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git.donarmstrong.com Git - biopieces.git/log
martinahansen [Tue, 24 May 2011 13:40:44 +0000 (13:40 +0000)]
working on clean_reads scripts
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1425
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martinahansen [Tue, 24 May 2011 13:36:23 +0000 (13:36 +0000)]
working on clean_reads scripts
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1424
74ccb610-7750-0410-82ae-
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martinahansen [Tue, 24 May 2011 12:36:45 +0000 (12:36 +0000)]
fixed strange bug in find_adaptor
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1423
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martinahansen [Tue, 24 May 2011 11:44:09 +0000 (11:44 +0000)]
fixed asseble_seq_velvet
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1422
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martinahansen [Tue, 24 May 2011 11:39:39 +0000 (11:39 +0000)]
fixed asseble_seq_idba
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1421
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martinahansen [Tue, 24 May 2011 09:11:38 +0000 (09:11 +0000)]
polished bp_scripts
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1420
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martinahansen [Mon, 23 May 2011 19:49:44 +0000 (19:49 +0000)]
fixed find_adaptor tests
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1419
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martinahansen [Mon, 23 May 2011 16:04:28 +0000 (16:04 +0000)]
polishing find_adaptor
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1418
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martinahansen [Mon, 23 May 2011 15:24:40 +0000 (15:24 +0000)]
fixed critical flaw in find_adaptor
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1416
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martinahansen [Mon, 23 May 2011 15:07:31 +0000 (15:07 +0000)]
fixed critical bug in biopieces.rb and reworked find_adaptor
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1415
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martinahansen [Mon, 23 May 2011 10:10:30 +0000 (10:10 +0000)]
committing major ruby overhaul
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1413
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martinahansen [Thu, 19 May 2011 13:49:59 +0000 (13:49 +0000)]
fiddleling with biopieces.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1412
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martinahansen [Thu, 19 May 2011 11:34:32 +0000 (11:34 +0000)]
preparing biopieces.rb rewrite
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1411
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martinahansen [Wed, 18 May 2011 15:50:33 +0000 (15:50 +0000)]
fixed a path in biopieces.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1410
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martinahansen [Wed, 18 May 2011 15:18:59 +0000 (15:18 +0000)]
fixed paths in assemble_seq_idba + velvet
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1409
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martinahansen [Wed, 18 May 2011 14:52:28 +0000 (14:52 +0000)]
refactored patternmatcher
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1408
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martinahansen [Fri, 13 May 2011 19:58:31 +0000 (19:58 +0000)]
updated 00README file in ruby dir
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1407
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martinahansen [Fri, 13 May 2011 19:55:33 +0000 (19:55 +0000)]
cleaning up old ruby trunk
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1406
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martinahansen [Fri, 13 May 2011 19:46:09 +0000 (19:46 +0000)]
changed layout of ruby source
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1405
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martinahansen [Fri, 13 May 2011 10:11:55 +0000 (10:11 +0000)]
add dist option to find_adaptor
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1403
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martinahansen [Thu, 12 May 2011 15:48:11 +0000 (15:48 +0000)]
upgraded add_ident tests
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1402
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martinahansen [Thu, 12 May 2011 15:43:47 +0000 (15:43 +0000)]
added offset switch to add_ident
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1400
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martinahansen [Wed, 11 May 2011 13:52:28 +0000 (13:52 +0000)]
1 vector only patternmatcher.rb now :o)
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1399
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martinahansen [Tue, 10 May 2011 16:49:36 +0000 (16:49 +0000)]
fixed pipes for adaptor removal
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1398
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martinahansen [Tue, 10 May 2011 14:15:02 +0000 (14:15 +0000)]
added fix for negative 454 decimal values
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1397
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martinahansen [Tue, 10 May 2011 10:35:48 +0000 (10:35 +0000)]
fixed type cast bug
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1396
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martinahansen [Tue, 10 May 2011 10:30:30 +0000 (10:30 +0000)]
added procedure switch to analyze_assembly
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1393
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martinahansen [Tue, 10 May 2011 10:27:31 +0000 (10:27 +0000)]
added procedure switch to find_genes
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1391
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martinahansen [Tue, 10 May 2011 08:20:09 +0000 (08:20 +0000)]
polished analyze_assembly
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1390
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martinahansen [Mon, 9 May 2011 11:13:31 +0000 (11:13 +0000)]
polishing gene cov feature in analyze_assembly
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1388
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martinahansen [Mon, 9 May 2011 10:32:57 +0000 (10:32 +0000)]
added gene coverage to analyze_assembly
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1386
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martinahansen [Mon, 9 May 2011 10:24:51 +0000 (10:24 +0000)]
added coverage method to prodigal.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1384
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martinahansen [Mon, 9 May 2011 09:23:40 +0000 (09:23 +0000)]
added fix to find_genes
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1383
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martinahansen [Mon, 9 May 2011 09:01:48 +0000 (09:01 +0000)]
ported find_genes to ruby
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1382
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martinahansen [Mon, 9 May 2011 08:57:58 +0000 (08:57 +0000)]
fixed indentation in uclust_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1381
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martinahansen [Mon, 9 May 2011 08:47:21 +0000 (08:47 +0000)]
added prodigal.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1380
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martinahansen [Mon, 9 May 2011 08:46:56 +0000 (08:46 +0000)]
updated genbank.rb to allow empty defaults
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1379
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martinahansen [Fri, 6 May 2011 12:42:30 +0000 (12:42 +0000)]
added full switch to find_genes
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1377
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martinahansen [Fri, 6 May 2011 06:31:11 +0000 (06:31 +0000)]
removing sequence file from assemble_seq*
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1376
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martinahansen [Thu, 5 May 2011 08:50:41 +0000 (08:50 +0000)]
polished asseble_seq_velvet
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1374
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martinahansen [Thu, 5 May 2011 08:47:55 +0000 (08:47 +0000)]
removed name option from asseble_seq_idba
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1372
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martinahansen [Wed, 4 May 2011 19:36:35 +0000 (19:36 +0000)]
added assemble_seq_velvet draft biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1371
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martinahansen [Wed, 4 May 2011 14:10:50 +0000 (14:10 +0000)]
fixed default cast for lists in biopieces.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1370
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martinahansen [Wed, 4 May 2011 11:19:07 +0000 (11:19 +0000)]
refactoring arg name in assemble_seq_idba
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1368
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martinahansen [Wed, 4 May 2011 11:08:27 +0000 (11:08 +0000)]
added --clean to assemble_seq_idba
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1366
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martinahansen [Tue, 3 May 2011 15:35:52 +0000 (15:35 +0000)]
polished assemble_seq_idba
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1361
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martinahansen [Tue, 3 May 2011 14:16:00 +0000 (14:16 +0000)]
added assemble_seq_idba
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1360
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martinahansen [Tue, 3 May 2011 12:46:45 +0000 (12:46 +0000)]
made plot_scores 1-based
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1359
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martinahansen [Tue, 3 May 2011 10:06:03 +0000 (10:06 +0000)]
corrected plot_matches missing -persists switch
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1358
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martinahansen [Tue, 3 May 2011 08:04:50 +0000 (08:04 +0000)]
added titles to plot_scores
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1356
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martinahansen [Mon, 2 May 2011 14:10:19 +0000 (14:10 +0000)]
fixed typo in analyce_gc
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1355
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martinahansen [Mon, 2 May 2011 13:59:01 +0000 (13:59 +0000)]
code update
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1354
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martinahansen [Mon, 2 May 2011 13:41:55 +0000 (13:41 +0000)]
ported plot_scores to ruby
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1352
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martinahansen [Mon, 2 May 2011 11:19:03 +0000 (11:19 +0000)]
removed redundant line from plot_scores
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1351
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martinahansen [Mon, 2 May 2011 09:36:40 +0000 (09:36 +0000)]
testing unspecified features
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1350
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martinahansen [Mon, 2 May 2011 07:56:38 +0000 (07:56 +0000)]
added tests to analyze_gc
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1349
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martinahansen [Tue, 26 Apr 2011 10:22:31 +0000 (10:22 +0000)]
adaptor script posilished
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1348
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martinahansen [Tue, 26 Apr 2011 08:34:24 +0000 (08:34 +0000)]
added useful biopiece scripts
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1347
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martinahansen [Tue, 19 Apr 2011 15:04:09 +0000 (15:04 +0000)]
fixed bit fields in pattern matcher
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1346
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martinahansen [Tue, 19 Apr 2011 10:10:48 +0000 (10:10 +0000)]
polishing find_adaptor
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1345
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martinahansen [Tue, 19 Apr 2011 08:35:40 +0000 (08:35 +0000)]
added cache option to find_adaptor
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1344
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martinahansen [Tue, 19 Apr 2011 08:31:17 +0000 (08:31 +0000)]
added cache option to find_adaptor
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1342
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martinahansen [Mon, 18 Apr 2011 14:17:30 +0000 (14:17 +0000)]
added clip_adaptor biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1340
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martinahansen [Mon, 18 Apr 2011 14:05:38 +0000 (14:05 +0000)]
added clip_adaptor biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1339
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martinahansen [Mon, 18 Apr 2011 12:32:34 +0000 (12:32 +0000)]
added tests for find_adaptor
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1336
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martinahansen [Mon, 18 Apr 2011 12:20:10 +0000 (12:20 +0000)]
fixed bug in find_adaptor
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1334
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martinahansen [Mon, 18 Apr 2011 10:09:59 +0000 (10:09 +0000)]
fixed bug in find_adaptor
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1333
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martinahansen [Mon, 18 Apr 2011 07:45:54 +0000 (07:45 +0000)]
added find_adaptor biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1330
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martinahansen [Sat, 16 Apr 2011 07:08:08 +0000 (07:08 +0000)]
cleaned patternmatcher code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1329
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martinahansen [Fri, 15 Apr 2011 12:38:49 +0000 (12:38 +0000)]
pattern hell
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1328
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martinahansen [Thu, 14 Apr 2011 14:27:47 +0000 (14:27 +0000)]
updated patternmatcher code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1327
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martinahansen [Thu, 14 Apr 2011 12:21:49 +0000 (12:21 +0000)]
added length check to read_454
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1326
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martinahansen [Thu, 14 Apr 2011 12:13:42 +0000 (12:13 +0000)]
fixed missing qual trimming in remove_mids
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1325
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martinahansen [Wed, 13 Apr 2011 11:36:12 +0000 (11:36 +0000)]
added remove_mids tests
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1324
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martinahansen [Wed, 13 Apr 2011 11:31:43 +0000 (11:31 +0000)]
added remove_mids
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1322
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martinahansen [Mon, 11 Apr 2011 10:46:01 +0000 (10:46 +0000)]
prettyfied gnuplots
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1319
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martinahansen [Mon, 11 Apr 2011 09:24:22 +0000 (09:24 +0000)]
added persist to gnuplot commands
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1318
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martinahansen [Wed, 30 Mar 2011 11:15:10 +0000 (11:15 +0000)]
reverted patternmatcher to original
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1316
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martinahansen [Wed, 30 Mar 2011 09:52:59 +0000 (09:52 +0000)]
removing Args.pyc from svn
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1315
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martinahansen [Wed, 30 Mar 2011 09:35:54 +0000 (09:35 +0000)]
updated find_mids
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1314
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martinahansen [Wed, 30 Mar 2011 09:30:55 +0000 (09:30 +0000)]
updated tests for find_mids
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1313
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martinahansen [Wed, 30 Mar 2011 09:24:21 +0000 (09:24 +0000)]
renamed find_mids.in file
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1312
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martinahansen [Wed, 30 Mar 2011 09:23:53 +0000 (09:23 +0000)]
renamed find_mids.in file
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1311
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martinahansen [Tue, 29 Mar 2011 17:41:04 +0000 (17:41 +0000)]
seq.rb update
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1310
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martinahansen [Tue, 29 Mar 2011 13:00:00 +0000 (13:00 +0000)]
added final unit test to test_patternmatcher.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1309
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martinahansen [Tue, 29 Mar 2011 10:14:12 +0000 (10:14 +0000)]
fixed Rakefile
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1308
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martinahansen [Tue, 29 Mar 2011 08:24:17 +0000 (08:24 +0000)]
removed amatch dependency in ruby code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1307
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martinahansen [Mon, 28 Mar 2011 21:22:26 +0000 (21:22 +0000)]
fixed patternmatcher.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1306
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martinahansen [Mon, 28 Mar 2011 14:46:16 +0000 (14:46 +0000)]
added PatternMatcher to ruby code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1305
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martinahansen [Sun, 20 Mar 2011 21:40:28 +0000 (21:40 +0000)]
plain and hd match in ruby Seq.rb now works
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1304
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martinahansen [Sat, 19 Mar 2011 21:07:42 +0000 (21:07 +0000)]
worked on match code in Seq.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1303
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martinahansen [Sat, 19 Mar 2011 20:40:01 +0000 (20:40 +0000)]
added rdoc stuff
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1302
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martinahansen [Sat, 19 Mar 2011 20:38:52 +0000 (20:38 +0000)]
worked on match code for ruby Seq class
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1301
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martinahansen [Sat, 19 Mar 2011 14:53:11 +0000 (14:53 +0000)]
added test_digest.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1300
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martinahansen [Sat, 19 Mar 2011 14:44:52 +0000 (14:44 +0000)]
split digest.rb from seq.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1299
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martinahansen [Sat, 19 Mar 2011 14:15:00 +0000 (14:15 +0000)]
removing align.rb code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1298
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martinahansen [Sat, 19 Mar 2011 14:14:39 +0000 (14:14 +0000)]
removing align.rb code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1297
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martinahansen [Sat, 19 Mar 2011 08:20:17 +0000 (08:20 +0000)]
cleanup of Filsys in ruby code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1296
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martinahansen [Fri, 18 Mar 2011 17:03:43 +0000 (17:03 +0000)]
filesys now polished
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1295
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martinahansen [Fri, 18 Mar 2011 17:00:13 +0000 (17:00 +0000)]
added filesys
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1294
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projects / biopieces.git / log