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git.donarmstrong.com Git - biopieces.git/log
martinahansen [Tue, 15 Mar 2011 10:31:54 +0000 (10:31 +0000)]
fixed bug in bwa_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1290
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martinahansen [Mon, 14 Mar 2011 13:43:27 +0000 (13:43 +0000)]
fixed missing license
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1289
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martinahansen [Tue, 8 Mar 2011 11:21:41 +0000 (11:21 +0000)]
updated remove_illumina_adaptor
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1286
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martinahansen [Mon, 7 Mar 2011 15:41:24 +0000 (15:41 +0000)]
updated remove_illumina_adaptor
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1283
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martinahansen [Mon, 7 Mar 2011 13:41:14 +0000 (13:41 +0000)]
added hamming distance to adaptor location/clipping in ruby lib
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1282
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martinahansen [Mon, 7 Mar 2011 12:00:19 +0000 (12:00 +0000)]
added hamming_dist method to bits.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1281
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martinahansen [Mon, 7 Mar 2011 09:46:22 +0000 (09:46 +0000)]
added bits.rb and test_bits.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1280
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martinahansen [Sun, 20 Feb 2011 13:45:37 +0000 (13:45 +0000)]
polished seq.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1279
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martinahansen [Sun, 20 Feb 2011 13:06:22 +0000 (13:06 +0000)]
added remove_illumina_adaptor Biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1277
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martinahansen [Sat, 19 Feb 2011 18:53:30 +0000 (18:53 +0000)]
added qual clipping to ruby code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1276
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martinahansen [Sat, 19 Feb 2011 15:27:44 +0000 (15:27 +0000)]
tried to fix unit testing errs in test_genbank.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1275
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martinahansen [Sat, 19 Feb 2011 15:03:56 +0000 (15:03 +0000)]
added Rakefile for unit testing of ruby code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1274
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martinahansen [Sat, 19 Feb 2011 14:51:05 +0000 (14:51 +0000)]
added adaptor_locate and adaptor_clip methods to ruby code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1273
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martinahansen [Fri, 11 Feb 2011 18:55:56 +0000 (18:55 +0000)]
fixed typo in sff.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1272
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martinahansen [Fri, 11 Feb 2011 18:42:48 +0000 (18:42 +0000)]
fixed typo in base36.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1271
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martinahansen [Fri, 11 Feb 2011 11:16:51 +0000 (11:16 +0000)]
updated tests for read_sff
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1270
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martinahansen [Fri, 11 Feb 2011 11:09:21 +0000 (11:09 +0000)]
added xy-coord extraction code to sff.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1268
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martinahansen [Fri, 11 Feb 2011 10:52:22 +0000 (10:52 +0000)]
added xy-coord extraction code to sff.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1266
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martinahansen [Fri, 11 Feb 2011 09:56:55 +0000 (09:56 +0000)]
added base36.rb Ruby library
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1265
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martinahansen [Tue, 8 Feb 2011 20:39:32 +0000 (20:39 +0000)]
removing stale test file
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1264
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martinahansen [Tue, 8 Feb 2011 20:38:46 +0000 (20:38 +0000)]
added read_sff biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1262
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martinahansen [Thu, 3 Feb 2011 19:04:29 +0000 (19:04 +0000)]
refactored shred_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1253
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martinahansen [Thu, 3 Feb 2011 18:44:14 +0000 (18:44 +0000)]
added subseq and subseq_rand methods to seq.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1252
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martinahansen [Thu, 3 Feb 2011 15:56:38 +0000 (15:56 +0000)]
crude polish of shred_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1251
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martinahansen [Wed, 2 Feb 2011 09:12:07 +0000 (09:12 +0000)]
added echo_yellow to testing code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1249
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martinahansen [Tue, 1 Feb 2011 13:55:08 +0000 (13:55 +0000)]
added analyze_assembly biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1247
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martinahansen [Tue, 1 Feb 2011 13:27:02 +0000 (13:27 +0000)]
added kmer_freq biopiece and tests
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1243
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martinahansen [Tue, 1 Feb 2011 12:53:36 +0000 (12:53 +0000)]
added generate_oligos method to seq.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1242
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martinahansen [Mon, 31 Jan 2011 21:06:54 +0000 (21:06 +0000)]
python update?
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1241
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martinahansen [Mon, 31 Jan 2011 21:05:30 +0000 (21:05 +0000)]
added tests of calc_N50
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1240
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martinahansen [Mon, 31 Jan 2011 21:01:59 +0000 (21:01 +0000)]
fixed bug in calc_N50
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1239
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martinahansen [Mon, 31 Jan 2011 20:47:49 +0000 (20:47 +0000)]
added calc_N50
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1238
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martinahansen [Mon, 31 Jan 2011 20:46:20 +0000 (20:46 +0000)]
remove calc_n50
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1237
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martinahansen [Mon, 31 Jan 2011 20:41:56 +0000 (20:41 +0000)]
removing calc_N50
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1236
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martinahansen@gmail.com [Mon, 31 Jan 2011 19:56:20 +0000 (19:56 +0000)]
argh!
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1235
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martinahansen [Mon, 31 Jan 2011 19:34:52 +0000 (19:34 +0000)]
added calc_N50 biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1233
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martinahansen [Mon, 31 Jan 2011 19:23:09 +0000 (19:23 +0000)]
add out accessor to Biopieces ruby code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1232
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martinahansen [Mon, 31 Jan 2011 18:31:07 +0000 (18:31 +0000)]
revoking data_out magic
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1231
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martinahansen [Mon, 31 Jan 2011 17:46:39 +0000 (17:46 +0000)]
added :data_out magic to Biopeices ruby code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1230
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martinahansen [Sun, 30 Jan 2011 18:24:27 +0000 (18:24 +0000)]
polished shred_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1229
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martinahansen [Sun, 30 Jan 2011 16:41:52 +0000 (16:41 +0000)]
polished shred_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1228
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martinahansen [Sat, 29 Jan 2011 16:21:40 +0000 (16:21 +0000)]
fixed bug in shred_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1227
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martinahansen [Sat, 29 Jan 2011 15:59:37 +0000 (15:59 +0000)]
added shred_seq tests
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1224
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martinahansen [Sat, 29 Jan 2011 15:45:25 +0000 (15:45 +0000)]
added shred_seq biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1222
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martinahansen [Sat, 29 Jan 2011 10:24:44 +0000 (10:24 +0000)]
added version test of perl and ruby
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1221
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martinahansen [Wed, 26 Jan 2011 09:03:19 +0000 (09:03 +0000)]
added warning in bashrc
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1220
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martinahansen [Sun, 23 Jan 2011 20:50:58 +0000 (20:50 +0000)]
added Seq#to_key method
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1218
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martinahansen [Sat, 22 Jan 2011 10:00:10 +0000 (10:00 +0000)]
changed seq names to 0 based in Digest#each
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1215
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martinahansen [Sat, 22 Jan 2011 09:59:15 +0000 (09:59 +0000)]
updated tests for digest_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1214
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martinahansen [Sat, 22 Jan 2011 09:45:27 +0000 (09:45 +0000)]
added S_BEG and S_END keys to digest_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1213
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martinahansen [Sat, 22 Jan 2011 09:28:13 +0000 (09:28 +0000)]
fixed missing upcase bug in ruby Seq#Digest::each
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1212
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martinahansen [Thu, 20 Jan 2011 12:55:59 +0000 (12:55 +0000)]
polish of bitarray.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1211
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martinahansen [Thu, 20 Jan 2011 09:33:41 +0000 (09:33 +0000)]
slight cleanup of find_gaps
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1210
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martinahansen [Mon, 17 Jan 2011 16:02:32 +0000 (16:02 +0000)]
added tests for find_gaps
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1208
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martinahansen [Mon, 17 Jan 2011 15:44:52 +0000 (15:44 +0000)]
fixed bug in Fasta.pm
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1207
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martinahansen [Fri, 14 Jan 2011 21:04:39 +0000 (21:04 +0000)]
finishing unit tests for bitarray.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1206
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martinahansen [Fri, 14 Jan 2011 20:30:41 +0000 (20:30 +0000)]
fixed license text
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1205
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martinahansen [Fri, 14 Jan 2011 16:29:16 +0000 (16:29 +0000)]
added S_LEN to find_gaps
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1203
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martinahansen [Fri, 14 Jan 2011 16:26:18 +0000 (16:26 +0000)]
added bitarray ruby code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1202
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martinahansen [Wed, 12 Jan 2011 14:02:41 +0000 (14:02 +0000)]
posished Calc::standard_deviation
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1201
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martinahansen [Mon, 10 Jan 2011 14:13:35 +0000 (14:13 +0000)]
fixed SEQ_LEN bug in transliterate_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1200
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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
74ccb610-7750-0410-82ae-
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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
74ccb610-7750-0410-82ae-
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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
74ccb610-7750-0410-82ae-
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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
74ccb610-7750-0410-82ae-
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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
74ccb610-7750-0410-82ae-
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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
74ccb610-7750-0410-82ae-
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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
74ccb610-7750-0410-82ae-
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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
74ccb610-7750-0410-82ae-
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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
74ccb610-7750-0410-82ae-
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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
74ccb610-7750-0410-82ae-
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