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git.donarmstrong.com Git - biopieces.git/log
martinahansen [Mon, 3 Jan 2011 12:49:50 +0000 (12:49 +0000)]
misq updates
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1199
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martinahansen [Fri, 31 Dec 2010 09:38:53 +0000 (09:38 +0000)]
polishing find_mids
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1198
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martinahansen [Tue, 21 Dec 2010 11:19:52 +0000 (11:19 +0000)]
fixed bug in bwa_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1196
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martinahansen [Fri, 17 Dec 2010 09:06:16 +0000 (09:06 +0000)]
added contributed biopieces calc_density
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1194
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martinahansen [Thu, 16 Dec 2010 13:07:14 +0000 (13:07 +0000)]
added min option to find_homopolymers
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1192
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martinahansen [Thu, 16 Dec 2010 12:24:36 +0000 (12:24 +0000)]
speedup fix of max_homopol again
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1191
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martinahansen [Thu, 16 Dec 2010 12:17:47 +0000 (12:17 +0000)]
speedup fix of max_homopol
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1190
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martinahansen [Thu, 16 Dec 2010 11:08:25 +0000 (11:08 +0000)]
added find_homopolymers biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1189
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martinahansen [Mon, 13 Dec 2010 14:00:55 +0000 (14:00 +0000)]
added QA_Solexa_report.sh
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1187
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martinahansen [Mon, 13 Dec 2010 09:26:34 +0000 (09:26 +0000)]
added QA_454_report.sh biopiece script
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1186
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martinahansen [Fri, 10 Dec 2010 16:40:43 +0000 (16:40 +0000)]
added join_seq biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1184
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martinahansen [Fri, 10 Dec 2010 13:25:27 +0000 (13:25 +0000)]
genbank.rb fixes
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1183
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martinahansen [Fri, 10 Dec 2010 11:31:53 +0000 (11:31 +0000)]
added shuffle_records
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1182
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martinahansen [Thu, 9 Dec 2010 15:56:59 +0000 (15:56 +0000)]
fixed get_seq in genbank.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1180
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martinahansen [Thu, 9 Dec 2010 15:55:12 +0000 (15:55 +0000)]
fixed another locator bug in genbank.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1179
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martinahansen [Thu, 9 Dec 2010 15:46:06 +0000 (15:46 +0000)]
fixed cryptic bug in genbank.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1178
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martinahansen [Thu, 9 Dec 2010 15:45:35 +0000 (15:45 +0000)]
fixed cryptic bug in genbank.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1177
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martinahansen [Thu, 9 Dec 2010 15:23:59 +0000 (15:23 +0000)]
small safety add in genbank.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1176
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martinahansen [Thu, 9 Dec 2010 12:37:04 +0000 (12:37 +0000)]
fixed read_genbank tests
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1175
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martinahansen [Thu, 9 Dec 2010 12:31:44 +0000 (12:31 +0000)]
fixed genbank.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1174
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martinahansen [Thu, 9 Dec 2010 12:28:53 +0000 (12:28 +0000)]
fixed genbank.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1173
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martinahansen [Wed, 8 Dec 2010 14:40:29 +0000 (14:40 +0000)]
added read_genbank
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1170
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martinahansen [Wed, 24 Nov 2010 15:11:08 +0000 (15:11 +0000)]
added tests for translate_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1169
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martinahansen [Wed, 24 Nov 2010 15:02:54 +0000 (15:02 +0000)]
added tests for uniq_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1168
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martinahansen [Thu, 18 Nov 2010 12:40:10 +0000 (12:40 +0000)]
fixed bug in uclust_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1167
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martinahansen [Thu, 18 Nov 2010 12:29:12 +0000 (12:29 +0000)]
added --comp switch to uclust_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1165
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martinahansen [Sun, 14 Nov 2010 17:27:58 +0000 (17:27 +0000)]
adding 00README file to code_ruby dir
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1163
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martinahansen [Sun, 14 Nov 2010 12:03:43 +0000 (12:03 +0000)]
added 00README to bp_test directory
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1162
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martinahansen [Wed, 10 Nov 2010 09:14:01 +0000 (09:14 +0000)]
fixed find_mids to locate even low q mids
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1160
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martinahansen [Tue, 9 Nov 2010 14:19:25 +0000 (14:19 +0000)]
added roche MID tags to find_mids
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1159
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martinahansen [Tue, 2 Nov 2010 15:14:59 +0000 (15:14 +0000)]
added find_mids biopiece tests
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1157
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martinahansen [Tue, 2 Nov 2010 13:36:54 +0000 (13:36 +0000)]
fixed bug in find_mids
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1155
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martinahansen [Tue, 2 Nov 2010 12:43:04 +0000 (12:43 +0000)]
added find_mids biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1154
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martinahansen [Tue, 2 Nov 2010 10:47:04 +0000 (10:47 +0000)]
fixed bug in clip_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1153
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martinahansen [Tue, 2 Nov 2010 10:40:16 +0000 (10:40 +0000)]
added clip_seq biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1152
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martinahansen [Mon, 1 Nov 2010 13:28:11 +0000 (13:28 +0000)]
removing patscan ruby crap
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1150
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martinahansen [Mon, 1 Nov 2010 09:14:12 +0000 (09:14 +0000)]
added patfind.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1149
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martinahansen [Sun, 31 Oct 2010 16:18:20 +0000 (16:18 +0000)]
fixed aliases in bashrc
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1144
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martinahansen [Wed, 20 Oct 2010 13:31:38 +0000 (13:31 +0000)]
added patscan.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1143
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martinahansen [Fri, 15 Oct 2010 14:14:08 +0000 (14:14 +0000)]
polishing min max sum etc
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1142
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martinahansen [Fri, 15 Oct 2010 13:46:32 +0000 (13:46 +0000)]
polished sum_vals and added tests
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1140
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martinahansen [Fri, 15 Oct 2010 10:04:59 +0000 (10:04 +0000)]
added tests for mean_vals
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1138
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martinahansen [Fri, 15 Oct 2010 09:17:51 +0000 (09:17 +0000)]
add tests for analyze_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1136
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martinahansen [Fri, 15 Oct 2010 08:15:47 +0000 (08:15 +0000)]
trouble shooting buffering problem
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1133
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martinahansen [Thu, 14 Oct 2010 14:04:50 +0000 (14:04 +0000)]
ported analyze_seq to ruby
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1132
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martinahansen [Thu, 14 Oct 2010 14:04:08 +0000 (14:04 +0000)]
ported analyze_seq to ruby
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1131
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martinahansen [Wed, 13 Oct 2010 12:11:28 +0000 (12:11 +0000)]
fixed scores in bwa_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1130
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martinahansen [Wed, 13 Oct 2010 12:00:52 +0000 (12:00 +0000)]
removed local logging causing trouble
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1129
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martinahansen [Wed, 13 Oct 2010 10:19:37 +0000 (10:19 +0000)]
fixed SAM.pm qual scores from phred-33 to phred-64
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1127
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martinahansen [Wed, 13 Oct 2010 09:27:48 +0000 (09:27 +0000)]
changed bowtie_seq to use phred64
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1126
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martinahansen [Wed, 13 Oct 2010 08:46:01 +0000 (08:46 +0000)]
polished read_454 and added tests
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1124
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martinahansen [Wed, 13 Oct 2010 08:28:36 +0000 (08:28 +0000)]
polished plot_scores
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1122
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martinahansen [Tue, 12 Oct 2010 15:18:53 +0000 (15:18 +0000)]
added align ruby lib
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1120
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martinahansen [Tue, 12 Oct 2010 15:17:34 +0000 (15:17 +0000)]
added fastq ruby lib
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1119
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martinahansen [Tue, 12 Oct 2010 15:14:34 +0000 (15:14 +0000)]
polished write_fastq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1118
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martinahansen [Tue, 12 Oct 2010 15:06:35 +0000 (15:06 +0000)]
slight bug fix of write_fastq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1116
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martinahansen [Tue, 12 Oct 2010 15:00:07 +0000 (15:00 +0000)]
upgraded scores_to_dec
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1114
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martinahansen [Tue, 12 Oct 2010 14:53:36 +0000 (14:53 +0000)]
upgraded mask_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1112
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martinahansen [Tue, 12 Oct 2010 14:31:38 +0000 (14:31 +0000)]
added solexa switch to read_fastq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1110
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martinahansen [Tue, 12 Oct 2010 09:16:31 +0000 (09:16 +0000)]
upgraded read_fastq and added tests
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1107
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martinahansen [Mon, 11 Oct 2010 12:48:23 +0000 (12:48 +0000)]
upgraded find_genes
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1106
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martinahansen [Tue, 28 Sep 2010 13:12:35 +0000 (13:12 +0000)]
AlignTwoSeq.pm briefly revisited
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1104
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martinahansen [Tue, 28 Sep 2010 09:02:04 +0000 (09:02 +0000)]
fixed indentation in perl code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1103
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martinahansen [Thu, 23 Sep 2010 11:46:43 +0000 (11:46 +0000)]
cleanup of uclust_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1102
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martinahansen [Wed, 22 Sep 2010 12:18:24 +0000 (12:18 +0000)]
polishing on uclust_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1101
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martinahansen [Tue, 21 Sep 2010 09:22:37 +0000 (09:22 +0000)]
added uclust_seq Biopiece - Work in progress!
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1100
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martinahansen [Mon, 20 Sep 2010 15:16:29 +0000 (15:16 +0000)]
fixed typo in text in digest_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1098
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martinahansen [Mon, 20 Sep 2010 08:40:00 +0000 (08:40 +0000)]
fixes and test for digest_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1096
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martinahansen [Mon, 20 Sep 2010 07:54:22 +0000 (07:54 +0000)]
added digest_seq Biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1094
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martinahansen [Fri, 17 Sep 2010 09:59:00 +0000 (09:59 +0000)]
added Digest class to ruby code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1093
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martinahansen [Thu, 16 Sep 2010 10:09:30 +0000 (10:09 +0000)]
added pcr_seq Biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1092
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martinahansen [Thu, 16 Sep 2010 10:08:39 +0000 (10:08 +0000)]
added reverse method to ruby Seq class
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1090
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martinahansen [Mon, 13 Sep 2010 08:10:55 +0000 (08:10 +0000)]
added bin_vals biopiece and tests
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1088
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martinahansen [Thu, 9 Sep 2010 11:41:03 +0000 (11:41 +0000)]
ported length_seq to ruby
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1087
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martinahansen [Thu, 9 Sep 2010 11:25:33 +0000 (11:25 +0000)]
fixing length_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1085
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martinahansen [Thu, 9 Sep 2010 11:20:56 +0000 (11:20 +0000)]
added Ruby version check
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1084
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martinahansen [Thu, 9 Sep 2010 08:41:24 +0000 (08:41 +0000)]
slight fix of trailing newline in progress_meter
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1083
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martinahansen [Thu, 9 Sep 2010 08:40:19 +0000 (08:40 +0000)]
slight fix of trailing newline in progress_meter
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1082
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martinahansen [Thu, 9 Sep 2010 08:38:36 +0000 (08:38 +0000)]
slight fix of trailing newline in progress_meter
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1081
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martinahansen [Thu, 9 Sep 2010 08:36:26 +0000 (08:36 +0000)]
slight fix of printf in progress_meter
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1080
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martinahansen [Thu, 9 Sep 2010 08:24:40 +0000 (08:24 +0000)]
added progress_meter biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1078
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martinahansen [Wed, 8 Sep 2010 07:21:41 +0000 (07:21 +0000)]
fixed minor bug in write_align of pairwise protein alignments
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1077
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martinahansen [Thu, 2 Sep 2010 08:01:47 +0000 (08:01 +0000)]
added scores_to_dec biopiece, wiki, and tests
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1075
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martinahansen [Wed, 1 Sep 2010 14:18:50 +0000 (14:18 +0000)]
reverting ruby unit test to old school
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1074
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martinahansen [Wed, 1 Sep 2010 13:48:50 +0000 (13:48 +0000)]
added tests for mask_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1073
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martinahansen [Wed, 1 Sep 2010 13:35:30 +0000 (13:35 +0000)]
added mask_seq biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1071
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martinahansen [Wed, 1 Sep 2010 13:03:31 +0000 (13:03 +0000)]
replaced option keys from strings to symbols in ruby code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1070
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martinahansen [Fri, 20 Aug 2010 12:40:02 +0000 (12:40 +0000)]
shifted ruby biopiece records to use symbols instead of strings
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1068
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martinahansen [Wed, 18 Aug 2010 19:48:50 +0000 (19:48 +0000)]
added zip reading to read_fasta
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1066
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martinahansen [Wed, 18 Aug 2010 11:20:24 +0000 (11:20 +0000)]
read_fasta now reads zipped fasta fails again
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1065
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martinahansen [Tue, 17 Aug 2010 14:03:22 +0000 (14:03 +0000)]
updating test_read_fasta
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1064
74ccb610-7750-0410-82ae-
013aeee3265d
martinahansen [Tue, 17 Aug 2010 13:50:14 +0000 (13:50 +0000)]
replacing read_fasta with ruby version
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1063
74ccb610-7750-0410-82ae-
013aeee3265d
martinahansen [Tue, 17 Aug 2010 13:48:11 +0000 (13:48 +0000)]
replacing read_fasta with ruby version
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1062
74ccb610-7750-0410-82ae-
013aeee3265d
martinahansen [Tue, 17 Aug 2010 13:48:00 +0000 (13:48 +0000)]
replacing read_fasta with ruby version
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1061
74ccb610-7750-0410-82ae-
013aeee3265d
martinahansen [Tue, 17 Aug 2010 13:47:33 +0000 (13:47 +0000)]
replacing read_fasta with ruby version
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1060
74ccb610-7750-0410-82ae-
013aeee3265d
martinahansen [Mon, 16 Aug 2010 10:14:19 +0000 (10:14 +0000)]
updating seq.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1059
74ccb610-7750-0410-82ae-
013aeee3265d
martinahansen [Mon, 16 Aug 2010 10:13:53 +0000 (10:13 +0000)]
updateing seq.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1058
74ccb610-7750-0410-82ae-
013aeee3265d
martinahansen [Fri, 13 Aug 2010 08:51:56 +0000 (08:51 +0000)]
fixed type bug in ruby code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1057
74ccb610-7750-0410-82ae-
013aeee3265d
martinahansen [Thu, 12 Aug 2010 09:59:26 +0000 (09:59 +0000)]
polishing testing suite
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1056
74ccb610-7750-0410-82ae-
013aeee3265d
martinahansen [Thu, 12 Aug 2010 09:29:39 +0000 (09:29 +0000)]
added test for blast biopieces
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1055
74ccb610-7750-0410-82ae-
013aeee3265d
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