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git.donarmstrong.com Git - biopieces.git/log
martinahansen [Tue, 8 Oct 2013 09:39:58 +0000 (09:39 +0000)]
refactoring of assemble_pairs
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2229
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martinahansen [Tue, 8 Oct 2013 08:46:04 +0000 (08:46 +0000)]
fixed seq qual length check
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2228
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martinahansen [Mon, 7 Oct 2013 15:05:20 +0000 (15:05 +0000)]
DRY refactorying of backtrack code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2227
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martinahansen [Mon, 7 Oct 2013 14:23:35 +0000 (14:23 +0000)]
gzip fiddling
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2226
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martinahansen [Mon, 7 Oct 2013 12:13:26 +0000 (12:13 +0000)]
exchanged zlib code with commandline gzip
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2225
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martinahansen [Mon, 7 Oct 2013 08:40:53 +0000 (08:40 +0000)]
fixed symlink flaw in file type detection
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2224
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martinahansen [Tue, 1 Oct 2013 18:33:22 +0000 (18:33 +0000)]
changed Seq.new argument to hash
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2223
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martinahansen [Thu, 26 Sep 2013 12:48:14 +0000 (12:48 +0000)]
added test for length of seq/qual mismatch
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2222
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martinahansen [Thu, 26 Sep 2013 10:18:14 +0000 (10:18 +0000)]
disabling buggy bzip2-ruby
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2221
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martinahansen [Thu, 26 Sep 2013 09:43:24 +0000 (09:43 +0000)]
temporary fix of bzip2 read problem
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2220
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martinahansen [Thu, 26 Sep 2013 08:09:07 +0000 (08:09 +0000)]
added prefix option to write_fasta_files and write_fastq_files
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2218
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martinahansen [Wed, 25 Sep 2013 20:06:28 +0000 (20:06 +0000)]
added bzip2-ruby gem requirement
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2216
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martinahansen [Wed, 25 Sep 2013 20:05:23 +0000 (20:05 +0000)]
added bzip2-ruby gem requirement
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2215
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martinahansen [Wed, 25 Sep 2013 19:50:03 +0000 (19:50 +0000)]
added gzip/bzip2 output option to write_fastq_files
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2214
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martinahansen [Wed, 25 Sep 2013 19:29:53 +0000 (19:29 +0000)]
added support for gzip/bzip2 in write_fasta_files (and wrap)
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2212
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martinahansen [Wed, 25 Sep 2013 14:34:00 +0000 (14:34 +0000)]
ported write_fasta to ruby enabling bzip2 support
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2210
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martinahansen [Wed, 25 Sep 2013 14:26:37 +0000 (14:26 +0000)]
added bzip output test to write_fastq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2209
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martinahansen [Wed, 25 Sep 2013 14:23:05 +0000 (14:23 +0000)]
adding bzip2 support in ruby
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2208
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martinahansen [Mon, 23 Sep 2013 12:29:14 +0000 (12:29 +0000)]
fixed isseu in find_orphans
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2207
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martinahansen [Mon, 23 Sep 2013 11:48:35 +0000 (11:48 +0000)]
created find_orphans Biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2205
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martinahansen [Wed, 18 Sep 2013 19:59:48 +0000 (19:59 +0000)]
beautifing ambiguity.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2204
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martinahansen [Wed, 18 Sep 2013 18:17:08 +0000 (18:17 +0000)]
implemented hamming_dist in inline C
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2203
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martinahansen [Wed, 18 Sep 2013 11:44:49 +0000 (11:44 +0000)]
add comments to ambiguity.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2202
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martinahansen [Wed, 18 Sep 2013 11:16:16 +0000 (11:16 +0000)]
fixed broken tests not workin with Ruby2
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2201
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martinahansen [Wed, 18 Sep 2013 10:30:49 +0000 (10:30 +0000)]
added amiguity.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2200
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martinahansen [Wed, 18 Sep 2013 10:29:46 +0000 (10:29 +0000)]
added mem.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2199
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martinahansen [Wed, 18 Sep 2013 10:17:27 +0000 (10:17 +0000)]
added ambiguity to hamming_distance
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2198
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martinahansen [Mon, 16 Sep 2013 14:46:00 +0000 (14:46 +0000)]
fixed overlap bug in patscan_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2197
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martinahansen [Fri, 13 Sep 2013 13:07:50 +0000 (13:07 +0000)]
added missing cpus switch to uclust_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2195
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martinahansen [Mon, 9 Sep 2013 19:05:50 +0000 (19:05 +0000)]
polish usearch_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2193
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martinahansen [Mon, 9 Sep 2013 19:04:47 +0000 (19:04 +0000)]
polish uclust_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2192
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martinahansen [Mon, 9 Sep 2013 18:58:53 +0000 (18:58 +0000)]
fixing usearch upgrade
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2190
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martinahansen [Fri, 6 Sep 2013 10:17:57 +0000 (10:17 +0000)]
upgraded uclust_seq to support usearch7
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2189
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martinahansen [Mon, 24 Jun 2013 10:55:33 +0000 (10:55 +0000)]
fixed genbank and embl parsing of 5'UTR and 3'UTR
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2187
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martinahansen [Mon, 24 Jun 2013 09:59:49 +0000 (09:59 +0000)]
added \r remove hack to genbank/embl parsers
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2186
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martinahansen [Sun, 23 Jun 2013 09:38:18 +0000 (09:38 +0000)]
moved inline C code to seperate file
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2185
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martinahansen [Fri, 21 Jun 2013 09:35:03 +0000 (09:35 +0000)]
added edit_distance method to seq.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2184
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martinahansen [Fri, 21 Jun 2013 09:09:29 +0000 (09:09 +0000)]
fixed ambiguity in levenshtein.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2183
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martinahansen [Thu, 20 Jun 2013 21:09:51 +0000 (21:09 +0000)]
added levenshtein edit distance calculator
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2182
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martinahansen [Thu, 20 Jun 2013 21:07:14 +0000 (21:07 +0000)]
added levenshtein edit distance calculator
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2181
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martinahansen [Thu, 20 Jun 2013 21:05:55 +0000 (21:05 +0000)]
added levenshtein edit distance calculator
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2180
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martinahansen [Mon, 17 Jun 2013 09:56:22 +0000 (09:56 +0000)]
updated patscan_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2179
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martinahansen [Mon, 17 Jun 2013 09:49:58 +0000 (09:49 +0000)]
updated patscan_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2177
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martinahansen [Tue, 4 Jun 2013 14:05:26 +0000 (14:05 +0000)]
added missing files
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2176
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martinahansen [Tue, 4 Jun 2013 14:00:16 +0000 (14:00 +0000)]
revamped find_homopolymers
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2174
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martinahansen [Thu, 16 May 2013 09:04:37 +0000 (09:04 +0000)]
more verbose grab output
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2172
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martinahansen [Thu, 16 May 2013 08:56:09 +0000 (08:56 +0000)]
added verbose count to grab
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2170
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martinahansen [Mon, 6 May 2013 09:17:39 +0000 (09:17 +0000)]
fixed QA_Illumina_report.rb encoding
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2169
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martinahansen [Mon, 29 Apr 2013 09:52:27 +0000 (09:52 +0000)]
fixed missing BP_TMP dir feature
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2167
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martinahansen [Thu, 18 Apr 2013 08:17:30 +0000 (08:17 +0000)]
fixed divide bug in compute
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2162
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martinahansen [Thu, 11 Apr 2013 17:29:24 +0000 (17:29 +0000)]
fixed bug in index_vals
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2157
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martinahansen [Thu, 11 Apr 2013 17:10:35 +0000 (17:10 +0000)]
added index_vals biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2155
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martinahansen [Wed, 20 Mar 2013 06:42:06 +0000 (06:42 +0000)]
corrected pcr_seq revcomp of patterns
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2153
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martinahansen [Sat, 16 Mar 2013 18:47:24 +0000 (18:47 +0000)]
changed upper/lower case output in assemble_pairs
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2151
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martinahansen [Wed, 13 Mar 2013 12:03:13 +0000 (12:03 +0000)]
dropped pandaseq requirement
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2150
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martinahansen [Wed, 13 Mar 2013 11:51:30 +0000 (11:51 +0000)]
fixed minor upcase bug in assemble.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2149
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martinahansen [Wed, 13 Mar 2013 11:46:21 +0000 (11:46 +0000)]
upgraded tests of read_sff
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2148
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martinahansen [Wed, 13 Mar 2013 11:41:49 +0000 (11:41 +0000)]
finish assemble_pairs revamp
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2147
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martinahansen [Wed, 13 Mar 2013 11:33:46 +0000 (11:33 +0000)]
assemble_pairs revamp
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2145
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martinahansen [Wed, 13 Mar 2013 10:30:54 +0000 (10:30 +0000)]
added comments to code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2142
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martinahansen [Wed, 13 Mar 2013 10:20:58 +0000 (10:20 +0000)]
added name check to assemble_pairs2
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2141
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martinahansen [Wed, 13 Mar 2013 09:59:23 +0000 (09:59 +0000)]
added check for minimum seq length
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2140
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martinahansen [Wed, 13 Mar 2013 09:58:08 +0000 (09:58 +0000)]
added check for minimum seq length
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2139
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martinahansen [Wed, 13 Mar 2013 09:25:30 +0000 (09:25 +0000)]
fixed defaults and key names
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2138
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martinahansen [Wed, 13 Mar 2013 09:12:52 +0000 (09:12 +0000)]
upgraded assemble.rb to chose proper residue when mismatch
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2137
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martinahansen [Wed, 13 Mar 2013 06:58:56 +0000 (06:58 +0000)]
added hacky thing to avoid warning from zlib
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2136
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martinahansen [Tue, 12 Mar 2013 21:33:40 +0000 (21:33 +0000)]
added keys to assemble_pairs2
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2135
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martinahansen [Tue, 12 Mar 2013 18:13:17 +0000 (18:13 +0000)]
added assemble_pairs2
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2134
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martinahansen [Tue, 12 Mar 2013 18:12:29 +0000 (18:12 +0000)]
added seq/assemble.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2133
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martinahansen [Tue, 12 Mar 2013 10:44:52 +0000 (10:44 +0000)]
fixed score base bug in sff.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2132
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martinahansen [Mon, 11 Mar 2013 18:15:08 +0000 (18:15 +0000)]
added word_size switch to blast_seq_pair
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2127
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martinahansen [Mon, 11 Mar 2013 14:49:14 +0000 (14:49 +0000)]
changed blast_seq_pair to do multiple pairs
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2125
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martinahansen [Mon, 11 Mar 2013 06:52:14 +0000 (06:52 +0000)]
added [] og []= to seq.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2124
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martinahansen [Fri, 8 Mar 2013 18:42:08 +0000 (18:42 +0000)]
added split_pair_seq biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2122
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martinahansen [Fri, 8 Mar 2013 14:41:32 +0000 (14:41 +0000)]
added new Biopiece merge_pair_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2121
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martinahansen [Fri, 8 Mar 2013 14:39:37 +0000 (14:39 +0000)]
added new Biopiece merge_pair_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2120
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martinahansen [Fri, 8 Mar 2013 13:10:10 +0000 (13:10 +0000)]
dropped cat_seq Biopieces since join_seq exists
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2118
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martinahansen [Fri, 8 Mar 2013 12:35:17 +0000 (12:35 +0000)]
added pair-end power to read_fastq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2117
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martinahansen [Fri, 8 Mar 2013 12:24:12 +0000 (12:24 +0000)]
added eof? method to filesys.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2115
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martinahansen [Fri, 8 Mar 2013 10:43:05 +0000 (10:43 +0000)]
refactoring of ruby code converting sequences types to symbols
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2114
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martinahansen [Fri, 8 Mar 2013 10:09:02 +0000 (10:09 +0000)]
added << method to Seq.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2113
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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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projects / biopieces.git / log