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from 5276924 use correct latex dependency new 17a2684 New upstream version 1.5.10+ds new 895438c Merge tag 'upstream/1.5.10+ds' new 80bbe17 WIP: ner upstream The 3 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: .travis.yml | 45 +- CHANGELOG | 19 +- Makefile | 15 +- VERSION | 2 +- debian/changelog | 7 + debian/genometools-common.install | 19 +- debian/patches/adding_soname | 4 +- debian/patches/libbam-fix | 6 +- debian/patches/reproducible | 4 +- debian/patches/series | 2 - doc/RELEASE | 4 - gtdata/modules/gtdoclib/docvisitorlatex.lua | 27 +- gtdata/modules/gtdoclib/gtscript_header.lp | 1 - gtdata/modules/gtdoclib/libgenometools_header.lp | 1 - gtpython/README | 2 +- scripts/SEmatch.rb | 151 + scripts/all-vs-all.sh | 6 +- scripts/alloutputoptions.rb | 44 +- scripts/build_dists.sh | 8 + scripts/check-fstperquery.rb | 55 + scripts/cleanpp.sh | 1 + scripts/cmp_db_query_exch.rb | 4 +- scripts/collect-mappings.rb | 26 - scripts/convert2myersformat.rb | 77 +- scripts/cutsequences.rb | 61 + scripts/enumkmers.rb | 26 + scripts/esq-in-bytes.sh | 25 +- scripts/estim-kmer-size.rb | 25 + scripts/evalue-filter.rb | 29 + scripts/extract-seed.rb | 18 + scripts/fasta.rb | 112 + scripts/findfasta.rb | 28 +- scripts/gen-display-struct.rb | 226 + scripts/gen-intsets.rb | 35 +- scripts/gen-radixsort-ip.rb | 466 +- scripts/gen-radixsort-ip.sh | 1 + scripts/gfa2lint.rb | 148 + scripts/manyshort-somelong.rb | 23 + scripts/matches-compare.rb | 396 + scripts/matches2ani.rb | 52 + scripts/mk_ft_longest_common.rb | 258 + scripts/print_sequence.rb | 7 + scripts/reverse-complement.rb | 19 + scripts/run-se-da.sh | 4 +- scripts/se-permutation.rb | 45 + scripts/seeds2maxmatches.rb | 95 + scripts/sensitivity-test.rb | 4 +- scripts/sim-read-mapping.sh | 60 +- scripts/single-read-mapping.sh | 30 + scripts/skmake.rb | 15 +- scripts/travis_installdeps.sh | 13 + scripts/{alloutputoptions.rb => turnwheel.rb} | 23 +- src/annotationsketch/custom_track_gc_content.c | 4 +- src/core/accspecialrange.gen | 50 + src/core/alphabet.c | 25 +- src/core/arraydef.h | 41 +- src/core/bitbuffer.c | 301 +- src/core/bitbuffer.h | 70 +- src/core/bitpackstringsimpleop.h | 11 +- src/core/colorspace.h | 6 +- src/core/csvline_reader.c | 302 + src/core/csvline_reader.h | 85 + src/core/encseq.c | 90 +- src/core/encseq.h | 19 +- src/core/fptr_api.h | 2 +- src/core/gtdatapath.c | 15 +- src/core/mail_address.h | 2 +- src/core/radix_sort.c | 241 +- src/core/radix_sort.h | 11 + src/core/radixsort-ip-flba.inc | 364 + src/core/radixsort-ip-uint64keypair.inc | 211 +- src/core/radixsort-ip-ulong.inc | 203 +- src/core/radixsort-ip-ulongpair.inc | 203 +- src/core/str.c | 7 + src/core/str.h | 2 + src/core/timer.c | 45 +- src/core/timer_api.h | 3 + src/core/unused_api.h | 6 + src/extended/alignment.c | 164 +- src/extended/alignment.h | 13 +- src/extended/assembly_stats_calculator.c | 95 +- src/extended/assembly_stats_calculator.h | 5 + src/extended/blast_process_call.h | 8 +- src/extended/compressed_bitsequence.h | 6 +- src/extended/condenseq.c | 170 +- src/extended/condenseq.h | 14 +- src/extended/condenseq_creator.c | 448 +- src/extended/condenseq_creator.h | 14 +- src/extended/condenseq_rep.h | 10 +- src/extended/condenseq_search_arguments.h | 2 + src/extended/editscript.c | 54 +- src/extended/editscript.h | 92 +- src/extended/elias_gamma.h | 2 +- src/extended/encdesc.c | 1 - src/extended/encdesc_header_io.h | 2 + src/extended/fasta_header_iterator.h | 6 +- src/extended/gff3_escaping.c | 14 +- src/extended/gff3_parser.c | 21 +- src/extended/huffcode.h | 2 +- src/extended/intset.h | 2 +- src/extended/intset_16.c | 37 +- src/extended/intset_16.h | 2 +- src/extended/intset_32.c | 37 +- src/extended/intset_32.h | 2 +- src/extended/intset_8.c | 37 +- src/extended/intset_8.h | 2 +- src/extended/io_function_pointers.h | 6 +- src/extended/linspace_management.c | 7 +- src/extended/match_blast.c | 61 +- src/extended/match_blast_api.h | 35 +- src/extended/match_iterator_blast.c | 59 +- src/extended/match_iterator_open.c | 11 +- src/extended/multieoplist.c | 16 +- src/extended/multieoplist.h | 26 +- src/extended/popcount_tab.h | 3 +- src/extended/ranked_list.c | 4 +- src/extended/rbtree.c | 51 +- src/extended/rbtree.h | 33 +- src/extended/rcr.h | 2 + src/extended/safe_popen.c | 9 +- src/extended/sam_alignment.h | 82 +- src/extended/sam_query_name_iterator.h | 4 +- src/extended/samfile_iterator.h | 2 +- src/extended/scorehandler.c | 12 + src/extended/scorehandler.h | 4 + src/extended/wtree.h | 7 +- src/extended/wtree_encseq.c | 4 +- src/gtt.c | 4 + src/match/asqg_writer.c | 2 +- src/match/asqg_writer.h | 2 +- src/match/chain2dim.c | 19 +- src/match/chainofin.c | 9 +- src/match/diagband-struct.c | 349 + src/match/diagband-struct.h | 170 + src/match/diagbandseed.c | 4556 +++++++++--- src/match/diagbandseed.h | 89 +- src/match/eis-bwtseq-context.c | 2 +- src/match/esa-mmsearch.c | 54 +- src/match/esa-mmsearch.h | 3 + src/match/ft-eoplist.c | 1349 ++++ src/match/ft-eoplist.h | 222 + src/match/ft-front-generation.c | 395 +- src/match/ft-front-generation.h | 58 +- src/match/ft-front-prune.c | 981 ++- src/match/ft-front-prune.h | 57 +- src/match/ft-longest-common.inc | 1839 +++++ src/match/ft-polish.c | 27 +- src/match/ft-polish.h | 25 +- src/match/ft-trimstat.c | 203 +- src/match/ft-trimstat.h | 36 +- src/match/gfa_writer.c | 227 + src/match/gfa_writer.h | 70 + src/match/karlin_altschul_stat.c | 945 +++ src/match/karlin_altschul_stat.h | 90 + src/match/lua_tools.h | 3 + src/match/querymatch-align.c | 967 +-- src/match/querymatch-align.h | 111 +- src/match/querymatch-display.c | 636 ++ src/match/querymatch-display.h | 67 + src/match/querymatch.c | 1475 +++- src/match/querymatch.h | 156 +- src/match/rdj-filesuf-def.h | 2 + src/match/rdj-spmfind.c | 1 + src/match/rdj-strgraph.c | 67 +- src/match/rdj-strgraph.h | 4 + src/match/rectangle-store.c | 158 + src/match/rectangle-store.h | 25 + src/match/se-display-fwd.inc | 85 + src/match/se-display.inc | 426 ++ src/match/seed-extend-iter.c | 231 +- src/match/seed-extend-iter.h | 99 +- src/match/seed-extend.c | 1395 ++-- src/match/seed-extend.h | 254 +- src/match/seed_extend_parts.c | 325 + src/match/seed_extend_parts.h | 73 + src/match/seq_or_encseq.h | 34 + src/match/seqabstract.c | 18 +- src/match/seqabstract.h | 2 +- src/match/sfx-diffcov.c | 8 +- src/match/sfx-run.c | 2 +- src/match/sfx-suffixgetset.c | 11 +- src/match/shu-dfs.h | 10 +- src/match/test-maxpairs.c | 18 +- src/tools/gt_condenseq_compress.c | 6 +- src/tools/gt_kmer_database.c | 4 +- src/tools/gt_readjoiner.c | 2 + src/tools/gt_readjoiner_asqg.c | 2 +- .../{gt_readjoiner_asqg.c => gt_readjoiner_gfa.c} | 147 +- .../lua_tools.h => tools/gt_readjoiner_gfa.h} | 13 +- src/tools/gt_repfind.c | 495 +- src/tools/gt_seed_extend.c | 813 ++- src/tools/gt_seqorder.c | 247 +- src/tools/gt_seqstat.c | 41 +- src/tools/gt_sfxmap.c | 6 +- src/tools/gt_show_seedext.c | 412 +- src/tools/gt_sortbench.c | 194 +- testdata/at-C99887-fwd.fna | 14 + testdata/at-C99887-rev.fna | 14 + testdata/at-C99930.fna | 12 + testdata/gt_seqorder_test_sortlength.fas | 34 + testdata/gt_sketch_textwidth.gff3 | 2 +- testdata/matchtool_see-ext.match | 72 + testdata/query-fwd.match | 55 + testdata/query-rev.match | 55 + testdata/readjoiner/30x_800nt.gfa1 | 64 + testdata/readjoiner/30x_800nt.gfa2 | 64 + testdata/readjoiner/30x_long_varlen.gfa1 | 73 + testdata/readjoiner/30x_long_varlen.gfa2 | 73 + testdata/readjoiner/70x_100nt.gfa1 | 82 + testdata/readjoiner/70x_100nt.gfa2 | 82 + testdata/readjoiner/contained_varlen.gfa1 | 11 + testdata/readjoiner/contained_varlen.gfa2 | 11 + .../at1MB-Atinsert-greedy-20-700-75-3-39-a | 1528 ++-- .../at1MB-U8-greedy-r-12-30-80-2-36-a | 1087 +-- .../repfind-result/at1MB-U8-xdrop-20-20-80-6-a | 359 +- .../repfind-result/at1MB-U8-xdrop-r-12-30-80-6-a | 562 +- .../repfind-result/at1MB-greedy-70-500-90-1-39-a | 1409 ++-- .../repfind-result/at1MB-greedy-r-14-32-80-2-36-a | 226 +- testdata/repfind-result/at1MB-xdrop-20-20-80-6 | 1 + .../repfind-result/at1MB-xdrop-70-500-90-1-39-a | 1297 ++-- testdata/repfind-result/at1MB-xdrop-r-14-32-80-6-a | 145 +- testdata/repfind-result/humhbb.fna-gr-ext.result | 1 + testdata/repfind-result/ychrIII.fna-gr-ext.result | 4 + testdata/see-ext-U8-evalue-bitscore.matches | 11 + testdata/see-ext-ani-at1MB-U8.txt | 6 + testdata/see-ext-at1MB-400-al-from-dtrace.matches | 7610 ++++++++++++++++++++ testdata/see-ext-at1MB-400-cigar.matches | 230 + testdata/see-ext-at1MB-400-cigarX.matches | 231 + testdata/see-ext-at1MB-400-dtrace.matches | 230 + testdata/see-ext-at1MB-400-evalue-bitscore.matches | 228 + testdata/see-ext-at1MB-400-seqdesc.matches | 230 + testdata/see-ext-at1MB-400-seqlength.matches | 228 + testdata/see-ext-at1MB-400-trace.matches | 230 + testdata/see-ext-at1MB-500-al.matches | 947 +++ ...ee-ext-at1MB-500-alignment-seed_in_algn.matches | 321 + testdata/see-ext-at1MB-500-failed_seed.matches | 1477 ++++ ...sert100-evalue-bitscore-cigar-seqlength.matches | 11 + ...ert100-evalue-bitscore-cigarX-seqlength.matches | 12 + .../see-ext-at1MB-U8-200-al-from-dtrace.matches | 47 + testdata/see-ext-at1MB-maxmat250.matches | 94 + .../see-ext-at1MB-mincoverage200-tabsep.matches | 750 ++ .../see-ext-at1MB-u8-failed_seed-evalue.matches | 21 + testdata/see-ext-at1MB-u8-maxmat30.matches | 27 + testdata/see-ext-at1MB-u8.matches | 1397 ++++ testdata/see-ext-at1MB.matches | 1865 +++++ testdata/see-ext-fastq_long-u8.matches | 108 + testdata/see-ext-fastq_long.matches | 39 + ...0_queries_300.fas => see-ext-paired-u8.matches} | 0 testdata/see-ext-paired.matches | 3 + testsuite/gt_condenseq_include.rb | 4 +- testsuite/gt_linspace_align_include.rb | 20 +- testsuite/gt_readjoiner_include.rb | 17 +- testsuite/gt_repfind_include.rb | 89 +- testsuite/gt_seed_extend_include.rb | 577 +- testsuite/gt_seqorder_include.rb | 9 + testsuite/gt_sortbench_include.rb | 3 +- testsuite/gt_suffixerator_include.rb | 2 +- www/genometools.org/htdocs/annotationsketch.html | 1 - .../htdocs/cgi-bin/annotationsketch_demo.cgi | 1 - .../htdocs/cgi-bin/gff3validator.cgi | 1 - www/genometools.org/htdocs/contract.html | 1 - www/genometools.org/htdocs/contribute.html | 1 - www/genometools.org/htdocs/customtracks.html | 1 - www/genometools.org/htdocs/design.html | 1 - www/genometools.org/htdocs/docs.html | 3 +- www/genometools.org/htdocs/documentation.html | 1 - www/genometools.org/htdocs/examples_tmpl.html | 1 - www/genometools.org/htdocs/index.html | 1 - www/genometools.org/htdocs/libgenometools.html | 75 +- www/genometools.org/htdocs/license.html | 1 - www/genometools.org/htdocs/manuals.html | 1 - www/genometools.org/htdocs/style_options.html | 1 - www/genometools.org/htdocs/tool.conf | 1 - www/genometools.org/htdocs/tool_list.conf | 1 - www/genometools.org/htdocs/tools.html | 1 - www/genometools.org/htdocs/tools/gt.html | 3 +- .../htdocs/tools/gt_bed_to_gff3.html | 3 +- www/genometools.org/htdocs/tools/gt_cds.html | 3 +- www/genometools.org/htdocs/tools/gt_chain2dim.html | 1 - www/genometools.org/htdocs/tools/gt_chseqids.html | 3 +- www/genometools.org/htdocs/tools/gt_clean.html | 3 +- www/genometools.org/htdocs/tools/gt_compreads.html | 3 +- .../htdocs/tools/gt_compreads_compress.html | 3 +- .../htdocs/tools/gt_compreads_decompress.html | 3 +- .../htdocs/tools/gt_compreads_refcompress.html | 3 +- .../htdocs/tools/gt_compreads_refdecompress.html | 3 +- www/genometools.org/htdocs/tools/gt_condenseq.html | 3 +- .../htdocs/tools/gt_congruence.html | 3 +- .../htdocs/tools/gt_congruence_spacedseed.html | 1 - .../htdocs/tools/gt_convertseq.html | 3 +- www/genometools.org/htdocs/tools/gt_csa.html | 3 +- www/genometools.org/htdocs/tools/gt_dot.html | 3 +- www/genometools.org/htdocs/tools/gt_dupfeat.html | 3 +- www/genometools.org/htdocs/tools/gt_encseq.html | 3 +- .../htdocs/tools/gt_encseq2spm.html | 3 +- .../htdocs/tools/gt_encseq_bench.html | 3 +- .../htdocs/tools/gt_encseq_bitextract.html | 3 +- .../htdocs/tools/gt_encseq_check.html | 3 +- .../htdocs/tools/gt_encseq_decode.html | 3 +- .../htdocs/tools/gt_encseq_encode.html | 3 +- .../htdocs/tools/gt_encseq_info.html | 3 +- .../htdocs/tools/gt_encseq_md5.html | 3 +- .../htdocs/tools/gt_encseq_sample.html | 3 +- www/genometools.org/htdocs/tools/gt_eval.html | 3 +- .../htdocs/tools/gt_extractfeat.html | 3 +- .../htdocs/tools/gt_extractseq.html | 3 +- .../htdocs/tools/gt_fastq_sample.html | 3 +- .../htdocs/tools/gt_featureindex.html | 3 +- .../htdocs/tools/gt_fingerprint.html | 3 +- .../htdocs/tools/gt_genomediff.html | 1 - www/genometools.org/htdocs/tools/gt_gff3.html | 3 +- .../htdocs/tools/gt_gff3_to_gtf.html | 3 +- .../htdocs/tools/gt_gff3validator.html | 3 +- .../htdocs/tools/gt_gtf_to_gff3.html | 3 +- www/genometools.org/htdocs/tools/gt_hop.html | 3 +- www/genometools.org/htdocs/tools/gt_id_to_md5.html | 3 +- .../htdocs/tools/gt_inlineseq_add.html | 3 +- .../htdocs/tools/gt_inlineseq_split.html | 3 +- www/genometools.org/htdocs/tools/gt_interfeat.html | 3 +- www/genometools.org/htdocs/tools/gt_loccheck.html | 3 +- .../htdocs/tools/gt_ltrclustering.html | 3 +- www/genometools.org/htdocs/tools/gt_ltrdigest.html | 3 +- .../htdocs/tools/gt_ltrharvest.html | 3 +- www/genometools.org/htdocs/tools/gt_matchtool.html | 3 +- www/genometools.org/htdocs/tools/gt_matstat.html | 1 - www/genometools.org/htdocs/tools/gt_md5_to_id.html | 3 +- www/genometools.org/htdocs/tools/gt_merge.html | 3 +- www/genometools.org/htdocs/tools/gt_mergefeat.html | 3 +- .../htdocs/tools/gt_mkfeatureindex.html | 3 +- .../htdocs/tools/gt_mmapandread.html | 3 +- www/genometools.org/htdocs/tools/gt_orffinder.html | 3 +- .../htdocs/tools/gt_packedindex.html | 3 +- www/genometools.org/htdocs/tools/gt_prebwt.html | 1 - .../htdocs/tools/gt_readjoiner.html | 3 +- .../htdocs/tools/gt_readjoiner_assembly.html | 3 +- .../htdocs/tools/gt_readjoiner_overlap.html | 3 +- .../htdocs/tools/gt_readjoiner_prefilter.html | 3 +- www/genometools.org/htdocs/tools/gt_repfind.html | 83 +- .../htdocs/tools/gt_scriptfilter.html | 3 +- .../htdocs/tools/gt_seed_extend.html | 132 +- www/genometools.org/htdocs/tools/gt_select.html | 3 +- www/genometools.org/htdocs/tools/gt_seq.html | 3 +- www/genometools.org/htdocs/tools/gt_seqfilter.html | 3 +- www/genometools.org/htdocs/tools/gt_seqids.html | 3 +- www/genometools.org/htdocs/tools/gt_seqmutate.html | 3 +- www/genometools.org/htdocs/tools/gt_seqorder.html | 11 +- www/genometools.org/htdocs/tools/gt_seqstat.html | 11 +- .../htdocs/tools/gt_seqtransform.html | 3 +- .../htdocs/tools/gt_seqtranslate.html | 3 +- www/genometools.org/htdocs/tools/gt_sequniq.html | 3 +- www/genometools.org/htdocs/tools/gt_shredder.html | 3 +- .../htdocs/tools/gt_shulengthdist.html | 1 - www/genometools.org/htdocs/tools/gt_simreads.html | 1 - www/genometools.org/htdocs/tools/gt_sketch.html | 3 +- .../htdocs/tools/gt_sketch_page.html | 3 +- www/genometools.org/htdocs/tools/gt_snpper.html | 3 +- www/genometools.org/htdocs/tools/gt_speck.html | 3 +- .../htdocs/tools/gt_splicesiteinfo.html | 3 +- .../htdocs/tools/gt_splitfasta.html | 3 +- www/genometools.org/htdocs/tools/gt_stat.html | 3 +- www/genometools.org/htdocs/tools/gt_tagerator.html | 1 - www/genometools.org/htdocs/tools/gt_tallymer.html | 3 +- .../htdocs/tools/gt_tallymer_mkindex.html | 1 - .../htdocs/tools/gt_tallymer_occratio.html | 1 - .../htdocs/tools/gt_tallymer_search.html | 1 - www/genometools.org/htdocs/tools/gt_tirvish.html | 3 +- www/genometools.org/htdocs/tools/gt_uniq.html | 3 +- www/genometools.org/htdocs/tools/gt_uniquesub.html | 1 - www/genometools.org/htdocs/tools/gt_wtree.html | 3 +- www/genometools.org/htdocs/trackselectors.html | 1 - 370 files changed, 43085 insertions(+), 9525 deletions(-) create mode 100644 scripts/SEmatch.rb create mode 100755 scripts/check-fstperquery.rb delete mode 100755 scripts/collect-mappings.rb create mode 100755 scripts/cutsequences.rb create mode 100755 scripts/enumkmers.rb create mode 100755 scripts/estim-kmer-size.rb create mode 100755 scripts/evalue-filter.rb create mode 100755 scripts/extract-seed.rb create mode 100644 scripts/fasta.rb create mode 100755 scripts/gen-display-struct.rb create mode 100755 scripts/gfa2lint.rb create mode 100755 scripts/manyshort-somelong.rb create mode 100755 scripts/matches-compare.rb create mode 100755 scripts/matches2ani.rb create mode 100755 scripts/mk_ft_longest_common.rb create mode 100644 scripts/print_sequence.rb create mode 100755 scripts/reverse-complement.rb create mode 100755 scripts/se-permutation.rb create mode 100755 scripts/seeds2maxmatches.rb create mode 100755 scripts/single-read-mapping.sh create mode 100755 scripts/travis_installdeps.sh copy scripts/{alloutputoptions.rb => turnwheel.rb} (55%) mode change 100755 => 100644 create mode 100644 src/core/csvline_reader.c create mode 100644 src/core/csvline_reader.h create mode 100644 src/core/radixsort-ip-flba.inc create mode 100644 src/match/diagband-struct.c create mode 100644 src/match/diagband-struct.h create mode 100644 src/match/ft-eoplist.c create mode 100644 src/match/ft-eoplist.h create mode 100644 src/match/ft-longest-common.inc create mode 100644 src/match/gfa_writer.c create mode 100644 src/match/gfa_writer.h create mode 100644 src/match/karlin_altschul_stat.c create mode 100644 src/match/karlin_altschul_stat.h create mode 100644 src/match/querymatch-display.c create mode 100644 src/match/querymatch-display.h create mode 100644 src/match/rectangle-store.c create mode 100644 src/match/rectangle-store.h create mode 100644 src/match/se-display-fwd.inc create mode 100644 src/match/se-display.inc create mode 100644 src/match/seed_extend_parts.c create mode 100644 src/match/seed_extend_parts.h copy src/tools/{gt_readjoiner_asqg.c => gt_readjoiner_gfa.c} (67%) copy src/{match/lua_tools.h => tools/gt_readjoiner_gfa.h} (78%) create mode 100644 testdata/at-C99887-fwd.fna create mode 100644 testdata/at-C99887-rev.fna create mode 100644 testdata/at-C99930.fna create mode 100644 testdata/gt_seqorder_test_sortlength.fas create mode 100644 testdata/matchtool_see-ext.match create mode 100644 testdata/query-fwd.match create mode 100644 testdata/query-rev.match create mode 100644 testdata/readjoiner/30x_800nt.gfa1 create mode 100644 testdata/readjoiner/30x_800nt.gfa2 create mode 100644 testdata/readjoiner/30x_long_varlen.gfa1 create mode 100644 testdata/readjoiner/30x_long_varlen.gfa2 create mode 100644 testdata/readjoiner/70x_100nt.gfa1 create mode 100644 testdata/readjoiner/70x_100nt.gfa2 create mode 100644 testdata/readjoiner/contained_varlen.gfa1 create mode 100644 testdata/readjoiner/contained_varlen.gfa2 create mode 100644 testdata/see-ext-U8-evalue-bitscore.matches create mode 100644 testdata/see-ext-ani-at1MB-U8.txt create mode 100644 testdata/see-ext-at1MB-400-al-from-dtrace.matches create mode 100644 testdata/see-ext-at1MB-400-cigar.matches create mode 100644 testdata/see-ext-at1MB-400-cigarX.matches create mode 100644 testdata/see-ext-at1MB-400-dtrace.matches create mode 100644 testdata/see-ext-at1MB-400-evalue-bitscore.matches create mode 100644 testdata/see-ext-at1MB-400-seqdesc.matches create mode 100644 testdata/see-ext-at1MB-400-seqlength.matches create mode 100644 testdata/see-ext-at1MB-400-trace.matches create mode 100644 testdata/see-ext-at1MB-500-al.matches create mode 100644 testdata/see-ext-at1MB-500-alignment-seed_in_algn.matches create mode 100644 testdata/see-ext-at1MB-500-failed_seed.matches create mode 100644 testdata/see-ext-at1MB-Atinsert100-evalue-bitscore-cigar-seqlength.matches create mode 100644 testdata/see-ext-at1MB-Atinsert100-evalue-bitscore-cigarX-seqlength.matches create mode 100644 testdata/see-ext-at1MB-U8-200-al-from-dtrace.matches create mode 100644 testdata/see-ext-at1MB-maxmat250.matches create mode 100644 testdata/see-ext-at1MB-mincoverage200-tabsep.matches create mode 100644 testdata/see-ext-at1MB-u8-failed_seed-evalue.matches create mode 100644 testdata/see-ext-at1MB-u8-maxmat30.matches create mode 100644 testdata/see-ext-at1MB-u8.matches create mode 100644 testdata/see-ext-at1MB.matches create mode 100644 testdata/see-ext-fastq_long-u8.matches create mode 100644 testdata/see-ext-fastq_long.matches copy testdata/{condenseq/varlen_0.01_50_queries_300.fas => see-ext-paired-u8.matches} (100%) create mode 100644 testdata/see-ext-paired.matches -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/genometools.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit