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git.donarmstrong.com Git - biopieces.git/log
martinahansen [Sun, 3 Jul 2011 18:40:37 +0000 (18:40 +0000)]
added warnings to bp_test
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1484
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martinahansen [Sun, 3 Jul 2011 18:38:37 +0000 (18:38 +0000)]
added warnings to bp_test
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1483
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martinahansen [Fri, 17 Jun 2011 13:48:04 +0000 (13:48 +0000)]
added sam.rb to ruby trunk
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1480
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martinahansen [Fri, 17 Jun 2011 13:47:30 +0000 (13:47 +0000)]
added sam.rb to ruby trunk
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1479
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martinahansen [Wed, 15 Jun 2011 10:00:23 +0000 (10:00 +0000)]
added tests for rename_keys
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1478
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martinahansen [Wed, 15 Jun 2011 07:00:37 +0000 (07:00 +0000)]
changed testing log file name
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1477
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martinahansen [Wed, 15 Jun 2011 06:47:36 +0000 (06:47 +0000)]
added tests for blast_seq_pair
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1476
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martinahansen [Tue, 14 Jun 2011 08:58:50 +0000 (08:58 +0000)]
hackery changes to plot_matches to deal with blast data
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1475
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martinahansen [Tue, 14 Jun 2011 08:38:50 +0000 (08:38 +0000)]
blast_seq_pair polish
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1474
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martinahansen [Tue, 14 Jun 2011 08:37:41 +0000 (08:37 +0000)]
blast_seq_pair polish
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1472
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martinahansen [Tue, 14 Jun 2011 08:32:11 +0000 (08:32 +0000)]
blast_seq_pair polish
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1471
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martinahansen [Tue, 14 Jun 2011 08:24:18 +0000 (08:24 +0000)]
added blast_seq_pair
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1470
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martinahansen [Mon, 13 Jun 2011 20:43:28 +0000 (20:43 +0000)]
added Seq.type_guess to ruby code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1468
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martinahansen [Wed, 8 Jun 2011 14:25:07 +0000 (14:25 +0000)]
added tests for remove_keys
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1467
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martinahansen [Wed, 8 Jun 2011 13:28:48 +0000 (13:28 +0000)]
added tests for remove_indels
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1466
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martinahansen [Wed, 8 Jun 2011 12:29:23 +0000 (12:29 +0000)]
added tests for reverse_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1465
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martinahansen [Wed, 8 Jun 2011 12:28:03 +0000 (12:28 +0000)]
added tests for complement_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1464
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martinahansen [Mon, 6 Jun 2011 15:21:33 +0000 (15:21 +0000)]
fixed cat_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1462
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martinahansen [Mon, 6 Jun 2011 14:58:49 +0000 (14:58 +0000)]
added cat_seq biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1460
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martinahansen [Sun, 5 Jun 2011 17:16:15 +0000 (17:16 +0000)]
shortened messages in test suite
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1459
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martinahansen [Sun, 5 Jun 2011 15:49:11 +0000 (15:49 +0000)]
added tests for uniq_vals
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1458
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martinahansen [Sun, 5 Jun 2011 15:41:03 +0000 (15:41 +0000)]
added tests for sort_records
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1457
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martinahansen [Sat, 4 Jun 2011 16:02:31 +0000 (16:02 +0000)]
added tests for transliterate_vals
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1456
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martinahansen [Sat, 4 Jun 2011 15:56:30 +0000 (15:56 +0000)]
added tests for transliterate_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1455
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martinahansen [Fri, 3 Jun 2011 12:56:58 +0000 (12:56 +0000)]
added tests for length_vals
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1454
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martinahansen [Fri, 3 Jun 2011 12:39:04 +0000 (12:39 +0000)]
added test for calc_bit_scores
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1453
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martinahansen [Tue, 31 May 2011 14:09:43 +0000 (14:09 +0000)]
added assemble_seq_ray
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1451
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martinahansen [Mon, 30 May 2011 15:12:22 +0000 (15:12 +0000)]
upgraded mean_scores
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1450
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martinahansen [Mon, 30 May 2011 11:14:40 +0000 (11:14 +0000)]
rename switch to something more appropriate
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1447
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martinahansen [Mon, 30 May 2011 08:46:04 +0000 (08:46 +0000)]
removed unused code from find_adaptor
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1443
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martinahansen [Mon, 30 May 2011 08:37:00 +0000 (08:37 +0000)]
added perl module and ruby gem test to bp_test
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1442
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martinahansen [Sun, 29 May 2011 08:17:01 +0000 (08:17 +0000)]
squashing bugs in find_adaptor
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1440
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martinahansen [Sun, 29 May 2011 07:59:24 +0000 (07:59 +0000)]
working on find_adaptor
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1439
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martinahansen [Sat, 28 May 2011 21:24:18 +0000 (21:24 +0000)]
added multithreading to find_adaptor
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1438
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martinahansen [Sat, 28 May 2011 20:54:36 +0000 (20:54 +0000)]
added multithreading to find_adaptor
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1437
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martinahansen [Thu, 26 May 2011 15:04:58 +0000 (15:04 +0000)]
added order_pairs
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1436
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martinahansen [Thu, 26 May 2011 12:55:58 +0000 (12:55 +0000)]
fixed type in assemble_seq_idba
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1434
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martinahansen [Thu, 26 May 2011 12:53:53 +0000 (12:53 +0000)]
fixed mate-pair name issue in assemble_seq_idba
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1433
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martinahansen [Wed, 25 May 2011 09:31:29 +0000 (09:31 +0000)]
added plot_distribution biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1431
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martinahansen [Wed, 25 May 2011 08:41:35 +0000 (08:41 +0000)]
polished plot_scores
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1430
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martinahansen [Tue, 24 May 2011 14:40:41 +0000 (14:40 +0000)]
upgraded bp_update alias due to complaints
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1428
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martinahansen [Tue, 24 May 2011 14:26:28 +0000 (14:26 +0000)]
fixed fence post bug in plot_lendist
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1426
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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
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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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projects / biopieces.git / log