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git.donarmstrong.com Git - biopieces.git/log
martinahansen [Wed, 19 Oct 2011 15:36:01 +0000 (15:36 +0000)]
worked on each_interval, but still too slow
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1587
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martinahansen [Wed, 19 Oct 2011 10:01:46 +0000 (10:01 +0000)]
speed optimized interval_set and interval_unset in bitarray.rb - now evil fast
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1586
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martinahansen [Tue, 18 Oct 2011 15:24:11 +0000 (15:24 +0000)]
rewrote interval_set in bitarray.rb = 20 x faster
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1585
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martinahansen [Tue, 18 Oct 2011 11:22:15 +0000 (11:22 +0000)]
memory optimization on bitarray.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1584
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martinahansen [Mon, 17 Oct 2011 19:34:22 +0000 (19:34 +0000)]
added more methods to bitarray.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1583
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martinahansen [Mon, 17 Oct 2011 14:40:37 +0000 (14:40 +0000)]
added methods to bitarray.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1582
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martinahansen [Mon, 17 Oct 2011 13:19:07 +0000 (13:19 +0000)]
bitarray.rb bits_on method speedup x 3
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1581
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martinahansen [Mon, 17 Oct 2011 12:56:54 +0000 (12:56 +0000)]
cleanup of bitarray.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1580
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martinahansen [Mon, 17 Oct 2011 12:40:14 +0000 (12:40 +0000)]
changed bitwise operators in bitarray to inline
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1579
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martinahansen [Mon, 17 Oct 2011 12:22:02 +0000 (12:22 +0000)]
upgraded bitarray to work with narray for speed
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1578
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martinahansen [Mon, 17 Oct 2011 10:29:34 +0000 (10:29 +0000)]
added comment to bitarray.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1577
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martinahansen [Fri, 14 Oct 2011 21:18:45 +0000 (21:18 +0000)]
fixed biopieces installer
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1575
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martinahansen [Fri, 14 Oct 2011 20:14:55 +0000 (20:14 +0000)]
slight change to installer
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1573
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martinahansen [Fri, 14 Oct 2011 19:46:04 +0000 (19:46 +0000)]
added biopieces installer
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1572
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martinahansen [Fri, 14 Oct 2011 09:50:26 +0000 (09:50 +0000)]
fixed critical missing uc bug in uniq_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1567
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martinahansen [Thu, 13 Oct 2011 12:32:53 +0000 (12:32 +0000)]
fixed fastq issue
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1565
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martinahansen [Thu, 13 Oct 2011 12:14:37 +0000 (12:14 +0000)]
fixed last of fasta problems
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1564
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martinahansen [Thu, 13 Oct 2011 12:11:20 +0000 (12:11 +0000)]
fixed assemblers
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1563
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martinahansen [Thu, 13 Oct 2011 11:40:44 +0000 (11:40 +0000)]
fixing broken biopieces
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1562
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martinahansen [Thu, 13 Oct 2011 10:09:23 +0000 (10:09 +0000)]
smoothed ruby code to get rid of warnings
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1561
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martinahansen [Thu, 13 Oct 2011 09:56:15 +0000 (09:56 +0000)]
beautifying fasta.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1560
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martinahansen [Thu, 13 Oct 2011 09:23:37 +0000 (09:23 +0000)]
added Class method Seq.new_bp to seq.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1559
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martinahansen [Thu, 13 Oct 2011 08:51:38 +0000 (08:51 +0000)]
added to_fastq method seq.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1558
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martinahansen [Wed, 12 Oct 2011 19:26:51 +0000 (19:26 +0000)]
adding tests for write_fastq_files
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1556
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martinahansen [Wed, 12 Oct 2011 19:16:27 +0000 (19:16 +0000)]
added write_fastq_files
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1555
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martinahansen [Wed, 12 Oct 2011 18:42:52 +0000 (18:42 +0000)]
added crufty puts method to fastq.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1551
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martinahansen [Wed, 12 Oct 2011 18:18:35 +0000 (18:18 +0000)]
variable rename
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1550
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martinahansen [Wed, 12 Oct 2011 15:15:42 +0000 (15:15 +0000)]
evil sort fix needed for assert_no_diff_dir
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1549
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martinahansen [Wed, 12 Oct 2011 14:59:36 +0000 (14:59 +0000)]
fixed .svn dir issue with assert_no_diff_dir
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1548
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martinahansen [Wed, 12 Oct 2011 14:45:42 +0000 (14:45 +0000)]
added tests for write_fasta_files
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1547
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martinahansen [Wed, 12 Oct 2011 14:29:40 +0000 (14:29 +0000)]
fortified test.sh
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1546
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martinahansen [Wed, 12 Oct 2011 14:20:55 +0000 (14:20 +0000)]
fortified assert_no_diff_dir function
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1545
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martinahansen [Wed, 12 Oct 2011 14:05:17 +0000 (14:05 +0000)]
added assert_no_diff_dir function to test code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1544
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martinahansen [Wed, 12 Oct 2011 13:34:09 +0000 (13:34 +0000)]
added biopieces write_fasta_files
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1542
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martinahansen [Thu, 6 Oct 2011 07:10:19 +0000 (07:10 +0000)]
fixed alignment descriptors in sam.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1541
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martinahansen [Wed, 5 Oct 2011 08:03:12 +0000 (08:03 +0000)]
cleanup
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1540
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martinahansen [Wed, 5 Oct 2011 07:56:41 +0000 (07:56 +0000)]
cleanup
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1539
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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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