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git.donarmstrong.com Git - biopieces.git/log
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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martinahansen [Mon, 7 Nov 2011 10:06:56 +0000 (10:06 +0000)]
added ruby version of read_sam
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1613
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martinahansen [Mon, 7 Nov 2011 10:06:18 +0000 (10:06 +0000)]
removed perl version of read_sam
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1612
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martinahansen [Wed, 2 Nov 2011 09:47:17 +0000 (09:47 +0000)]
added length check to bowtie_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1611
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martinahansen [Wed, 2 Nov 2011 09:46:06 +0000 (09:46 +0000)]
added length check to bowtie_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1610
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martinahansen [Wed, 2 Nov 2011 09:31:08 +0000 (09:31 +0000)]
fixed qual argument for bowtie on fasta only
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1609
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martinahansen [Tue, 1 Nov 2011 15:20:47 +0000 (15:20 +0000)]
added quality_trim to seq.rb along with unit tests
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1608
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martinahansen [Tue, 1 Nov 2011 13:43:51 +0000 (13:43 +0000)]
fixed unit tests for reverse and revcomp in seq.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1607
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martinahansen [Tue, 1 Nov 2011 13:24:05 +0000 (13:24 +0000)]
fixed return on reverse_complement in seq.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1606
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martinahansen [Mon, 31 Oct 2011 13:36:44 +0000 (13:36 +0000)]
added metagenome flag to assemble_seq_idba
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1605
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martinahansen [Fri, 28 Oct 2011 14:58:51 +0000 (14:58 +0000)]
added reversing of qual to reverse
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1603
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martinahansen [Thu, 27 Oct 2011 13:06:45 +0000 (13:06 +0000)]
removed biopieces find_mids remove_mids read_solexa
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1602
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martinahansen [Thu, 27 Oct 2011 08:19:25 +0000 (08:19 +0000)]
added QA_454_report ruby script
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1601
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martinahansen [Tue, 25 Oct 2011 14:52:19 +0000 (14:52 +0000)]
added find_barcodes biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1599
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martinahansen [Tue, 25 Oct 2011 06:27:06 +0000 (06:27 +0000)]
added png terminal to plot_histogram
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1597
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martinahansen [Sun, 23 Oct 2011 12:41:50 +0000 (12:41 +0000)]
updated biopieces_installer - adding bash check
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1596
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martinahansen [Sat, 22 Oct 2011 08:07:15 +0000 (08:07 +0000)]
added version number to biopieces_installer
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1595
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martinahansen [Sat, 22 Oct 2011 08:03:23 +0000 (08:03 +0000)]
added more control to appending of .bashrc in biopieces_installer.sh
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1594
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martinahansen [Fri, 21 Oct 2011 12:14:33 +0000 (12:14 +0000)]
added shuffle! method to seq.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1592
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martinahansen [Thu, 20 Oct 2011 08:21:27 +0000 (08:21 +0000)]
ported trim_seq to ruby and added tests
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1591
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martinahansen [Wed, 19 Oct 2011 20:34:16 +0000 (20:34 +0000)]
updated biopieces_installer.sh
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1589
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martinahansen [Wed, 19 Oct 2011 19:01:42 +0000 (19:01 +0000)]
revoked to old working version of each_interval in bitarray.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1588
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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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