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git.donarmstrong.com Git - biopieces.git/log
martinahansen [Tue, 18 Mar 2014 19:24:13 +0000 (19:24 +0000)]
removed debug message
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2296
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martinahansen [Tue, 18 Mar 2014 19:15:59 +0000 (19:15 +0000)]
fixed file bug
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2295
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martinahansen [Tue, 18 Mar 2014 16:21:34 +0000 (16:21 +0000)]
added file check
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2294
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martinahansen [Tue, 18 Mar 2014 16:21:16 +0000 (16:21 +0000)]
polish of fastq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2293
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martinahansen [Thu, 6 Feb 2014 10:33:20 +0000 (10:33 +0000)]
fixed typo in max_vals
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2290
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martinahansen [Mon, 13 Jan 2014 10:50:03 +0000 (10:50 +0000)]
fixed each_orf
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2288
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martinahansen [Mon, 13 Jan 2014 10:38:40 +0000 (10:38 +0000)]
refactor subseq to Seq#[]
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2287
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martinahansen [Mon, 13 Jan 2014 10:04:41 +0000 (10:04 +0000)]
removed subseq and subseq! methods in favor of []
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2286
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martinahansen [Mon, 13 Jan 2014 09:39:43 +0000 (09:39 +0000)]
exchanged subseq with seq[]
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2285
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martinahansen [Mon, 13 Jan 2014 09:29:50 +0000 (09:29 +0000)]
exchanged subseq with seq[]
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2284
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martinahansen [Mon, 13 Jan 2014 09:21:41 +0000 (09:21 +0000)]
refactor foo to record
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2283
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martinahansen [Thu, 19 Dec 2013 12:35:36 +0000 (12:35 +0000)]
fixed missing field problem in analyze_vals
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2282
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martinahansen [Wed, 18 Dec 2013 17:18:24 +0000 (17:18 +0000)]
upgraded dependencies
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2281
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martinahansen [Wed, 18 Dec 2013 17:17:50 +0000 (17:17 +0000)]
upgraded installer deps
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2280
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martinahansen [Wed, 18 Dec 2013 17:16:12 +0000 (17:16 +0000)]
updateing to idba hybrid
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2279
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martinahansen [Fri, 13 Dec 2013 10:37:23 +0000 (10:37 +0000)]
changed fasta parse to allow leading empty lines
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2278
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martinahansen [Wed, 11 Dec 2013 11:14:16 +0000 (11:14 +0000)]
fixed wrap bug in seq.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2277
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martinahansen [Thu, 5 Dec 2013 14:16:58 +0000 (14:16 +0000)]
fixed qual scores in sam.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2275
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martinahansen [Thu, 5 Dec 2013 14:07:59 +0000 (14:07 +0000)]
fixed qual scores in sam.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2274
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martinahansen [Thu, 5 Dec 2013 13:45:19 +0000 (13:45 +0000)]
fixed encoding bug in bowtie_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2273
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martinahansen [Wed, 4 Dec 2013 10:45:23 +0000 (10:45 +0000)]
added ugly fix to ruby gnuplot dumb print problem
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2272
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martinahansen [Tue, 3 Dec 2013 11:42:43 +0000 (11:42 +0000)]
fixed name issue in uclust_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2271
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martinahansen [Mon, 2 Dec 2013 21:27:33 +0000 (21:27 +0000)]
finishing slice_align biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2269
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martinahansen [Mon, 2 Dec 2013 21:22:21 +0000 (21:22 +0000)]
finishing slice_align biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2268
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martinahansen [Mon, 2 Dec 2013 21:21:54 +0000 (21:21 +0000)]
added more tests to slice_align
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2267
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martinahansen [Mon, 2 Dec 2013 19:45:39 +0000 (19:45 +0000)]
added tests for slice_align
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2266
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martinahansen [Mon, 2 Dec 2013 14:44:35 +0000 (14:44 +0000)]
fixed bug in assemble_pairs
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2264
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martinahansen [Fri, 29 Nov 2013 21:32:41 +0000 (21:32 +0000)]
fixed read_454 tests
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2263
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martinahansen [Fri, 29 Nov 2013 21:07:46 +0000 (21:07 +0000)]
added tests to find_orfs
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2262
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martinahansen [Fri, 29 Nov 2013 20:58:58 +0000 (20:58 +0000)]
fixed another each_orf bug
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2261
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martinahansen [Fri, 29 Nov 2013 20:14:12 +0000 (20:14 +0000)]
fixed bug in find_orfs
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2260
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martinahansen [Fri, 29 Nov 2013 15:08:04 +0000 (15:08 +0000)]
added slice_align biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2259
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martinahansen [Mon, 25 Nov 2013 20:49:29 +0000 (20:49 +0000)]
fixed encoding bug in read_454
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2257
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martinahansen [Mon, 25 Nov 2013 20:32:12 +0000 (20:32 +0000)]
fixed encoding in write_454
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2256
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martinahansen [Mon, 25 Nov 2013 15:36:04 +0000 (15:36 +0000)]
plot_scores max length set to 100K
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2255
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martinahansen [Thu, 7 Nov 2013 12:38:38 +0000 (12:38 +0000)]
fixed installer issue
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2254
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martinahansen [Wed, 30 Oct 2013 21:37:08 +0000 (21:37 +0000)]
fixed bug in pair assembler
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2253
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martinahansen [Wed, 30 Oct 2013 10:56:28 +0000 (10:56 +0000)]
added patscan_trim method to Seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2252
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martinahansen [Fri, 25 Oct 2013 10:29:33 +0000 (10:29 +0000)]
fixed analyze_vals issue
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2251
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martinahansen [Fri, 25 Oct 2013 09:42:48 +0000 (09:42 +0000)]
added -o and -x to analyze_vals
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2250
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martinahansen [Thu, 24 Oct 2013 10:05:05 +0000 (10:05 +0000)]
refactored backtrack methods to use options hash in method invocations
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2248
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martinahansen [Thu, 24 Oct 2013 09:25:12 +0000 (09:25 +0000)]
fixed Seq object creation in sff.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2247
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martinahansen [Thu, 24 Oct 2013 08:49:27 +0000 (08:49 +0000)]
now using roche mid module for find_barcodes
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2246
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martinahansen [Thu, 24 Oct 2013 08:41:23 +0000 (08:41 +0000)]
added roche mid module
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2245
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martinahansen [Thu, 24 Oct 2013 08:19:44 +0000 (08:19 +0000)]
adding table.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2244
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martinahansen [Wed, 23 Oct 2013 12:47:14 +0000 (12:47 +0000)]
removed commented out stale code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2243
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martinahansen [Fri, 18 Oct 2013 13:01:02 +0000 (13:01 +0000)]
fixed method name change
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2242
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martinahansen [Thu, 17 Oct 2013 12:24:07 +0000 (12:24 +0000)]
fixed QA_454_report.rb to work with new analyze_vals
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2241
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martinahansen [Thu, 17 Oct 2013 12:13:57 +0000 (12:13 +0000)]
fixed QA_454_report.rb to work with new analyze_vals
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2240
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martinahansen [Thu, 17 Oct 2013 11:12:41 +0000 (11:12 +0000)]
fixed QA_454_report.rb to work with new analyze_vals
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2239
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martinahansen [Thu, 17 Oct 2013 07:34:56 +0000 (07:34 +0000)]
fixed QA_454_report.rb to work with new analyze_vals
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2238
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martinahansen [Wed, 16 Oct 2013 08:02:04 +0000 (08:02 +0000)]
cleanup of analyze_vals added analyze_scores
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2236
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martinahansen [Tue, 15 Oct 2013 20:06:45 +0000 (20:06 +0000)]
rewrote analyze_vals
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2234
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martinahansen [Tue, 15 Oct 2013 17:48:22 +0000 (17:48 +0000)]
rewrote write_tab
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2232
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martinahansen [Tue, 15 Oct 2013 17:45:28 +0000 (17:45 +0000)]
rewrote write_tab
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2231
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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
74ccb610-7750-0410-82ae-
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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
74ccb610-7750-0410-82ae-
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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
74ccb610-7750-0410-82ae-
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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
74ccb610-7750-0410-82ae-
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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
74ccb610-7750-0410-82ae-
013aeee3265d
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
74ccb610-7750-0410-82ae-
013aeee3265d
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
74ccb610-7750-0410-82ae-
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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
74ccb610-7750-0410-82ae-
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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
74ccb610-7750-0410-82ae-
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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
74ccb610-7750-0410-82ae-
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projects / biopieces.git / log