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git.donarmstrong.com Git - biopieces.git/log
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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martinahansen [Fri, 18 Mar 2011 16:29:49 +0000 (16:29 +0000)]
fixed stdin read for fastq and ruby code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1293
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martinahansen [Fri, 18 Mar 2011 15:18:19 +0000 (15:18 +0000)]
polishing stdin for ruby code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1292
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martinahansen [Thu, 17 Mar 2011 14:02:17 +0000 (14:02 +0000)]
ruby cleanup
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1291
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martinahansen [Tue, 15 Mar 2011 10:31:54 +0000 (10:31 +0000)]
fixed bug in bwa_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1290
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martinahansen [Mon, 14 Mar 2011 13:43:27 +0000 (13:43 +0000)]
fixed missing license
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1289
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martinahansen [Tue, 8 Mar 2011 11:21:41 +0000 (11:21 +0000)]
updated remove_illumina_adaptor
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1286
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martinahansen [Mon, 7 Mar 2011 15:41:24 +0000 (15:41 +0000)]
updated remove_illumina_adaptor
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1283
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martinahansen [Mon, 7 Mar 2011 13:41:14 +0000 (13:41 +0000)]
added hamming distance to adaptor location/clipping in ruby lib
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1282
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martinahansen [Mon, 7 Mar 2011 12:00:19 +0000 (12:00 +0000)]
added hamming_dist method to bits.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1281
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martinahansen [Mon, 7 Mar 2011 09:46:22 +0000 (09:46 +0000)]
added bits.rb and test_bits.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1280
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martinahansen [Sun, 20 Feb 2011 13:45:37 +0000 (13:45 +0000)]
polished seq.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1279
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martinahansen [Sun, 20 Feb 2011 13:06:22 +0000 (13:06 +0000)]
added remove_illumina_adaptor Biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1277
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martinahansen [Sat, 19 Feb 2011 18:53:30 +0000 (18:53 +0000)]
added qual clipping to ruby code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1276
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martinahansen [Sat, 19 Feb 2011 15:27:44 +0000 (15:27 +0000)]
tried to fix unit testing errs in test_genbank.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1275
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martinahansen [Sat, 19 Feb 2011 15:03:56 +0000 (15:03 +0000)]
added Rakefile for unit testing of ruby code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1274
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martinahansen [Sat, 19 Feb 2011 14:51:05 +0000 (14:51 +0000)]
added adaptor_locate and adaptor_clip methods to ruby code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1273
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martinahansen [Fri, 11 Feb 2011 18:55:56 +0000 (18:55 +0000)]
fixed typo in sff.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1272
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martinahansen [Fri, 11 Feb 2011 18:42:48 +0000 (18:42 +0000)]
fixed typo in base36.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1271
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martinahansen [Fri, 11 Feb 2011 11:16:51 +0000 (11:16 +0000)]
updated tests for read_sff
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1270
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martinahansen [Fri, 11 Feb 2011 11:09:21 +0000 (11:09 +0000)]
added xy-coord extraction code to sff.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1268
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martinahansen [Fri, 11 Feb 2011 10:52:22 +0000 (10:52 +0000)]
added xy-coord extraction code to sff.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1266
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martinahansen [Fri, 11 Feb 2011 09:56:55 +0000 (09:56 +0000)]
added base36.rb Ruby library
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1265
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martinahansen [Tue, 8 Feb 2011 20:39:32 +0000 (20:39 +0000)]
removing stale test file
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1264
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martinahansen [Tue, 8 Feb 2011 20:38:46 +0000 (20:38 +0000)]
added read_sff biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1262
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martinahansen [Thu, 3 Feb 2011 19:04:29 +0000 (19:04 +0000)]
refactored shred_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1253
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martinahansen [Thu, 3 Feb 2011 18:44:14 +0000 (18:44 +0000)]
added subseq and subseq_rand methods to seq.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1252
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martinahansen [Thu, 3 Feb 2011 15:56:38 +0000 (15:56 +0000)]
crude polish of shred_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1251
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martinahansen [Wed, 2 Feb 2011 09:12:07 +0000 (09:12 +0000)]
added echo_yellow to testing code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1249
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martinahansen [Tue, 1 Feb 2011 13:55:08 +0000 (13:55 +0000)]
added analyze_assembly biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1247
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martinahansen [Tue, 1 Feb 2011 13:27:02 +0000 (13:27 +0000)]
added kmer_freq biopiece and tests
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1243
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martinahansen [Tue, 1 Feb 2011 12:53:36 +0000 (12:53 +0000)]
added generate_oligos method to seq.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1242
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martinahansen [Mon, 31 Jan 2011 21:06:54 +0000 (21:06 +0000)]
python update?
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1241
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martinahansen [Mon, 31 Jan 2011 21:05:30 +0000 (21:05 +0000)]
added tests of calc_N50
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1240
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martinahansen [Mon, 31 Jan 2011 21:01:59 +0000 (21:01 +0000)]
fixed bug in calc_N50
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1239
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martinahansen [Mon, 31 Jan 2011 20:47:49 +0000 (20:47 +0000)]
added calc_N50
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1238
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martinahansen [Mon, 31 Jan 2011 20:46:20 +0000 (20:46 +0000)]
remove calc_n50
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1237
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martinahansen [Mon, 31 Jan 2011 20:41:56 +0000 (20:41 +0000)]
removing calc_N50
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1236
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martinahansen@gmail.com [Mon, 31 Jan 2011 19:56:20 +0000 (19:56 +0000)]
argh!
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1235
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martinahansen [Mon, 31 Jan 2011 19:34:52 +0000 (19:34 +0000)]
added calc_N50 biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1233
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