[med-svn] [genometools] branch upstream updated (a84e526 -> 17a2684)
Sascha Steinbiss
satta at debian.org
Sun Aug 6 14:14:47 UTC 2017
This is an automated email from the git hooks/post-receive script.
satta pushed a change to branch upstream
in repository genometools.
from a84e526 Imported Upstream version 1.5.9+ds
new 17a2684 New upstream version 1.5.10+ds
The 1 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 +-
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 -
364 files changed, 43070 insertions(+), 9498 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
--
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