[med-svn] [genometools] branch upstream updated (a84e526 -> 17a2684)

Sascha Steinbiss satta at debian.org
Sun Aug 6 14:14:47 UTC 2017


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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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