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git.donarmstrong.com Git - biopieces.git/log
martinahansen [Fri, 8 Mar 2013 09:29:16 +0000 (09:29 +0000)]
rewrite of FASTQ internals
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2111
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martinahansen [Fri, 1 Mar 2013 11:23:46 +0000 (11:23 +0000)]
fixed bug in plot_scores
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2110
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martinahansen [Thu, 28 Feb 2013 14:34:26 +0000 (14:34 +0000)]
finished refactoring s/has_key?/[]/
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2109
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martinahansen [Thu, 28 Feb 2013 14:17:03 +0000 (14:17 +0000)]
refactoring of ruby code s/has_key?/[]/
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2108
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martinahansen [Thu, 28 Feb 2013 13:56:09 +0000 (13:56 +0000)]
fixed global SCORE_BASE in mean_scores
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2107
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martinahansen [Thu, 28 Feb 2013 12:36:22 +0000 (12:36 +0000)]
refactoring of revcomp in seq.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2106
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martinahansen [Thu, 28 Feb 2013 10:21:22 +0000 (10:21 +0000)]
added Seq.shuffle method and tests
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2105
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martinahansen [Thu, 28 Feb 2013 08:46:32 +0000 (08:46 +0000)]
updated find_SNPs tests
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2104
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martinahansen [Mon, 25 Feb 2013 19:17:08 +0000 (19:17 +0000)]
fixed SCORE_BASE global var
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2101
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martinahansen [Thu, 21 Feb 2013 18:57:55 +0000 (18:57 +0000)]
added coverage to find_SNPs
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2100
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martinahansen [Thu, 21 Feb 2013 13:46:28 +0000 (13:46 +0000)]
fixed nasty bug in grab where -E and pattern 0 failed
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2099
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martinahansen [Thu, 21 Feb 2013 13:45:21 +0000 (13:45 +0000)]
fixed nasty bug in grab where -E and pattern 0 failed
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2098
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martinahansen [Wed, 20 Feb 2013 10:07:15 +0000 (10:07 +0000)]
made find_adaptor ignore too short sequences
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2096
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martinahansen [Tue, 19 Feb 2013 14:08:15 +0000 (14:08 +0000)]
added write_sam biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2095
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martinahansen [Tue, 19 Feb 2013 13:51:25 +0000 (13:51 +0000)]
disabled encoding validity check
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2094
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martinahansen [Tue, 19 Feb 2013 13:40:46 +0000 (13:40 +0000)]
added provisional write sam support
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2093
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martinahansen [Tue, 19 Feb 2013 13:40:21 +0000 (13:40 +0000)]
polished read_sam
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2092
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martinahansen [Fri, 8 Feb 2013 07:48:39 +0000 (07:48 +0000)]
fixed quality score validity check
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2091
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martinahansen [Wed, 6 Feb 2013 14:23:13 +0000 (14:23 +0000)]
disable validity check
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2090
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martinahansen [Mon, 4 Feb 2013 13:50:07 +0000 (13:50 +0000)]
added quality score check to read_fastq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2089
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martinahansen [Mon, 4 Feb 2013 13:37:39 +0000 (13:37 +0000)]
added qual_valid? method to Seq.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2088
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martinahansen [Sat, 2 Feb 2013 21:37:11 +0000 (21:37 +0000)]
fixed minor bug in error handling
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2087
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martinahansen [Tue, 22 Jan 2013 13:52:35 +0000 (13:52 +0000)]
fixed axis titles
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2086
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martinahansen [Tue, 22 Jan 2013 11:50:56 +0000 (11:50 +0000)]
added plot_stacked_histogram biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2085
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martinahansen [Mon, 21 Jan 2013 13:45:03 +0000 (13:45 +0000)]
added pandaseq prerequisite
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2084
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martinahansen [Mon, 21 Jan 2013 13:42:13 +0000 (13:42 +0000)]
added tests for assemble_pairs biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2083
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martinahansen [Mon, 21 Jan 2013 13:37:11 +0000 (13:37 +0000)]
added assemble_pairs biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2081
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martinahansen [Sun, 20 Jan 2013 19:03:41 +0000 (19:03 +0000)]
added substitute_vals biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2079
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martinahansen [Wed, 16 Jan 2013 09:47:10 +0000 (09:47 +0000)]
fixed bad tests in match.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2078
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martinahansen [Tue, 15 Jan 2013 12:16:44 +0000 (12:16 +0000)]
added png term to plot_matches
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2076
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martinahansen [Mon, 14 Jan 2013 18:33:13 +0000 (18:33 +0000)]
added tests for create_seq_index and get_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2075
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martinahansen [Mon, 14 Jan 2013 17:38:28 +0000 (17:38 +0000)]
fixed apparent change in Carp yielding an extra . after error msg
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2074
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martinahansen [Mon, 14 Jan 2013 17:27:06 +0000 (17:27 +0000)]
removed error check
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2072
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martinahansen [Fri, 11 Jan 2013 14:36:57 +0000 (14:36 +0000)]
added bowtie2 biopieces
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2071
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martinahansen [Wed, 9 Jan 2013 14:24:28 +0000 (14:24 +0000)]
adding kmer to contigs
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2069
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martinahansen [Wed, 9 Jan 2013 11:20:20 +0000 (11:20 +0000)]
fixed up assemble_seq_velvet
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2067
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martinahansen [Wed, 9 Jan 2013 10:19:07 +0000 (10:19 +0000)]
rewrote assemble_seq_velvet
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2066
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martinahansen [Wed, 9 Jan 2013 09:38:45 +0000 (09:38 +0000)]
fixed pair end issue
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2065
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martinahansen [Wed, 9 Jan 2013 09:15:41 +0000 (09:15 +0000)]
set cutoff to auto in velvet
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2064
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martinahansen [Wed, 9 Jan 2013 09:10:53 +0000 (09:10 +0000)]
renamed assemle_seq_idba assemble_seq_idba
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2060
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martinahansen [Wed, 9 Jan 2013 09:09:55 +0000 (09:09 +0000)]
renamed assemble_seq_idba_ud assemle_seq_idba
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2059
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martinahansen [Wed, 9 Jan 2013 09:09:18 +0000 (09:09 +0000)]
removed old assemle_seq_idba
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2058
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martinahansen [Fri, 4 Jan 2013 10:53:03 +0000 (10:53 +0000)]
fixed to_i bug in pcr_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2057
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martinahansen [Fri, 4 Jan 2013 10:25:24 +0000 (10:25 +0000)]
updated report
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2056
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martinahansen [Fri, 4 Jan 2013 10:23:15 +0000 (10:23 +0000)]
updated pcr_seq and added tests
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2054
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martinahansen [Thu, 3 Jan 2013 15:15:12 +0000 (15:15 +0000)]
polished pairwise alignment code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2053
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martinahansen [Wed, 2 Jan 2013 11:12:51 +0000 (11:12 +0000)]
added new match.rb and tests
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2052
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martinahansen [Wed, 2 Jan 2013 11:10:11 +0000 (11:10 +0000)]
added new match.rb and tests
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2051
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martinahansen [Wed, 2 Jan 2013 09:51:15 +0000 (09:51 +0000)]
added test for align dir
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2050
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martinahansen [Wed, 2 Jan 2013 09:49:50 +0000 (09:49 +0000)]
renaming match.rb to matches.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2049
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martinahansen [Wed, 2 Jan 2013 09:40:08 +0000 (09:40 +0000)]
moved mum.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2048
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martinahansen [Thu, 20 Dec 2012 21:25:23 +0000 (21:25 +0000)]
clearnup of pair align code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2047
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martinahansen [Thu, 13 Dec 2012 10:44:37 +0000 (10:44 +0000)]
fixed minor bug in grab for exact_in where no key would give undef warning
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2045
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martinahansen [Wed, 12 Dec 2012 08:38:37 +0000 (08:38 +0000)]
fixed QA_Illumina_report.rb SEQ_LEN > 20
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2044
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martinahansen [Wed, 12 Dec 2012 08:33:01 +0000 (08:33 +0000)]
changed to new find_adaptor
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2043
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martinahansen [Tue, 11 Dec 2012 08:52:30 +0000 (08:52 +0000)]
added unit test to backtrack code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2042
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martinahansen [Mon, 10 Dec 2012 18:38:02 +0000 (18:38 +0000)]
removed debug code from find_adaptor
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2041
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martinahansen [Mon, 10 Dec 2012 18:34:35 +0000 (18:34 +0000)]
unrolling new find_adaptor
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2039
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martinahansen [Mon, 10 Dec 2012 18:28:52 +0000 (18:28 +0000)]
fixed bug in backtrack.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2038
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martinahansen [Mon, 10 Dec 2012 08:42:53 +0000 (08:42 +0000)]
fixed unit tests for backtrack.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2037
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martinahansen [Thu, 6 Dec 2012 11:15:19 +0000 (11:15 +0000)]
fixed unit tests
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2036
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martinahansen [Wed, 5 Dec 2012 10:24:11 +0000 (10:24 +0000)]
renamed patternmatcher to dynamic
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2035
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martinahansen [Wed, 5 Dec 2012 10:22:29 +0000 (10:22 +0000)]
renamed patternmatcher to dynamic
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2034
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martinahansen [Wed, 5 Dec 2012 10:22:01 +0000 (10:22 +0000)]
fixing name space collision
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2033
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martinahansen [Wed, 5 Dec 2012 10:21:36 +0000 (10:21 +0000)]
refactorying PatternMatcher to Dynamic
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2032
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martinahansen [Wed, 5 Dec 2012 10:20:05 +0000 (10:20 +0000)]
renamed patternmatcher to dynamic
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2031
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martinahansen [Wed, 5 Dec 2012 10:19:39 +0000 (10:19 +0000)]
cleaned comments
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2030
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martinahansen [Wed, 5 Dec 2012 09:33:29 +0000 (09:33 +0000)]
refactor match->patmatch scan->patscan
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2029
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martinahansen [Wed, 5 Dec 2012 09:32:46 +0000 (09:32 +0000)]
refactor match->patmatch scan->patscan
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2028
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martinahansen [Tue, 4 Dec 2012 12:51:49 +0000 (12:51 +0000)]
added patmatch method to backtrack.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2027
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martinahansen [Tue, 4 Dec 2012 10:37:46 +0000 (10:37 +0000)]
added private to patternmatcher
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2026
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martinahansen [Tue, 4 Dec 2012 10:35:06 +0000 (10:35 +0000)]
fixed unit tests for patternmatcher
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2025
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martinahansen [Tue, 4 Dec 2012 07:03:41 +0000 (07:03 +0000)]
added some text
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2024
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martinahansen [Mon, 3 Dec 2012 21:45:58 +0000 (21:45 +0000)]
fixed constants for align.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2023
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martinahansen [Mon, 3 Dec 2012 21:45:03 +0000 (21:45 +0000)]
ported patternmatcher to C
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2022
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martinahansen [Fri, 30 Nov 2012 11:29:07 +0000 (11:29 +0000)]
finished backtrack drama
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2021
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martinahansen [Fri, 30 Nov 2012 11:21:41 +0000 (11:21 +0000)]
added state to backtrack.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2020
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martinahansen [Fri, 30 Nov 2012 11:21:06 +0000 (11:21 +0000)]
done revert of test_backtrack.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2019
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martinahansen [Fri, 30 Nov 2012 11:13:09 +0000 (11:13 +0000)]
reverted test_backtrack.rb to r1827
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2018
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martinahansen [Fri, 30 Nov 2012 11:05:08 +0000 (11:05 +0000)]
reverted backtrack.rb to 2006 prior to struct version
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2017
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martinahansen [Thu, 29 Nov 2012 20:12:34 +0000 (20:12 +0000)]
disabling backtrack which causes compile error
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2016
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martinahansen [Thu, 29 Nov 2012 13:12:46 +0000 (13:12 +0000)]
added 3 parameters to blast_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2009
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martinahansen [Wed, 28 Nov 2012 18:08:46 +0000 (18:08 +0000)]
fixing up backtrack code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2008
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martinahansen [Wed, 28 Nov 2012 10:35:46 +0000 (10:35 +0000)]
added output of mis ind and del to backtrack code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2007
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martinahansen [Tue, 27 Nov 2012 20:52:44 +0000 (20:52 +0000)]
polished backtrack.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2006
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martinahansen [Tue, 27 Nov 2012 18:06:20 +0000 (18:06 +0000)]
backtrack.rb polish
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2005
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martinahansen [Tue, 27 Nov 2012 07:22:55 +0000 (07:22 +0000)]
added -c to nuc dist plot
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2004
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martinahansen [Tue, 27 Nov 2012 07:21:04 +0000 (07:21 +0000)]
added -c to plot_nuc_dist
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2003
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martinahansen [Tue, 27 Nov 2012 07:17:20 +0000 (07:17 +0000)]
added missing seq fix to plot_nucleotide_distribution
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2001
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martinahansen [Tue, 27 Nov 2012 07:03:54 +0000 (07:03 +0000)]
added relative count to plot_nucleotide_distribution
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2000
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martinahansen [Tue, 27 Nov 2012 06:38:53 +0000 (06:38 +0000)]
more power to the QA
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1999
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martinahansen [Mon, 26 Nov 2012 22:16:58 +0000 (22:16 +0000)]
more power to the QA
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1998
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martinahansen [Mon, 26 Nov 2012 16:26:00 +0000 (16:26 +0000)]
added adaptor removal to QA
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1997
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martinahansen [Mon, 26 Nov 2012 08:35:58 +0000 (08:35 +0000)]
polish of QA_Illumina_report.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1995
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martinahansen [Fri, 23 Nov 2012 21:31:58 +0000 (21:31 +0000)]
small fix QA_Illumina_report.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1994
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martinahansen [Fri, 23 Nov 2012 20:46:50 +0000 (20:46 +0000)]
added QA_Illumina_report.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1993
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martinahansen [Wed, 21 Nov 2012 09:30:07 +0000 (09:30 +0000)]
added exception handling for missing SFF coordinates
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1992
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martinahansen [Tue, 20 Nov 2012 09:00:05 +0000 (09:00 +0000)]
added uchime to usearch
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1991
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martinahansen [Mon, 19 Nov 2012 14:20:46 +0000 (14:20 +0000)]
add uchime_seq biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1989
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martinahansen [Fri, 2 Nov 2012 13:33:34 +0000 (13:33 +0000)]
added tests for find_pairs
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1987
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