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satta pushed a change to branch master
in repository genometools.
from 5276924 use correct latex dependency
new 17a2684 New upstream version 1.5.10+ds
new 895438c Merge tag 'upstream/1.5.10+ds'
new 80bbe17 WIP: ner upstream
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:
.travis.yml | 45 +-
CHANGELOG | 19 +-
Makefile | 15 +-
VERSION | 2 +-
debian/changelog | 7 +
debian/genometools-common.install | 19 +-
debian/patches/adding_soname | 4 +-
debian/patches/libbam-fix | 6 +-
debian/patches/reproducible | 4 +-
debian/patches/series | 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 -
370 files changed, 43085 insertions(+), 9525 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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