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git.donarmstrong.com Git - biopieces.git/log
martinahansen [Mon, 26 Mar 2012 18:18:35 +0000 (18:18 +0000)]
fixed ugly 1-off bug in locator
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1776
74ccb610-7750-0410-82ae-
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martinahansen [Mon, 26 Mar 2012 18:15:15 +0000 (18:15 +0000)]
fixed ugly 1-off bug in locator.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1775
74ccb610-7750-0410-82ae-
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martinahansen [Mon, 26 Mar 2012 18:14:41 +0000 (18:14 +0000)]
fixed ugly 1-off bug in locator.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1774
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martinahansen [Thu, 22 Mar 2012 08:29:21 +0000 (08:29 +0000)]
added bitmap.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1773
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martinahansen [Tue, 20 Mar 2012 14:05:03 +0000 (14:05 +0000)]
fixed issues in bwa_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1772
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martinahansen [Fri, 16 Mar 2012 09:51:01 +0000 (09:51 +0000)]
added closed? method to filesys.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1771
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martinahansen [Wed, 14 Mar 2012 08:07:19 +0000 (08:07 +0000)]
added check for empty files in usearch.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1770
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martinahansen [Tue, 13 Mar 2012 10:44:28 +0000 (10:44 +0000)]
fixed dir in bwa_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1769
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martinahansen [Tue, 13 Mar 2012 10:06:13 +0000 (10:06 +0000)]
fixed minor issue in align.rb tests
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1768
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martinahansen [Tue, 13 Mar 2012 09:58:04 +0000 (09:58 +0000)]
addid missing S_END to sam.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1767
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martinahansen [Tue, 13 Mar 2012 09:49:33 +0000 (09:49 +0000)]
ported bwa_seq to ruby for better SAM support
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1766
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martinahansen [Wed, 7 Mar 2012 09:26:10 +0000 (09:26 +0000)]
fixed overflow bug in align.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1764
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martinahansen [Mon, 5 Mar 2012 18:37:08 +0000 (18:37 +0000)]
changed align.to_s
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1762
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martinahansen [Fri, 2 Mar 2012 11:23:06 +0000 (11:23 +0000)]
major upgrade of denoise_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1759
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martinahansen [Fri, 2 Mar 2012 11:12:30 +0000 (11:12 +0000)]
major upgrade of align.rb for denoising
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1758
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martinahansen [Thu, 1 Mar 2012 09:56:30 +0000 (09:56 +0000)]
fixed bug in each_alignment
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1757
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martinahansen [Thu, 23 Feb 2012 08:29:07 +0000 (08:29 +0000)]
added duplicate_record biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1750
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martinahansen [Thu, 9 Feb 2012 11:20:31 +0000 (11:20 +0000)]
added force to rm of tmpdir
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1749
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martinahansen [Tue, 7 Feb 2012 14:34:26 +0000 (14:34 +0000)]
added raw data reading to read_fasta and read_fastq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1748
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martinahansen [Tue, 7 Feb 2012 13:38:44 +0000 (13:38 +0000)]
fixed indentation in biopieces.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1747
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martinahansen [Fri, 3 Feb 2012 09:06:53 +0000 (09:06 +0000)]
rounding up work on denoise_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1745
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martinahansen [Fri, 3 Feb 2012 08:05:58 +0000 (08:05 +0000)]
added denoise_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1743
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martinahansen [Fri, 3 Feb 2012 07:38:30 +0000 (07:38 +0000)]
fixed attributes
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1742
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martinahansen [Fri, 3 Feb 2012 07:28:09 +0000 (07:28 +0000)]
added FastqIndex to fastq.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1741
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martinahansen [Fri, 3 Feb 2012 07:10:13 +0000 (07:10 +0000)]
added ustar and each_alignment methods to usearch.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1740
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martinahansen [Fri, 3 Feb 2012 07:09:49 +0000 (07:09 +0000)]
added masks to align.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1739
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martinahansen [Tue, 31 Jan 2012 20:25:25 +0000 (20:25 +0000)]
major rewrite of align.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1738
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martinahansen [Tue, 31 Jan 2012 10:55:06 +0000 (10:55 +0000)]
add ustar method to usearch.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1737
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martinahansen [Fri, 27 Jan 2012 13:09:20 +0000 (13:09 +0000)]
final touches to align.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1735
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martinahansen [Tue, 24 Jan 2012 08:34:23 +0000 (08:34 +0000)]
fixed indels in methods mask_seq_hard/soft
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1734
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martinahansen [Mon, 23 Jan 2012 21:27:03 +0000 (21:27 +0000)]
fixed broken pcr_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1733
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martinahansen [Mon, 23 Jan 2012 14:30:52 +0000 (14:30 +0000)]
polish seq.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1732
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martinahansen [Mon, 23 Jan 2012 14:16:33 +0000 (14:16 +0000)]
rewrote mask_seq_hard and mask_seq_soft methods to NArrays for speed
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1731
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martinahansen [Sun, 22 Jan 2012 19:18:56 +0000 (19:18 +0000)]
fixed popen3 issue in align.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1730
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martinahansen [Fri, 20 Jan 2012 14:09:51 +0000 (14:09 +0000)]
changed Align.muscle to file based instead of popen3
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1729
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martinahansen [Wed, 18 Jan 2012 14:51:57 +0000 (14:51 +0000)]
added additional prerequisite check for RubyInline
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1728
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martinahansen [Thu, 12 Jan 2012 13:19:03 +0000 (13:19 +0000)]
fixed typo
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1727
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martinahansen [Thu, 12 Jan 2012 12:45:57 +0000 (12:45 +0000)]
added check for duplicate seq_names to align.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1726
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martinahansen [Thu, 12 Jan 2012 12:42:45 +0000 (12:42 +0000)]
added preservation of indels and case to align.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1725
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martinahansen [Thu, 12 Jan 2012 11:09:58 +0000 (11:09 +0000)]
added align.rb to ruby code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1724
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martinahansen [Wed, 11 Jan 2012 17:02:00 +0000 (17:02 +0000)]
added remove_indels method
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1723
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martinahansen [Tue, 3 Jan 2012 14:24:42 +0000 (14:24 +0000)]
fixed issue in compute
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1720
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martinahansen [Tue, 3 Jan 2012 14:17:38 +0000 (14:17 +0000)]
fixed issue in compute
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1718
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martinahansen [Mon, 2 Jan 2012 12:17:04 +0000 (12:17 +0000)]
fixed missing ; in create_blast_index
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1717
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martinahansen [Thu, 29 Dec 2011 15:07:53 +0000 (15:07 +0000)]
added extra RL tags to find_barcodes
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1716
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martinahansen [Thu, 22 Dec 2011 14:32:14 +0000 (14:32 +0000)]
increaded database size for blast
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1715
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martinahansen [Tue, 20 Dec 2011 14:55:52 +0000 (14:55 +0000)]
fixed --rev swith in usearch.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1714
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martinahansen [Thu, 15 Dec 2011 10:17:42 +0000 (10:17 +0000)]
fixed typo in replace_vals
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1713
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martinahansen [Thu, 15 Dec 2011 10:13:38 +0000 (10:13 +0000)]
fixed typo in replace_vals
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1712
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martinahansen [Mon, 12 Dec 2011 11:35:04 +0000 (11:35 +0000)]
add tests for read_embl
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1705
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martinahansen [Mon, 12 Dec 2011 11:21:42 +0000 (11:21 +0000)]
added new read_embl (ruby)
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1704
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martinahansen [Mon, 12 Dec 2011 11:18:26 +0000 (11:18 +0000)]
removed old read_embl (perl)
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1703
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martinahansen [Mon, 12 Dec 2011 11:17:20 +0000 (11:17 +0000)]
added embl.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1702
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martinahansen [Mon, 12 Dec 2011 08:18:01 +0000 (08:18 +0000)]
split off locator stuff from genbank.rb to locator.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1701
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martinahansen [Thu, 8 Dec 2011 15:00:41 +0000 (15:00 +0000)]
added check for duplicate keys in replace_vals
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1700
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martinahansen [Thu, 8 Dec 2011 14:39:10 +0000 (14:39 +0000)]
added replace_vals biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1698
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martinahansen [Wed, 7 Dec 2011 15:23:27 +0000 (15:23 +0000)]
added new biopeice remove_indel_columns
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1696
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martinahansen [Wed, 7 Dec 2011 10:46:55 +0000 (10:46 +0000)]
minor tweak to genbank.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1695
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martinahansen [Tue, 6 Dec 2011 16:13:30 +0000 (16:13 +0000)]
fixed count bug in sff.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1694
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martinahansen [Tue, 6 Dec 2011 09:07:59 +0000 (09:07 +0000)]
minor tweaks added to installer
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1693
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martinahansen [Mon, 5 Dec 2011 14:36:19 +0000 (14:36 +0000)]
upgraded mask_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1692
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martinahansen [Fri, 25 Nov 2011 13:38:46 +0000 (13:38 +0000)]
cleanup of usearch.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1689
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martinahansen [Fri, 25 Nov 2011 12:31:49 +0000 (12:31 +0000)]
moved usearch code to external file
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1688
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martinahansen [Thu, 24 Nov 2011 12:58:47 +0000 (12:58 +0000)]
removed bp_doc/ and content
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1684
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martinahansen [Thu, 24 Nov 2011 10:57:17 +0000 (10:57 +0000)]
fixed regex in backtrack.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1683
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martinahansen [Wed, 23 Nov 2011 13:50:50 +0000 (13:50 +0000)]
removed stale unit tests from test_biopieces.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1681
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martinahansen [Wed, 23 Nov 2011 13:48:06 +0000 (13:48 +0000)]
fixed glob unit test in test_biopieces.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1680
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martinahansen [Wed, 23 Nov 2011 13:30:04 +0000 (13:30 +0000)]
removed comma
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1679
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martinahansen [Tue, 22 Nov 2011 15:24:57 +0000 (15:24 +0000)]
got rid of nasty to_sym in biopieces.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1678
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martinahansen [Tue, 22 Nov 2011 15:24:41 +0000 (15:24 +0000)]
got rid of nasty to_sym in biopieces.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1677
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martinahansen [Tue, 22 Nov 2011 14:56:12 +0000 (14:56 +0000)]
got rid of type in filesys.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1676
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martinahansen [Tue, 22 Nov 2011 14:30:03 +0000 (14:30 +0000)]
beautifying backtrack.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1675
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martinahansen [Tue, 22 Nov 2011 11:17:46 +0000 (11:17 +0000)]
slight cleanup of backtrack code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1674
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martinahansen [Mon, 21 Nov 2011 10:35:59 +0000 (10:35 +0000)]
made --rev defacto in useach_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1673
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martinahansen [Mon, 21 Nov 2011 10:29:30 +0000 (10:29 +0000)]
upgraded usearch_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1671
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martinahansen [Mon, 21 Nov 2011 06:31:34 +0000 (06:31 +0000)]
added tests for uclust_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1668
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martinahansen [Sat, 19 Nov 2011 09:10:21 +0000 (09:10 +0000)]
fixed bug in uniq_vals causing clusters named 0 to be ignored
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1667
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martinahansen [Fri, 18 Nov 2011 10:57:25 +0000 (10:57 +0000)]
rewriting uclust_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1665
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martinahansen [Thu, 17 Nov 2011 20:06:24 +0000 (20:06 +0000)]
fixed bug in grab
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1663
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martinahansen [Thu, 17 Nov 2011 19:57:32 +0000 (19:57 +0000)]
added tests to remove_primers
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1662
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martinahansen [Thu, 17 Nov 2011 16:53:31 +0000 (16:53 +0000)]
fixed remove_primers
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1661
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martinahansen [Thu, 17 Nov 2011 14:50:32 +0000 (14:50 +0000)]
fixed bug in remove_primers
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1659
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martinahansen [Thu, 17 Nov 2011 14:16:16 +0000 (14:16 +0000)]
added remove_primers biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1658
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martinahansen [Thu, 17 Nov 2011 10:59:54 +0000 (10:59 +0000)]
fixed stupid windows \r bug in Patscan::read_patterns
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1657
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martinahansen [Thu, 17 Nov 2011 09:34:12 +0000 (09:34 +0000)]
added requirement of RubyInline
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1656
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martinahansen [Thu, 17 Nov 2011 07:28:58 +0000 (07:28 +0000)]
fixed ins/del reverse
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1655
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martinahansen [Wed, 16 Nov 2011 13:31:52 +0000 (13:31 +0000)]
fixed FLAG bug in sam.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1654
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martinahansen [Wed, 16 Nov 2011 10:24:44 +0000 (10:24 +0000)]
disabled inline
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1653
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martinahansen [Wed, 16 Nov 2011 10:18:46 +0000 (10:18 +0000)]
fixed bug in backtrack.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1651
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martinahansen [Tue, 15 Nov 2011 19:40:12 +0000 (19:40 +0000)]
fixed digest.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1649
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martinahansen [Tue, 15 Nov 2011 15:14:59 +0000 (15:14 +0000)]
added backtrack.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1648
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martinahansen [Tue, 15 Nov 2011 15:14:46 +0000 (15:14 +0000)]
added backtrack.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1647
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martinahansen [Mon, 14 Nov 2011 15:30:00 +0000 (15:30 +0000)]
upgraded uclust_seq to work with useach 5.1.221
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1644
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martinahansen [Sun, 13 Nov 2011 19:41:55 +0000 (19:41 +0000)]
added backtrack.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1640
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martinahansen [Sun, 13 Nov 2011 19:18:07 +0000 (19:18 +0000)]
fixed digest_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1639
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martinahansen [Sun, 13 Nov 2011 18:58:16 +0000 (18:58 +0000)]
cleaning up digest.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1638
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martinahansen [Wed, 9 Nov 2011 15:28:46 +0000 (15:28 +0000)]
added Backtrack.pm
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1618
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martinahansen [Wed, 9 Nov 2011 15:20:40 +0000 (15:20 +0000)]
fixed bug in seq.to_fasta
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1617
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martinahansen [Wed, 9 Nov 2011 13:25:06 +0000 (13:25 +0000)]
fixed bugs in installer
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1616
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martinahansen [Tue, 8 Nov 2011 12:46:07 +0000 (12:46 +0000)]
fixed bug in QA_454_report.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1615
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projects / biopieces.git / log