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git.donarmstrong.com Git - biopieces.git/log
martinahansen [Tue, 7 Aug 2012 17:33:50 +0000 (17:33 +0000)]
upgraded prodigal
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1886
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martinahansen [Tue, 7 Aug 2012 13:41:32 +0000 (13:41 +0000)]
fixed typo
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1885
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martinahansen [Tue, 7 Aug 2012 11:48:20 +0000 (11:48 +0000)]
added assemble_seq_idba_ud
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1882
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martinahansen [Tue, 7 Aug 2012 09:34:18 +0000 (09:34 +0000)]
added relative count to plot_scores + rewrite for speed
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1878
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martinahansen [Mon, 6 Aug 2012 14:43:28 +0000 (14:43 +0000)]
removed outdated installer
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1876
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martinahansen [Mon, 6 Aug 2012 14:42:46 +0000 (14:42 +0000)]
updated biopieces installer
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1875
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martinahansen [Fri, 13 Jul 2012 14:43:11 +0000 (14:43 +0000)]
fixed another bug in find orfs
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1872
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martinahansen [Fri, 13 Jul 2012 14:32:53 +0000 (14:32 +0000)]
fixed bug in orf finder
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1871
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martinahansen [Fri, 13 Jul 2012 14:15:39 +0000 (14:15 +0000)]
fixed grave bug in find_orfs
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1870
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martinahansen [Fri, 13 Jul 2012 13:54:49 +0000 (13:54 +0000)]
made orf finder case insensitive
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1868
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martinahansen [Fri, 13 Jul 2012 13:52:36 +0000 (13:52 +0000)]
added find_orfs
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1867
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martinahansen [Fri, 13 Jul 2012 13:51:58 +0000 (13:51 +0000)]
added orf finder to seq.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1866
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martinahansen [Tue, 10 Jul 2012 13:46:26 +0000 (13:46 +0000)]
ported align_pair_seq to ruby
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1865
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martinahansen [Tue, 10 Jul 2012 13:37:10 +0000 (13:37 +0000)]
added align/pair.rb to ruby trunk
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1864
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martinahansen [Tue, 10 Jul 2012 13:35:54 +0000 (13:35 +0000)]
fixed align.rb up a bit
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1863
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martinahansen [Tue, 10 Jul 2012 12:09:03 +0000 (12:09 +0000)]
minor fix to find_adaptor 2
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1862
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martinahansen [Tue, 10 Jul 2012 12:06:09 +0000 (12:06 +0000)]
minor fix to find_adaptor
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1861
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martinahansen [Tue, 10 Jul 2012 09:38:29 +0000 (09:38 +0000)]
added -m hardcoded option to prodigal.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1860
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martinahansen [Tue, 10 Jul 2012 08:52:14 +0000 (08:52 +0000)]
fixed bug for missing sequence in genbank parser
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1858
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martinahansen [Mon, 2 Jul 2012 09:12:17 +0000 (09:12 +0000)]
added mum.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1857
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martinahansen [Mon, 2 Jul 2012 09:00:04 +0000 (09:00 +0000)]
updated order_pairs
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1856
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martinahansen [Mon, 2 Jul 2012 08:59:44 +0000 (08:59 +0000)]
updated order_pairs
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1855
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martinahansen [Fri, 29 Jun 2012 18:27:56 +0000 (18:27 +0000)]
clean-up of ruby code to remove rake warnings
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1852
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martinahansen [Fri, 29 Jun 2012 18:27:21 +0000 (18:27 +0000)]
rewrote mean_scores to fix bug
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1851
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martinahansen [Fri, 29 Jun 2012 13:44:59 +0000 (13:44 +0000)]
added scores_mean method to seq.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1850
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martinahansen [Thu, 28 Jun 2012 11:29:22 +0000 (11:29 +0000)]
cleanup of pair stuff in align.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1849
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martinahansen [Wed, 27 Jun 2012 20:04:21 +0000 (20:04 +0000)]
fixed inline code warning
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1848
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martinahansen [Mon, 25 Jun 2012 11:36:40 +0000 (11:36 +0000)]
fixed bug in findsim.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1847
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martinahansen [Mon, 25 Jun 2012 09:04:40 +0000 (09:04 +0000)]
added max_diversity swith to findsim.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1846
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martinahansen [Mon, 25 Jun 2012 09:02:40 +0000 (09:02 +0000)]
added max_diversity swith to findsim.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1845
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martinahansen [Mon, 25 Jun 2012 09:01:26 +0000 (09:01 +0000)]
added max_diversity swith to findsim.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1844
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martinahansen [Wed, 20 Jun 2012 11:19:35 +0000 (11:19 +0000)]
classify_taxonomy work
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1843
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martinahansen [Wed, 20 Jun 2012 09:38:04 +0000 (09:38 +0000)]
classify_taxonomy work
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1842
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martinahansen [Wed, 13 Jun 2012 13:50:15 +0000 (13:50 +0000)]
added classify_taxonomy (unfinished biopiece)
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1841
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martinahansen [Fri, 8 Jun 2012 09:42:04 +0000 (09:42 +0000)]
fixed raw intput bug in read_fasta and read_fastq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1840
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martinahansen [Fri, 8 Jun 2012 09:14:16 +0000 (09:14 +0000)]
refactoring biopieces.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1839
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martinahansen [Fri, 8 Jun 2012 09:07:26 +0000 (09:07 +0000)]
fixed unit tests for test_trim.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1838
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martinahansen [Fri, 1 Jun 2012 09:43:20 +0000 (09:43 +0000)]
added illumina 1.8 name scheme support to order pairs
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1836
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martinahansen [Thu, 31 May 2012 14:22:57 +0000 (14:22 +0000)]
fixed bad error msg
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1835
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martinahansen [Wed, 30 May 2012 11:41:17 +0000 (11:41 +0000)]
fixed bug in sff.rb clip and mask methods
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1834
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martinahansen [Wed, 30 May 2012 11:39:48 +0000 (11:39 +0000)]
fixed bug in sff.rb to_seq method
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1833
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martinahansen [Wed, 30 May 2012 11:37:01 +0000 (11:37 +0000)]
added to_seq method to sff.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1832
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martinahansen [Fri, 25 May 2012 09:27:49 +0000 (09:27 +0000)]
fixed trim_seq tests
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1830
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martinahansen [Thu, 24 May 2012 20:49:05 +0000 (20:49 +0000)]
fixed ugly bug in trim.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1829
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martinahansen [Thu, 24 May 2012 13:35:10 +0000 (13:35 +0000)]
moved patscan.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1828
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martinahansen [Thu, 24 May 2012 13:32:20 +0000 (13:32 +0000)]
moved backtrack.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1827
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martinahansen [Thu, 24 May 2012 13:30:02 +0000 (13:30 +0000)]
moved patternmatcher.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1826
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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
74ccb610-7750-0410-82ae-
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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
74ccb610-7750-0410-82ae-
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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
74ccb610-7750-0410-82ae-
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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
74ccb610-7750-0410-82ae-
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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
74ccb610-7750-0410-82ae-
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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
74ccb610-7750-0410-82ae-
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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
74ccb610-7750-0410-82ae-
013aeee3265d
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