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Update AliTV perl interface to version 1.0.0
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@iimog
iimog committed Apr 13, 2017
1 parent eb8fbbe commit f965055
Showing 1 changed file with 1 addition and 1 deletion.
2 changes: 1 addition & 1 deletion AliTV-perl-interface
Submodule AliTV-perl-interface updated 53 files
+25 −3 MANIFEST
+6 −1 Makefile.PL
+0 −40 README
+379 −0 bin/alitv-filter.pl
+171 −41 bin/alitv.pl
+110 −0 data/chloroset/importer.yml
+17 −0 data/chloroset/input.yml
+1,246 −0 data/chloroset/pregenerated_maf/temp9PSge.maf
+1,210 −0 data/chloroset/pregenerated_maf/tempLdMGL.maf
+1,370 −0 data/chloroset/pregenerated_maf/tempRBBMe.maf
+498 −0 data/chloroset/pregenerated_maf/tempTSbMa.maf
+1,198 −0 data/chloroset/pregenerated_maf/tempiUqZk.maf
+862 −0 data/chloroset/pregenerated_maf/tempqPXZ7.maf
+1,614 −0 data/chloroset/pregenerated_maf/tempsYXwN.maf
+638 −0 data/chloroset/pregenerated_maf/tempzWY0h.maf
+14 −0 data/single_genome_with_alignment.yml
+74 −0 data/vectors/001_uniq.maf
+30 −0 data/vectors/002_uniq.maf
+38 −0 data/vectors/003_uniq.maf
+42 −0 data/vectors/004_uniq.maf
+29 −0 data/vectors/importer.yml
+328 −59 lib/AliTV.pm
+182 −16 lib/AliTV/Alignment.pm
+60 −0 lib/AliTV/Alignment/importer.pm
+13 −7 lib/AliTV/Alignment/lastz.pm
+64 −0 lib/AliTV/Alignment/template.pm
+1 −1 lib/AliTV/Base/Version.pm
+33 −29 lib/AliTV/Genome.pm
+83 −1 lib/AliTV/Tree.pm
+3 −3 t/112_AliTV-Tree-tree_2_json_structure.t
+50 −15 t/113_AliTV-Tree-balance_node_depth.t
+68 −0 t/116_AliTV-Tree-_ladderize.t
+46 −0 t/117_AliTV-Tree-get_genome_order.t
+30 −0 t/504_AliTV-file.t
+7 −4 t/505_AliTV-get_default_settings.t
+29 −0 t/506_AliTV-project.t
+75 −0 t/507_AliTV-_write_mapping_file.t
+82 −0 t/508_AliTV-maximum_seq_length_in_json.t
+53 −0 t/509_AliTV-_calculate_tick_distance.t
+5 −2 t/510_AliTV-run_working.t
+4 −2 t/520_AliTV-_generate_seq_set.t
+14 −1 t/607_AliTV-Genome-get_features.t
+32 −2 t/610_AliTV-Genome-set_uniq_seq_names.t
+0 −32 t/645_AliTV-Genome-fix_maf_revcomp.t
+44 −0 t/712_AliTV-Alignment-sequence_set.t
+12 −4 t/713_AliTV-Alignment-parameters.t
+15 −0 t/714_AliTV-Alignment-_check_if_maf_fix_is_required.t
+34 −23 t/735_AliTV-Alignment-import_alignments.t
+36 −5 t/737_AliTV-Alignment-export-to-genome.t
+19 −17 t/752_AliTV-Alignment-lastz-run.t
+5 −0 t/760_AliTV-Alignment-importer.t
+17 −0 t/761_AliTV-Alignment-importer-_check.t
+17 −0 t/762_AliTV-Alignment-importer-run.t

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