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git.donarmstrong.com Git - biopieces.git/log
martinahansen [Thu, 29 Sep 2011 09:12:55 +0000 (09:12 +0000)]
added delimiter to join_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1537
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martinahansen [Mon, 26 Sep 2011 08:43:04 +0000 (08:43 +0000)]
fixed bug in patscan_seq arguments
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1536
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martinahansen [Fri, 23 Sep 2011 12:27:59 +0000 (12:27 +0000)]
fixed patscan_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1535
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martinahansen [Fri, 23 Sep 2011 09:59:49 +0000 (09:59 +0000)]
removed bad method from fastq.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1534
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martinahansen [Fri, 23 Sep 2011 09:57:25 +0000 (09:57 +0000)]
fixed mistakes in test_fasta.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1533
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martinahansen [Fri, 23 Sep 2011 09:44:31 +0000 (09:44 +0000)]
fixed newline to rec seperator in seq.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1532
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martinahansen [Tue, 20 Sep 2011 15:06:09 +0000 (15:06 +0000)]
updated patscan_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1529
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martinahansen [Mon, 19 Sep 2011 11:43:36 +0000 (11:43 +0000)]
fixed grave bug in genbank.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1527
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martinahansen [Wed, 7 Sep 2011 06:25:51 +0000 (06:25 +0000)]
Cholhee fixed bug in lowercase_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1524
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martinahansen [Tue, 6 Sep 2011 11:47:33 +0000 (11:47 +0000)]
fixed typo in test_biopieces.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1523
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martinahansen [Tue, 6 Sep 2011 09:53:26 +0000 (09:53 +0000)]
rewrote remove_mids again
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1521
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martinahansen [Tue, 6 Sep 2011 08:19:10 +0000 (08:19 +0000)]
fixed bug in remove_mids
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1520
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martinahansen [Tue, 6 Sep 2011 06:26:08 +0000 (06:26 +0000)]
added tests to remove_mids
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1519
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martinahansen [Mon, 5 Sep 2011 20:43:34 +0000 (20:43 +0000)]
updated remove_mids
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1518
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martinahansen [Mon, 5 Sep 2011 13:47:15 +0000 (13:47 +0000)]
added hamming_distance method to seq.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1516
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martinahansen [Mon, 5 Sep 2011 13:34:21 +0000 (13:34 +0000)]
polishing on sam.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1515
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martinahansen [Mon, 5 Sep 2011 13:23:30 +0000 (13:23 +0000)]
speedup of bits.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1514
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martinahansen [Mon, 5 Sep 2011 13:23:08 +0000 (13:23 +0000)]
speedup of bits.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1513
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martinahansen [Mon, 5 Sep 2011 06:30:51 +0000 (06:30 +0000)]
polished test_cigar.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1512
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martinahansen [Thu, 1 Sep 2011 14:29:29 +0000 (14:29 +0000)]
fixed bug in find_SNPs
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1511
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martinahansen [Thu, 1 Sep 2011 14:01:40 +0000 (14:01 +0000)]
added tests for find_SNPs
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1510
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martinahansen [Thu, 1 Sep 2011 13:36:19 +0000 (13:36 +0000)]
added find_SNPs biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1508
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martinahansen [Thu, 1 Sep 2011 12:24:39 +0000 (12:24 +0000)]
polish of cigar.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1507
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martinahansen [Wed, 31 Aug 2011 14:27:37 +0000 (14:27 +0000)]
corrected bug in sam.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1506
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martinahansen [Wed, 31 Aug 2011 13:14:11 +0000 (13:14 +0000)]
sam update
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1504
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martinahansen [Wed, 31 Aug 2011 12:41:48 +0000 (12:41 +0000)]
worked on sam - added 1 to phred score check in seq.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1503
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martinahansen [Mon, 29 Aug 2011 13:10:51 +0000 (13:10 +0000)]
added cigar.rb and test_cigar.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1502
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martinahansen [Mon, 29 Aug 2011 09:51:05 +0000 (09:51 +0000)]
working on sam.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1501
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martinahansen [Wed, 24 Aug 2011 21:22:48 +0000 (21:22 +0000)]
worked on unit tests for sam.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1500
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martinahansen [Wed, 24 Aug 2011 21:03:15 +0000 (21:03 +0000)]
worked on unit tests for sam.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1499
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martinahansen [Wed, 24 Aug 2011 20:56:05 +0000 (20:56 +0000)]
worked on unit tests for sam.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1498
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martinahansen [Wed, 24 Aug 2011 20:54:33 +0000 (20:54 +0000)]
worked on unit tests for sam.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1497
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martinahansen [Wed, 24 Aug 2011 19:23:46 +0000 (19:23 +0000)]
worked on unit tests for sam.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1496
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martinahansen [Wed, 24 Aug 2011 19:22:39 +0000 (19:22 +0000)]
worked on unit tests for sam.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1495
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martinahansen [Tue, 23 Aug 2011 15:14:06 +0000 (15:14 +0000)]
worked on unit tests for sam.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1494
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martinahansen [Tue, 23 Aug 2011 14:29:01 +0000 (14:29 +0000)]
worked on unit tests for sam.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1493
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martinahansen [Tue, 23 Aug 2011 14:06:02 +0000 (14:06 +0000)]
worked on unit tests for sam.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1492
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martinahansen [Tue, 23 Aug 2011 13:51:19 +0000 (13:51 +0000)]
worked on unit tests for sam.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1491
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martinahansen [Tue, 23 Aug 2011 11:03:26 +0000 (11:03 +0000)]
worked on unit tests for sam.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1490
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martinahansen [Mon, 22 Aug 2011 20:12:22 +0000 (20:12 +0000)]
worked on sam.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1489
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martinahansen [Mon, 4 Jul 2011 05:18:30 +0000 (05:18 +0000)]
s/Checking/Testing
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1488
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martinahansen [Mon, 4 Jul 2011 05:16:58 +0000 (05:16 +0000)]
fixed typo
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1487
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martinahansen [Mon, 4 Jul 2011 05:16:20 +0000 (05:16 +0000)]
fixed typo
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1486
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martinahansen [Mon, 4 Jul 2011 05:15:30 +0000 (05:15 +0000)]
fixed typo
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1485
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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
74ccb610-7750-0410-82ae-
013aeee3265d
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
74ccb610-7750-0410-82ae-
013aeee3265d
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
74ccb610-7750-0410-82ae-
013aeee3265d
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
74ccb610-7750-0410-82ae-
013aeee3265d
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
74ccb610-7750-0410-82ae-
013aeee3265d
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
74ccb610-7750-0410-82ae-
013aeee3265d
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
74ccb610-7750-0410-82ae-
013aeee3265d
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
74ccb610-7750-0410-82ae-
013aeee3265d
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
74ccb610-7750-0410-82ae-
013aeee3265d
projects / biopieces.git / log