[med-svn] [genometools] 02/03: Merge tag 'upstream/1.5.10+ds'
Sascha Steinbiss
satta at debian.org
Sun Aug 6 14:14:46 UTC 2017
This is an automated email from the git hooks/post-receive script.
satta pushed a commit to branch master
in repository genometools.
commit 895438c4ec2e91ab7970fc7f2611c58df10d5403
Merge: 5276924 17a2684
Author: Sascha Steinbiss <satta at 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 | 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 +
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 | 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 -
364 files changed, 43070 insertions(+), 9498 deletions(-)
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