[med-svn] [genometools] branch master updated (ce6f539 -> f73a143)
Sascha Steinbiss
satta at debian.org
Fri Jul 22 11:13:19 UTC 2016
This is an automated email from the git hooks/post-receive script.
satta pushed a change to branch master
in repository genometools.
from ce6f539 bump Standards-Version
new a84e526 Imported Upstream version 1.5.9+ds
new 6928fbb Merge tag 'upstream/1.5.9+ds'
new f73a143 new upstream release
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:
.github/ISSUE_TEMPLATE.md | 19 +
.github/PULL_REQUEST_TEMPLATE.md | 12 +
.gitignore | 1 +
CHANGELOG | 16 +
INSTALL | 25 +-
LICENSE | 33 +-
Makefile | 425 ++--
VERSION | 2 +-
debian/changelog | 7 +
debian/patches/adding_soname | 12 +-
debian/patches/gtdoc-traverse-sorted | 4 +-
debian/patches/ignore-m32-m64.patch | 2 +-
debian/patches/libbam-fix | 27 +-
debian/patches/remove_png_timestamps | 12 +-
debian/patches/series | 2 -
debian/patches/spelling | 292 ---
debian/patches/split-manuals | 14 +-
debian/patches/use-mx32 | 2 +-
debian/patches/use-pkgconfig | 191 --
doc/devguide/devguide.tex | 27 +-
doc/manuals/annotationsketch.tex | 6 +
doc/manuals/genomediff.tex | 1 +
doc/manuals/hop.tex | 1 +
doc/manuals/ltrdigest.tex | 1 +
doc/manuals/ltrharvest.tex | 1 +
doc/manuals/mgth.tex | 1 +
doc/manuals/packedindex.tex | 1 +
doc/manuals/readjoiner.tex | 1 +
doc/manuals/repfind.tex | 1 +
doc/manuals/tagerator.tex | 1 +
doc/manuals/tallymer.tex | 1 +
doc/manuals/uniquesub.tex | 1 +
gtdata/doc/extractseq.lua | 2 +-
gtdata/doc/fingerprint.lua | 2 +-
gtdata/modules/external/des56.lua | 1 +
gtdata/modules/external/md5.lua | 21 +-
gtdata/modules/gtdoclib/class_latex.lp | 4 +-
gtdata/modules/gtdoclib/classes_latex.lp | 3 +-
gtdata/modules/gtdoclib/docvisitorlatex.lua | 31 +-
gtdata/modules/gtdoclib/footer.lp | 2 +-
.../gtdoclib/libgenometools_header_latex.lp | 3 +-
gtdata/modules/gtdoclib/method_latex.lp | 5 +-
gtdata/modules/gtdoclib/module_latex.lp | 2 +-
gtdata/modules/gtdoclib/modules_latex.lp | 1 +
gtdata/modules/gtdoclib/sole_function_latex.lp | 3 +-
gtdata/spec/output_drivers/tabular | 72 +
gtdata/spec/speclib.lua | 14 +
gtpython/tests/test_version.py | 4 +-
gtscripts/gtdoc.lua | 16 +-
scripts/collect-mappings.rb | 26 +
scripts/coverage-MEM.rb | 97 +
scripts/esq-in-bytes.sh | 5 +-
scripts/gen-intsets.rb | 28 +-
scripts/gen-randseq.rb | 42 +-
scripts/sim-read-mapping.sh | 87 +
src/core/compact_ulong_store.h | 2 +-
src/core/encseq.c | 13 +-
src/core/encseq_col.c | 26 +-
src/core/error_api.h | 2 +-
src/core/fa.h | 2 +-
src/core/grep.c | 2 +-
src/core/hashtable.h | 4 +-
src/core/intbits.h | 2 +-
src/core/option_api.h | 4 +-
src/core/seq_iterator_api.h | 2 +-
src/extended/affinealign.c | 147 +-
src/extended/affinealign.h | 81 +-
src/extended/alignment.c | 63 +-
src/extended/cds_check_visitor.c | 29 +-
src/extended/compressed_bitsequence.c | 6 +-
src/extended/compressed_bitsequence.h | 6 +-
src/extended/condenseq.c | 26 +-
src/extended/condenseq.h | 15 +-
src/extended/condenseq_creator.c | 6 +-
src/extended/condenseq_rep.h | 34 +-
src/extended/diagonalbandalign.c | 237 +--
src/extended/diagonalbandalign.h | 85 +-
src/extended/diagonalbandalign_affinegapcost.c | 416 ++--
src/extended/diagonalbandalign_affinegapcost.h | 94 +-
src/extended/editscript.c | 150 +-
src/extended/elias_gamma.h | 2 +-
src/extended/encdesc.c | 14 +-
src/extended/encdesc.h | 17 +-
src/extended/golomb.c | 4 +-
src/extended/golomb.h | 12 +-
src/extended/hcr.c | 15 +-
src/extended/hcr.h | 17 +-
src/extended/huffcode.h | 73 +-
src/extended/intset_16.c | 28 +-
src/extended/intset_16.h | 4 +-
src/extended/intset_32.c | 28 +-
src/extended/intset_32.h | 4 +-
src/extended/intset_8.c | 28 +-
src/extended/intset_8.h | 4 +-
src/extended/linearalign.c | 266 +--
src/extended/linearalign.h | 101 +-
src/extended/linearalign_affinegapcost.c | 341 ++--
src/extended/linearalign_affinegapcost.h | 123 +-
src/extended/linspace_management.c | 101 +-
src/extended/linspace_management.h | 83 +-
src/extended/maxcoordvalue.c | 73 +-
src/extended/maxcoordvalue.h | 42 +-
src/extended/node_stream_api.h | 2 +-
src/extended/popcount_tab.h | 14 +-
src/extended/rcr.c | 33 +-
src/extended/rcr.h | 2 +-
src/extended/reconstructalignment.c | 93 +-
src/extended/reconstructalignment.h | 87 +-
src/extended/sam_alignment.c | 2 +-
src/extended/sam_alignment_rep.h | 2 +-
src/extended/samfile_iterator.c | 2 +-
src/extended/scorehandler.c | 2 +-
src/extended/scorehandler.h | 31 +-
src/extended/spec_results.c | 21 +-
src/extended/spec_results.h | 3 +
src/extended/squarealign.c | 183 +-
src/extended/squarealign.h | 83 +-
src/extended/type_node.c | 2 +-
src/gth/align_protein.c | 2 +-
src/gth/intermediate.c | 4 +-
src/gth/parse_options.c | 2 +-
src/gtlua/region_mapping_lua.c | 117 +-
src/gtlua/region_mapping_lua.h | 18 +
src/gtr.c | 8 +-
src/interactive.c | 3 +-
src/ltr/ltrdigest_file_out_stream.c | 6 +-
src/match/declare-readfunc.h | 61 +
src/match/diagbandseed.c | 2052 +++++++++++++-------
src/match/diagbandseed.h | 84 +-
src/match/eis-encidxseq-construct.h | 2 +-
src/match/eis-encidxseq.c | 2 +-
src/match/eis-encidxseq.h | 4 +-
src/match/esa-mmsearch.c | 10 +-
src/match/querymatch-align.c | 26 +-
src/match/querymatch-align.h | 7 +-
src/match/querymatch.c | 228 ++-
src/match/querymatch.h | 21 +-
src/match/rdj-filesuf-def.h | 1 +
src/match/rdj-strgraph.c | 290 ++-
src/match/rdj-strgraph.h | 13 +
src/match/sarr-def.h | 37 +-
src/match/seed-extend-iter.c | 25 +-
src/match/seed-extend-iter.h | 12 +-
src/match/seed-extend.c | 35 +-
src/match/seed-extend.h | 15 +-
src/match/seqabstract.c | 11 +
src/match/seqabstract.h | 3 +
src/match/sfx-suffixer.c | 232 ++-
src/match/sfx-suffixer.h | 17 +
src/tools/gt_compreads_decompress.c | 2 +-
src/tools/gt_condenseq_compress.c | 2 +-
src/tools/gt_encseq_sample.c | 2 +-
src/tools/gt_encseq_sample.h | 2 +-
src/tools/gt_fastq_sample.c | 2 +-
src/tools/gt_fastq_sample.h | 2 +-
src/tools/gt_kmer_database.c | 2 +-
src/tools/gt_linspace_align.c | 22 +-
src/tools/gt_paircmp.c | 20 +-
src/tools/gt_readjoiner_assembly.c | 2 +-
src/tools/gt_readjoiner_graph.c | 95 +-
src/tools/gt_repfind.c | 49 +-
src/tools/gt_seed_extend.c | 607 +++---
src/tools/gt_seed_extend.h | 4 +-
src/tools/gt_seq.c | 183 +-
src/tools/gt_seqorder.c | 113 +-
src/tools/gt_show_seedext.c | 56 +-
src/tools/gt_show_seedext.h | 2 +-
src/tools/gt_speck.c | 12 +-
testdata/gt_encseq_col_test1.fasta | 428 ++++
testdata/gt_gff3_phases1.gff3 | 8 +
testdata/gt_gff3_phases1.out | 9 +
testdata/gt_gff3_phases2.gff3 | 8 +
testdata/gt_gff3_phases3.gff3 | 24 +
testdata/gt_gff3_phases3.out | 26 +
testdata/gt_gff3_phases4.gff3 | 10 +
testdata/gt_gff3_phases5.gff3 | 10 +
testdata/gt_gff3_phases6.gff3 | 10 +
testdata/gt_gff3_phases7.gff3 | 10 +
..._test_sort.fas => gt_seqorder_test_sorthdr.fas} | 44 +-
testdata/seedextend2.out.gz | Bin 233341 -> 233171 bytes
testsuite/gt_chain2dim_include.rb | 4 +-
testsuite/gt_extractseq_include.rb | 6 +-
testsuite/gt_gff3_include.rb | 30 +
testsuite/gt_ltrdigest_include.rb | 12 +
testsuite/gt_mergeesa_include.rb | 6 +-
testsuite/gt_repfind_include.rb | 68 +-
testsuite/gt_scripts_include.rb | 2 +-
testsuite/gt_seed_extend_include.rb | 248 ++-
testsuite/gt_seqorder_include.rb | 20 +
testsuite/gt_suffixerator_include.rb | 2 +-
testsuite/gt_tallymer_include.rb | 4 +-
testsuite/testsuite.rb | 6 +-
www/genometools.org/htdocs/docs.html | 13 +-
www/genometools.org/htdocs/libgenometools.html | 10 +-
www/genometools.org/htdocs/license.html | 6 +-
www/genometools.org/htdocs/tool.conf | 2 +-
www/genometools.org/htdocs/tool_list.conf | 2 +-
www/genometools.org/htdocs/tools.html | 2 +-
www/genometools.org/htdocs/tools/gt.html | 2 +-
.../htdocs/tools/gt_bed_to_gff3.html | 2 +-
www/genometools.org/htdocs/tools/gt_cds.html | 2 +-
www/genometools.org/htdocs/tools/gt_chain2dim.html | 2 +-
www/genometools.org/htdocs/tools/gt_chseqids.html | 2 +-
www/genometools.org/htdocs/tools/gt_clean.html | 2 +-
www/genometools.org/htdocs/tools/gt_compreads.html | 2 +-
.../htdocs/tools/gt_compreads_compress.html | 2 +-
.../htdocs/tools/gt_compreads_decompress.html | 4 +-
.../htdocs/tools/gt_compreads_refcompress.html | 2 +-
.../htdocs/tools/gt_compreads_refdecompress.html | 2 +-
www/genometools.org/htdocs/tools/gt_condenseq.html | 2 +-
.../htdocs/tools/gt_congruence.html | 2 +-
.../htdocs/tools/gt_congruence_spacedseed.html | 2 +-
.../htdocs/tools/gt_convertseq.html | 2 +-
www/genometools.org/htdocs/tools/gt_csa.html | 2 +-
www/genometools.org/htdocs/tools/gt_dot.html | 2 +-
www/genometools.org/htdocs/tools/gt_dupfeat.html | 2 +-
www/genometools.org/htdocs/tools/gt_encseq.html | 2 +-
.../htdocs/tools/gt_encseq2spm.html | 2 +-
.../htdocs/tools/gt_encseq_bench.html | 2 +-
.../htdocs/tools/gt_encseq_bitextract.html | 2 +-
.../htdocs/tools/gt_encseq_check.html | 2 +-
.../htdocs/tools/gt_encseq_decode.html | 2 +-
.../htdocs/tools/gt_encseq_encode.html | 2 +-
.../htdocs/tools/gt_encseq_info.html | 2 +-
.../htdocs/tools/gt_encseq_md5.html | 2 +-
.../htdocs/tools/gt_encseq_sample.html | 2 +-
www/genometools.org/htdocs/tools/gt_eval.html | 2 +-
.../htdocs/tools/gt_extractfeat.html | 2 +-
.../htdocs/tools/gt_extractseq.html | 4 +-
.../htdocs/tools/gt_fastq_sample.html | 2 +-
.../htdocs/tools/gt_featureindex.html | 2 +-
.../htdocs/tools/gt_fingerprint.html | 4 +-
.../htdocs/tools/gt_genomediff.html | 2 +-
www/genometools.org/htdocs/tools/gt_gff3.html | 2 +-
.../htdocs/tools/gt_gff3_to_gtf.html | 2 +-
.../htdocs/tools/gt_gff3validator.html | 2 +-
.../htdocs/tools/gt_gtf_to_gff3.html | 2 +-
www/genometools.org/htdocs/tools/gt_hop.html | 2 +-
www/genometools.org/htdocs/tools/gt_id_to_md5.html | 2 +-
.../htdocs/tools/gt_inlineseq_add.html | 2 +-
.../htdocs/tools/gt_inlineseq_split.html | 2 +-
www/genometools.org/htdocs/tools/gt_interfeat.html | 2 +-
www/genometools.org/htdocs/tools/gt_loccheck.html | 2 +-
.../htdocs/tools/gt_ltrclustering.html | 2 +-
www/genometools.org/htdocs/tools/gt_ltrdigest.html | 2 +-
.../htdocs/tools/gt_ltrharvest.html | 2 +-
www/genometools.org/htdocs/tools/gt_matchtool.html | 2 +-
www/genometools.org/htdocs/tools/gt_matstat.html | 2 +-
www/genometools.org/htdocs/tools/gt_md5_to_id.html | 2 +-
www/genometools.org/htdocs/tools/gt_merge.html | 2 +-
www/genometools.org/htdocs/tools/gt_mergefeat.html | 2 +-
.../htdocs/tools/gt_mkfeatureindex.html | 2 +-
.../htdocs/tools/gt_mmapandread.html | 2 +-
www/genometools.org/htdocs/tools/gt_orffinder.html | 2 +-
.../htdocs/tools/gt_packedindex.html | 2 +-
www/genometools.org/htdocs/tools/gt_prebwt.html | 2 +-
.../htdocs/tools/gt_readjoiner.html | 2 +-
.../htdocs/tools/gt_readjoiner_assembly.html | 2 +-
.../htdocs/tools/gt_readjoiner_overlap.html | 2 +-
.../htdocs/tools/gt_readjoiner_prefilter.html | 2 +-
www/genometools.org/htdocs/tools/gt_repfind.html | 2 +-
.../htdocs/tools/gt_scriptfilter.html | 2 +-
.../tools/{gt_repfind.html => gt_seed_extend.html} | 86 +-
www/genometools.org/htdocs/tools/gt_select.html | 2 +-
www/genometools.org/htdocs/tools/gt_seq.html | 28 +-
www/genometools.org/htdocs/tools/gt_seqfilter.html | 2 +-
www/genometools.org/htdocs/tools/gt_seqids.html | 2 +-
www/genometools.org/htdocs/tools/gt_seqmutate.html | 2 +-
www/genometools.org/htdocs/tools/gt_seqorder.html | 20 +-
www/genometools.org/htdocs/tools/gt_seqstat.html | 2 +-
.../htdocs/tools/gt_seqtransform.html | 2 +-
.../htdocs/tools/gt_seqtranslate.html | 2 +-
www/genometools.org/htdocs/tools/gt_sequniq.html | 2 +-
www/genometools.org/htdocs/tools/gt_shredder.html | 2 +-
.../htdocs/tools/gt_shulengthdist.html | 2 +-
www/genometools.org/htdocs/tools/gt_simreads.html | 2 +-
www/genometools.org/htdocs/tools/gt_sketch.html | 2 +-
.../htdocs/tools/gt_sketch_page.html | 2 +-
www/genometools.org/htdocs/tools/gt_snpper.html | 2 +-
www/genometools.org/htdocs/tools/gt_speck.html | 4 +-
.../htdocs/tools/gt_splicesiteinfo.html | 2 +-
.../htdocs/tools/gt_splitfasta.html | 2 +-
www/genometools.org/htdocs/tools/gt_stat.html | 2 +-
www/genometools.org/htdocs/tools/gt_tagerator.html | 2 +-
www/genometools.org/htdocs/tools/gt_tallymer.html | 2 +-
.../htdocs/tools/gt_tallymer_mkindex.html | 2 +-
.../htdocs/tools/gt_tallymer_occratio.html | 2 +-
.../htdocs/tools/gt_tallymer_search.html | 2 +-
www/genometools.org/htdocs/tools/gt_tirvish.html | 2 +-
www/genometools.org/htdocs/tools/gt_uniq.html | 2 +-
www/genometools.org/htdocs/tools/gt_uniquesub.html | 2 +-
www/genometools.org/htdocs/tools/gt_wtree.html | 2 +-
292 files changed, 6874 insertions(+), 4016 deletions(-)
create mode 100644 .github/ISSUE_TEMPLATE.md
create mode 100644 .github/PULL_REQUEST_TEMPLATE.md
create mode 100644 gtdata/modules/external/des56.lua
create mode 100644 gtdata/spec/output_drivers/tabular
create mode 100755 scripts/collect-mappings.rb
create mode 100755 scripts/coverage-MEM.rb
create mode 100755 scripts/sim-read-mapping.sh
create mode 100644 src/match/declare-readfunc.h
create mode 100644 testdata/gt_encseq_col_test1.fasta
create mode 100644 testdata/gt_gff3_phases1.gff3
create mode 100644 testdata/gt_gff3_phases1.out
create mode 100644 testdata/gt_gff3_phases2.gff3
create mode 100644 testdata/gt_gff3_phases3.gff3
create mode 100644 testdata/gt_gff3_phases3.out
create mode 100644 testdata/gt_gff3_phases4.gff3
create mode 100644 testdata/gt_gff3_phases5.gff3
create mode 100644 testdata/gt_gff3_phases6.gff3
create mode 100644 testdata/gt_gff3_phases7.gff3
copy testdata/{gt_seqorder_test_sort.fas => gt_seqorder_test_sorthdr.fas} (100%)
copy www/genometools.org/htdocs/tools/{gt_repfind.html => gt_seed_extend.html} (59%)
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/genometools.git
More information about the debian-med-commit
mailing list