueDestructor_::destruct(TIterator) [with TIterator = seqan::Tuple, 21, seqan::BitPacked<> >*]’ ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h:461:26: required from ‘void seqan::valueDestruct(TIterator) [with TIterator = seqan::Tuple, 21, seqan::BitPacked<> >*]’ ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h:732:22: required from ‘void seqan::_arrayDestructDefault(TIterator1, TIterator2) [with TIterator1 = seqan::Tuple, 21, seqan::BitPacked<> >*; TIterator2 = seqan::Tuple, 21, seqan::BitPacked<> >*]’ ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h:1489:26: required from ‘void seqan::_arrayDestructPointer(TValue*, TValue*, seqan::False) [with TValue = seqan::Tuple, 21, seqan::BitPacked<> >]’ ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h:1498:26: required from ‘void seqan::arrayDestruct(TValue*, TValue*) [with TValue = seqan::Tuple, 21, seqan::BitPacked<> >]’ ./SeqAn-1.4.2/seqan/sequence/string_alloc.h:188:22: required from ‘seqan::String >::~String() [with TValue = seqan::Tuple, 21, seqan::BitPacked<> >; TSpec = void]’ ./SeqAn-1.4.2/seqan/sequence/string_packed.h:145:7: required from here ./SeqAn-1.4.2/seqan/basic/tuple_bit_compressed.h:185:17: warning: taking address of packed member of ‘seqan::Tuple, 21, seqan::BitPacked<> >’ may result in an unaligned pointer value [-Waddress-of-packed-member] 185 | return &i; | ^ In file included from ./SeqAn-1.4.2/seqan/basic/basic_fundamental.h:79, from ./SeqAn-1.4.2/seqan/basic.h:58, from ./SeqAn-1.4.2/seqan/sequence.h:51, from juncs_db.cpp:26: ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]’: ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]’ ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, seqan::True) [with TValueSource = seqan::SimpleType; TValueTarget = seqan::SimpleType]’ ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = seqan::SimpleType; TValueTarget = seqan::SimpleType]’ ./SeqAn-1.4.2/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::SimpleType; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagExact_]’ ./SeqAn-1.4.2/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::SimpleType; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagExact_; typename seqan::Size >::Type = unsigned int]’ ./SeqAn-1.4.2/seqan/sequence/string_alloc.h:131:16: required from ‘seqan::String >::String(const seqan::String >&) [with TValue = seqan::SimpleType; TSpec = void]’ juncs_db.cpp:417:64: required from here ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./SeqAn-1.4.2/seqan/basic/basic_alphabet.h:84, from ./SeqAn-1.4.2/seqan/basic.h:68, from ./SeqAn-1.4.2/seqan/sequence.h:51, from juncs_db.cpp:26: ./SeqAn-1.4.2/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ mv -f .deps/juncs_db.Tpo .deps/juncs_db.Po g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -L./samtools-0.1.18 -L./samtools-0.1.18 -L/usr/lib -L./samtools-0.1.18 -L/usr/lib -o juncs_db juncs_db.o libtophat.a -lbam -lz g++ -DHAVE_CONFIG_H -I. -I.. -O2 -march=i586 -mtune=i686 -std=c++14 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -MT long_spanning_reads.o -MD -MP -MF .deps/long_spanning_reads.Tpo -c -o long_spanning_reads.o long_spanning_reads.cpp In file included from ./SeqAn-1.4.2/seqan/basic/basic_fundamental.h:79, from ./SeqAn-1.4.2/seqan/basic.h:58, from ./SeqAn-1.4.2/seqan/sequence.h:51, from long_spanning_reads.cpp:30: ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h: In instantiation of ‘void seqan::_arrayCopyForwardPointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType]’: ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h:1542:29: required from ‘void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType]’ ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h:1398:21: required from ‘void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, seqan::True) [with TValueSource = seqan::SimpleType; TValueTarget = seqan::SimpleType]’ ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h:1429:31: required from ‘void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = seqan::SimpleType; TValueTarget = seqan::SimpleType]’ ./SeqAn-1.4.2/seqan/sequence/string_base.h:1840:27: required from ‘void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::SimpleType; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagExact_]’ ./SeqAn-1.4.2/seqan/sequence/string_base.h:1855:20: required from ‘typename seqan::Size >::Type seqan::reserve(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::SimpleType; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagExact_; typename seqan::Size >::Type = unsigned int]’ ./SeqAn-1.4.2/seqan/sequence/string_alloc.h:131:16: required from ‘seqan::String >::String(const seqan::String >&) [with TValue = seqan::SimpleType; TSpec = void]’ long_spanning_reads.cpp:316:81: required from here ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h:1521:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class seqan::SimpleType’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1521 | ::std::memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./SeqAn-1.4.2/seqan/basic/basic_alphabet.h:84, from ./SeqAn-1.4.2/seqan/basic.h:68, from ./SeqAn-1.4.2/seqan/sequence.h:51, from long_spanning_reads.cpp:30: ./SeqAn-1.4.2/seqan/basic/alphabet_simple_type.h:116:7: note: ‘class seqan::SimpleType’ declared here 116 | class SimpleType | ^~~~~~~~~~ In file included from ./SeqAn-1.4.2/seqan/basic/basic_aggregate.h:60, from ./SeqAn-1.4.2/seqan/basic.h:71, from ./SeqAn-1.4.2/seqan/sequence.h:51, from long_spanning_reads.cpp:30: ./SeqAn-1.4.2/seqan/basic/tuple_bit_compressed.h: In instantiation of ‘seqan::Tuple >::TBitVector* seqan::Tuple >::operator&() [with TValue = seqan::SimpleType; unsigned int SIZE = 21; seqan::Tuple >::TBitVector = long long unsigned int]’: ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h:406:19: required from ‘static void seqan::ValueDestructor_::destruct(TIterator) [with TIterator = seqan::Tuple, 21, seqan::BitPacked<> >*]’ ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h:461:26: required from ‘void seqan::valueDestruct(TIterator) [with TIterator = seqan::Tuple, 21, seqan::BitPacked<> >*]’ ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h:732:22: required from ‘void seqan::_arrayDestructDefault(TIterator1, TIterator2) [with TIterator1 = seqan::Tuple, 21, seqan::BitPacked<> >*; TIterator2 = seqan::Tuple, 21, seqan::BitPacked<> >*]’ ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h:1489:26: required from ‘void seqan::_arrayDestructPointer(TValue*, TValue*, seqan::False) [with TValue = seqan::Tuple, 21, seqan::BitPacked<> >]’ ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h:1498:26: required from ‘void seqan::arrayDestruct(TValue*, TValue*) [with TValue = seqan::Tuple, 21, seqan::BitPacked<> >]’ ./SeqAn-1.4.2/seqan/sequence/string_alloc.h:188:22: required from ‘seqan::String >::~String() [with TValue = seqan::Tuple, 21, seqan::BitPacked<> >; TSpec = void]’ ./SeqAn-1.4.2/seqan/sequence/string_packed.h:155:5: required from ‘seqan::String >::String() [with TValue = seqan::SimpleType; THostspec = seqan::Alloc<>]’ long_spanning_reads.cpp:72:76: required from here ./SeqAn-1.4.2/seqan/basic/tuple_bit_compressed.h:185:17: warning: taking address of packed member of ‘seqan::Tuple, 21, seqan::BitPacked<> >’ may result in an unaligned pointer value [-Waddress-of-packed-member] 185 | return &i; | ^ mv -f .deps/long_spanning_reads.Tpo .deps/long_spanning_reads.Po g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -L./samtools-0.1.18 -L./samtools-0.1.18 -L/usr/lib -L/usr/lib -L./samtools-0.1.18 -L/usr/lib -o long_spanning_reads long_spanning_reads.o libtophat.a -lboost_thread -lbam -lz g++ -DHAVE_CONFIG_H -I. -I.. -O2 -march=i586 -mtune=i686 -std=c++14 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -MT bam_merge.o -MD -MP -MF .deps/bam_merge.Tpo -c -o bam_merge.o bam_merge.cpp mv -f .deps/bam_merge.Tpo .deps/bam_merge.Po g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -L./samtools-0.1.18 -L./samtools-0.1.18 -L/usr/lib -L./samtools-0.1.18 -L/usr/lib -o bam_merge bam_merge.o libtophat.a libgc.a -lbam -lz g++ -DHAVE_CONFIG_H -I. -I.. -O2 -march=i586 -mtune=i686 -std=c++14 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -MT map2gtf.o -MD -MP -MF .deps/map2gtf.Tpo -c -o map2gtf.o map2gtf.cpp mv -f .deps/map2gtf.Tpo .deps/map2gtf.Po g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -L./samtools-0.1.18 -L./samtools-0.1.18 -L/usr/lib -L./samtools-0.1.18 -L/usr/lib -o map2gtf map2gtf.o libtophat.a libgc.a -lbam -lz g++ -DHAVE_CONFIG_H -I. -I.. -O2 -march=i586 -mtune=i686 -std=c++14 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -MT tophat_reports.o -MD -MP -MF .deps/tophat_reports.Tpo -c -o tophat_reports.o tophat_reports.cpp tophat_reports.cpp: In constructor ‘MultipleBAMReader::MultipleBAMReader(ReadTable&, RefSequenceTable&, const std::vector >&, long int, long int)’: tophat_reports.cpp:1806:68: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=] 1806 | sprintf(suffix, "%lu.bam", j); | ~~^ ~ | | | | | size_t {aka unsigned int} | long unsigned int | %u tophat_reports.cpp: In function ‘void print_alnStats(SAlignStats&)’: tophat_reports.cpp:2131:46: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘int64_t’ {aka ‘long long int’} [-Wformat=] 2131 | fprintf(f, " Input : %9ld\n", total_left); | ~~~^ ~~~~~~~~~~ | | | | | int64_t {aka long long int} | long int | %9lld tophat_reports.cpp:2133:46: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘int64_t’ {aka ‘long long int’} [-Wformat=] 2133 | fprintf(f, " Mapped : %9ld (%4.1f%% of input)\n", | ~~~^ | | | long int | %9lld 2134 | alnStats.num_aligned_left, perc); | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | int64_t {aka long long int} tophat_reports.cpp:2137:46: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘int64_t’ {aka ‘long long int’} [-Wformat=] 2137 | fprintf(f," of these: %9ld (%4.1f%%) have multiple alignments (%ld have >%d)\n", | ~~~^ | | | long int | %9lld 2138 | alnStats.num_aligned_left_multi, perc, alnStats.num_aligned_left_xmulti, max_multihits); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | int64_t {aka long long int} tophat_reports.cpp:2137:86: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘int64_t’ {aka ‘long long int’} [-Wformat=] 2137 | fprintf(f," of these: %9ld (%4.1f%%) have multiple alignments (%ld have >%d)\n", | ~~^ | | | long int | %lld 2138 | alnStats.num_aligned_left_multi, perc, alnStats.num_aligned_left_xmulti, max_multihits); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | int64_t {aka long long int} tophat_reports.cpp:2149:54: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘int64_t’ {aka ‘long long int’} [-Wformat=] 2149 | fprintf(f, " Input : %9ld\n", total_right); | ~~~^ ~~~~~~~~~~~ | | | | | int64_t {aka long long int} | long int | %9lld tophat_reports.cpp:2152:54: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘int64_t’ {aka ‘long long int’} [-Wformat=] 2152 | fprintf(f, " Mapped : %9ld (%4.1f%% of input)\n", | ~~~^ | | | long int | %9lld 2153 | alnStats.num_aligned_right, perc); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | int64_t {aka long long int} tophat_reports.cpp:2156:61: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘int64_t’ {aka ‘long long int’} [-Wformat=] 2156 | fprintf(f," of these: %9ld (%4.1f%%) have multiple alignments (%ld have >%d)\n", | ~~~^ | | | long int | %9lld 2157 | alnStats.num_aligned_right_multi, perc, alnStats.num_aligned_right_xmulti, max_multihits); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | int64_t {aka long long int} tophat_reports.cpp:2156:101: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘int64_t’ {aka ‘long long int’} [-Wformat=] 2156 | fprintf(f," of these: %9ld (%4.1f%%) have multiple alignments (%ld have >%d)\n", | ~~^ | | | long int | %lld 2157 | alnStats.num_aligned_right_multi, perc, alnStats.num_aligned_right_xmulti, max_multihits); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | int64_t {aka long long int} tophat_reports.cpp:2164:70: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘int64_t’ {aka ‘long long int’} [-Wformat=] 2164 | fprintf(f, " Input : %9ld\n", total_unpaired); | ~~~^ ~~~~~~~~~~~~~~ | | | | | int64_t {aka long long int} | long int | %9lld tophat_reports.cpp:2167:70: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘int64_t’ {aka ‘long long int’} [-Wformat=] 2167 | fprintf(f, " Mapped : %9ld (%4.1f%% of input)\n", | ~~~^ | | | long int | %9lld 2168 | alnStats.num_aligned_unpaired, perc); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | int64_t {aka long long int} tophat_reports.cpp:2171:77: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘int64_t’ {aka ‘long long int’} [-Wformat=] 2171 | fprintf(f," of these: %9ld (%4.1f%%) have multiple alignments (%ld have >%d)\n", | ~~~^ | | | long int | %9lld 2172 | alnStats.num_aligned_unpaired_multi, perc, alnStats.num_aligned_unpaired_xmulti, max_multihits); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | int64_t {aka long long int} tophat_reports.cpp:2171:117: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘int64_t’ {aka ‘long long int’} [-Wformat=] 2171 | fprintf(f," of these: %9ld (%4.1f%%) have multiple alignments (%ld have >%d)\n", | ~~^ | | | long int | %lld 2172 | alnStats.num_aligned_unpaired_multi, perc, alnStats.num_aligned_unpaired_xmulti, max_multihits); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | int64_t {aka long long int} tophat_reports.cpp:2180:49: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘int64_t’ {aka ‘long long int’} [-Wformat=] 2180 | fprintf(f, "\nAligned pairs: %9ld\n", alnStats.num_aligned_pairs); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | long int int64_t {aka long long int} | %9lld tophat_reports.cpp:2183:49: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘int64_t’ {aka ‘long long int’} [-Wformat=] 2183 | fprintf(f, " of these: %9ld (%4.1f%%) have multiple alignments\n", | ~~~^ | | | long int | %9lld 2184 | alnStats.num_aligned_pairs_multi, perc); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | int64_t {aka long long int} tophat_reports.cpp:2188:49: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘int64_t’ {aka ‘long long int’} [-Wformat=] 2188 | fprintf(f, " %9ld (%4.1f%%) are discordant alignments\n", | ~~~^ | | | long int | %9lld 2189 | alnStats.num_aligned_pairs_disc, perc); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | int64_t {aka long long int} In file included from ./SeqAn-1.4.2/seqan/basic/basic_aggregate.h:60, from ./SeqAn-1.4.2/seqan/basic.h:71, from ./SeqAn-1.4.2/seqan/sequence.h:51, from tophat_reports.cpp:31: ./SeqAn-1.4.2/seqan/basic/tuple_bit_compressed.h: In instantiation of ‘seqan::Tuple >::TBitVector* seqan::Tuple >::operator&() [with TValue = seqan::SimpleType; unsigned int SIZE = 21; seqan::Tuple >::TBitVector = long long unsigned int]’: ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h:406:19: required from ‘static void seqan::ValueDestructor_::destruct(TIterator) [with TIterator = seqan::Tuple, 21, seqan::BitPacked<> >*]’ ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h:461:26: required from ‘void seqan::valueDestruct(TIterator) [with TIterator = seqan::Tuple, 21, seqan::BitPacked<> >*]’ ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h:732:22: required from ‘void seqan::_arrayDestructDefault(TIterator1, TIterator2) [with TIterator1 = seqan::Tuple, 21, seqan::BitPacked<> >*; TIterator2 = seqan::Tuple, 21, seqan::BitPacked<> >*]’ ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h:1489:26: required from ‘void seqan::_arrayDestructPointer(TValue*, TValue*, seqan::False) [with TValue = seqan::Tuple, 21, seqan::BitPacked<> >]’ ./SeqAn-1.4.2/seqan/basic/array_construct_destruct.h:1498:26: required from ‘void seqan::arrayDestruct(TValue*, TValue*) [with TValue = seqan::Tuple, 21, seqan::BitPacked<> >]’ ./SeqAn-1.4.2/seqan/sequence/string_alloc.h:188:22: required from ‘seqan::String >::~String() [with TValue = seqan::Tuple, 21, seqan::BitPacked<> >; TSpec = void]’ ./SeqAn-1.4.2/seqan/sequence/string_packed.h:155:5: required from ‘seqan::String >::String() [with TValue = seqan::SimpleType; THostspec = seqan::Alloc<>]’ tophat_reports.cpp:70:76: required from here ./SeqAn-1.4.2/seqan/basic/tuple_bit_compressed.h:185:17: warning: taking address of packed member of ‘seqan::Tuple, 21, seqan::BitPacked<> >’ may result in an unaligned pointer value [-Waddress-of-packed-member] 185 | return &i; | ^ mv -f .deps/tophat_reports.Tpo .deps/tophat_reports.Po g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -L./samtools-0.1.18 -L./samtools-0.1.18 -L/usr/lib -L/usr/lib -L./samtools-0.1.18 -L/usr/lib -o tophat_reports tophat_reports.o libtophat.a -lboost_thread -lbam -lz g++ -DHAVE_CONFIG_H -I. -I.. -O2 -march=i586 -mtune=i686 -std=c++14 -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -MT sam_juncs.o -MD -MP -MF .deps/sam_juncs.Tpo -c -o sam_juncs.o sam_juncs.cpp sam_juncs.cpp: In function ‘void driver(FILE*)’: sam_juncs.cpp:106:38: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘std::map::size_type’ {aka ‘unsigned int’} [-Wformat=] 106 | fprintf(stderr, "Extracted %lu junctions\n", junctions.size()); | ~~^ ~~~~~~~~~~~~~~~~ | | | | long unsigned int std::map::size_type {aka unsigned int} | %u mv -f .deps/sam_juncs.Tpo .deps/sam_juncs.Po g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -march=i586 -mtune=i686 -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/include -I./SeqAn-1.4.2 -L./samtools-0.1.18 -L./samtools-0.1.18 -L/usr/lib -L./samtools-0.1.18 -L/usr/lib -o sam_juncs sam_juncs.o libtophat.a -lbam -lz cp tophat2.sh tophat2 && chmod 755 tophat2 sed -e 's|__VERSION__|2.1.2|' tophat.py > tophat && chmod 755 tophat make[2]: Leaving directory '/usr/src/slapt-src/academic/tophat/tophat-2.1.2/src' make[2]: Entering directory '/usr/src/slapt-src/academic/tophat/tophat-2.1.2' make[2]: Leaving directory '/usr/src/slapt-src/academic/tophat/tophat-2.1.2' make[1]: Leaving directory '/usr/src/slapt-src/academic/tophat/tophat-2.1.2' Making install in src make[1]: Entering directory '/usr/src/slapt-src/academic/tophat/tophat-2.1.2/src' Makefile:1880: warning: overriding recipe for target 'samtools_0.1.18' Makefile:1427: warning: ignoring old recipe for target 'samtools_0.1.18' Makefile:1883: warning: overriding recipe for target 'libbam.a' Makefile:1372: warning: ignoring old recipe for target 'libbam.a' make[2]: Entering directory '/usr/src/slapt-src/academic/tophat/tophat-2.1.2/src' Makefile:1880: warning: overriding recipe for target 'samtools_0.1.18' Makefile:1427: warning: ignoring old recipe for target 'samtools_0.1.18' Makefile:1883: warning: overriding recipe for target 'libbam.a' Makefile:1372: warning: ignoring old recipe for target 'libbam.a' /usr/bin/mkdir -p '/usr/src/slapt-src/academic/tophat/package-tophat/usr/bin' /usr/bin/ginstall -c samtools_0.1.18 prep_reads gtf_to_fasta fix_map_ordering bam2fastx segment_juncs gtf_juncs juncs_db long_spanning_reads bam_merge map2gtf tophat_reports sam_juncs '/usr/src/slapt-src/academic/tophat/package-tophat/usr/bin' /usr/bin/mkdir -p '/usr/src/slapt-src/academic/tophat/package-tophat/usr/bin' /usr/bin/ginstall -c tophat2 tophat '/usr/src/slapt-src/academic/tophat/package-tophat/usr/bin' /usr/bin/mkdir -p '/usr/src/slapt-src/academic/tophat/package-tophat/usr/bin' /usr/bin/ginstall -c contig_to_chr_coords bed_to_juncs sra_to_solid tophat-fusion-post '/usr/src/slapt-src/academic/tophat/package-tophat/usr/bin' /usr/bin/mkdir -p '/usr/src/slapt-src/academic/tophat/package-tophat/usr/lib' /usr/bin/ginstall -c -m 644 libtophat.a libgc.a '/usr/src/slapt-src/academic/tophat/package-tophat/usr/lib' ( cd '/usr/src/slapt-src/academic/tophat/package-tophat/usr/lib' && ranlib libtophat.a ) ( cd '/usr/src/slapt-src/academic/tophat/package-tophat/usr/lib' && ranlib libgc.a ) make install-data-hook make[3]: Entering directory '/usr/src/slapt-src/academic/tophat/tophat-2.1.2/src' Makefile:1880: warning: overriding recipe for target 'samtools_0.1.18' Makefile:1427: warning: ignoring old recipe for target 'samtools_0.1.18' Makefile:1883: warning: overriding recipe for target 'libbam.a' Makefile:1372: warning: ignoring old recipe for target 'libbam.a' cp -r intervaltree sortedcontainers /usr/src/slapt-src/academic/tophat/package-tophat/usr/bin make[3]: Leaving directory '/usr/src/slapt-src/academic/tophat/tophat-2.1.2/src' make[2]: Leaving directory '/usr/src/slapt-src/academic/tophat/tophat-2.1.2/src' make[1]: Leaving directory '/usr/src/slapt-src/academic/tophat/tophat-2.1.2/src' make[1]: Entering directory '/usr/src/slapt-src/academic/tophat/tophat-2.1.2' make[2]: Entering directory '/usr/src/slapt-src/academic/tophat/tophat-2.1.2' make[2]: Nothing to be done for 'install-exec-am'. make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/usr/src/slapt-src/academic/tophat/tophat-2.1.2' make[1]: Leaving directory '/usr/src/slapt-src/academic/tophat/tophat-2.1.2' Slackware package maker, version 3.14159265. Searching for symbolic links: No symbolic links were found, so we won't make an installation script. You can make your own later in ./install/doinst.sh and rebuild the package if you like. This next step is optional - you can set the directories in your package to some sane permissions. If any of the directories in your package have special permissions, then DO NOT reset them here! Would you like to reset all directory permissions to 755 (drwxr-xr-x) and directory ownerships to root.root ([y]es, [n]o)? n Creating Slackware package: /usr/src/slapt-src/academic/tophat/tophat-2.1.2-i586-2salix15.0.txz ./ install/ install/slack-desc usr/ usr/bin/ usr/bin/bam2fastx usr/bin/bam_merge usr/bin/bed_to_juncs usr/bin/contig_to_chr_coords usr/bin/fix_map_ordering usr/bin/gtf_juncs usr/bin/gtf_to_fasta usr/bin/intervaltree/ usr/bin/intervaltree/__init__.py usr/bin/intervaltree/interval.py usr/bin/intervaltree/intervaltree.py usr/bin/intervaltree/node.py usr/bin/juncs_db usr/bin/long_spanning_reads usr/bin/map2gtf usr/bin/prep_reads usr/bin/sam_juncs usr/bin/samtools_0.1.18 usr/bin/segment_juncs usr/bin/sortedcontainers/ usr/bin/sortedcontainers/__init__.py usr/bin/sortedcontainers/sorteddict.py usr/bin/sortedcontainers/sortedlist.py usr/bin/sortedcontainers/sortedlistwithkey.py usr/bin/sortedcontainers/sortedset.py usr/bin/sra_to_solid usr/bin/tophat usr/bin/tophat-fusion-post usr/bin/tophat2 usr/bin/tophat_reports usr/doc/ usr/doc/tophat-2.1.2/ usr/doc/tophat-2.1.2/AUTHORS usr/doc/tophat-2.1.2/INSTALL usr/doc/tophat-2.1.2/LICENSE usr/doc/tophat-2.1.2/NEWS usr/doc/tophat-2.1.2/README usr/doc/tophat-2.1.2/References usr/doc/tophat-2.1.2/THANKS usr/doc/tophat-2.1.2/tophat.SlackBuild usr/lib/ usr/lib/libgc.a usr/lib/libtophat.a Slackware package /usr/src/slapt-src/academic/tophat/tophat-2.1.2-i586-2salix15.0.txz created. Installing package tophat-2.1.2-i586-2salix15.0... | tophat (Splice junction mapper for RNA-Seq reads) | | TopHat is a fast splice junction mapper for RNA-Seq reads. It | aligns RNA-Seq reads to mammalian-sized genomes using the ultra | high-throughput short read aligner Bowtie, and then analyzes the | mapping results to identify splice junctions between exons. | | Home: http://tophat.cbcb.umd.edu/ | https://github.com/infphilo/tophat/ | | | |