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git.donarmstrong.com Git - biopieces.git/log
martinahansen [Thu, 24 May 2012 13:09:11 +0000 (13:09 +0000)]
moving digest.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1825
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martinahansen [Thu, 24 May 2012 09:00:48 +0000 (09:00 +0000)]
upgraded trim_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1823
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martinahansen [Wed, 23 May 2012 17:42:56 +0000 (17:42 +0000)]
refactored SeqError/TrimError
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1822
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martinahansen [Wed, 23 May 2012 14:14:54 +0000 (14:14 +0000)]
rewrite of seq.rb and addition of seq/trim.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1821
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martinahansen [Wed, 23 May 2012 09:54:00 +0000 (09:54 +0000)]
refactored argument precise to realign
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1820
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martinahansen [Tue, 8 May 2012 11:08:31 +0000 (11:08 +0000)]
reverted findsim_seq and renamed precise switch to realign
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1817
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martinahansen [Wed, 2 May 2012 19:15:04 +0000 (19:15 +0000)]
finishing hmmer_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1815
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martinahansen [Wed, 2 May 2012 17:57:20 +0000 (17:57 +0000)]
added hmmer_seq biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1814
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martinahansen [Mon, 30 Apr 2012 10:20:17 +0000 (10:20 +0000)]
upgraded write_fixedstep
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1812
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martinahansen [Tue, 24 Apr 2012 12:28:24 +0000 (12:28 +0000)]
added split of quality scores to split_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1810
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martinahansen [Mon, 23 Apr 2012 11:17:50 +0000 (11:17 +0000)]
added precise switch to findsim
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1808
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martinahansen [Mon, 23 Apr 2012 11:15:00 +0000 (11:15 +0000)]
workied on pair wise aligner
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1807
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martinahansen [Thu, 19 Apr 2012 09:29:24 +0000 (09:29 +0000)]
added precise alignment option to findsim.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1806
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martinahansen [Thu, 19 Apr 2012 09:28:57 +0000 (09:28 +0000)]
fixed double insertion of indels in alignments (missing .dup)
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1805
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martinahansen [Wed, 18 Apr 2012 17:02:20 +0000 (17:02 +0000)]
added identity method to align.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1804
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martinahansen [Wed, 18 Apr 2012 09:07:10 +0000 (09:07 +0000)]
changed report_scores to max_hits in findsim.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1801
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martinahansen [Wed, 18 Apr 2012 09:06:27 +0000 (09:06 +0000)]
changed record_scores to max_hits refactoring
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1800
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martinahansen [Wed, 18 Apr 2012 08:10:47 +0000 (08:10 +0000)]
added findsim_seq biopieces
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1799
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martinahansen [Wed, 18 Apr 2012 08:07:05 +0000 (08:07 +0000)]
added to_bp method to findsim.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1798
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martinahansen [Wed, 18 Apr 2012 07:44:22 +0000 (07:44 +0000)]
fixed issue 32
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1797
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martinahansen [Wed, 18 Apr 2012 07:28:38 +0000 (07:28 +0000)]
fixed x bug in compute
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1796
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martinahansen [Wed, 18 Apr 2012 07:09:49 +0000 (07:09 +0000)]
added q_id and s_id options to findsim.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1795
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martinahansen [Tue, 17 Apr 2012 10:09:56 +0000 (10:09 +0000)]
added findsim.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1794
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martinahansen [Wed, 11 Apr 2012 08:15:25 +0000 (08:15 +0000)]
ported write_fastq to ruby and allowed different encoding support
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1792
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martinahansen [Wed, 11 Apr 2012 08:07:42 +0000 (08:07 +0000)]
cleanup in read_fastq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1791
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martinahansen [Tue, 10 Apr 2012 19:05:02 +0000 (19:05 +0000)]
fixed comment
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1788
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martinahansen [Tue, 10 Apr 2012 19:04:36 +0000 (19:04 +0000)]
upgraded read_fastq to handle illumina1.8 better
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1787
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martinahansen [Tue, 10 Apr 2012 19:03:10 +0000 (19:03 +0000)]
upgraded tests for read_fastq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1786
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martinahansen [Tue, 10 Apr 2012 18:57:55 +0000 (18:57 +0000)]
removing stale test in files
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1785
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martinahansen [Tue, 10 Apr 2012 18:08:36 +0000 (18:08 +0000)]
making changes to accomodate Illumina18 qual scores
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1784
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martinahansen [Fri, 6 Apr 2012 13:47:14 +0000 (13:47 +0000)]
upgraded bitmap.rb to a 64bit version
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1783
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martinahansen [Tue, 3 Apr 2012 13:24:51 +0000 (13:24 +0000)]
upgraded bitmap.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1777
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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
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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
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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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