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commit 895438c4ec2e91ab7970fc7f2611c58df10d5403 Merge: 5276924 17a2684 Author: Sascha Steinbiss <sa...@debian.org> Date: Sun Aug 6 15:45:45 2017 +0200 Merge tag 'upstream/1.5.10+ds' Upstream version 1.5.10+ds .travis.yml | 45 +- CHANGELOG | 19 +- Makefile | 15 +- VERSION | 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 | 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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 + testdata/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 | 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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 - 364 files changed, 43070 insertions(+), 9498 deletions(-) -- 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