biopieces.git
5 years agoremoved debug message master
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agofixed file bug
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agoadded file check
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agopolish of fastq
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agofixed typo in max_vals
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agofixed each_orf
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agorefactor subseq to Seq#[]
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agoremoved subseq and subseq! methods in favor of []
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agoexchanged subseq with seq[]
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agoexchanged subseq with seq[]
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agorefactor foo to record
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agofixed missing field problem in analyze_vals
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agoupgraded dependencies
martinahansen [Wed, 18 Dec 2013 17:18:24 +0000 (17:18 +0000)]
upgraded dependencies

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2281 74ccb610-7750-0410-82ae-013aeee3265d

5 years agoupgraded installer deps
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agoupdateing to idba hybrid
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agochanged fasta parse to allow leading empty lines
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agofixed wrap bug in seq.rb
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agofixed qual scores in sam.rb
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agofixed qual scores in sam.rb
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agofixed encoding bug in bowtie_seq
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agoadded ugly fix to ruby gnuplot dumb print problem
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agofixed name issue in uclust_seq
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agofinishing slice_align biopiece
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agofinishing slice_align biopiece
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agoadded more tests to slice_align
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agoadded tests for slice_align
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agofixed bug in assemble_pairs
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agofixed read_454 tests
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agoadded tests to find_orfs
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agofixed another each_orf bug
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agofixed bug in find_orfs
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agoadded slice_align biopiece
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agofixed encoding bug in read_454
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agofixed encoding in write_454
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agoplot_scores max length set to 100K
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agofixed installer issue
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agofixed bug in pair assembler
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agoadded patscan_trim method to Seq
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agofixed analyze_vals issue
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agoadded -o and -x to analyze_vals
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agorefactored backtrack methods to use options hash in method invocations
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agofixed Seq object creation in sff.rb
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agonow using roche mid module for find_barcodes
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agoadded roche mid module
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agoadding table.rb
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agoremoved commented out stale code
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agofixed method name change
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agofixed QA_454_report.rb to work with new analyze_vals
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agofixed QA_454_report.rb to work with new analyze_vals
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agofixed QA_454_report.rb to work with new analyze_vals
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agofixed QA_454_report.rb to work with new analyze_vals
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agocleanup of analyze_vals added analyze_scores
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agorewrote analyze_vals
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agorewrote write_tab
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agorewrote write_tab
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agorefactoring of assemble_pairs
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agofixed seq qual length check
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agoDRY refactorying of backtrack code
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agogzip fiddling
martinahansen [Mon, 7 Oct 2013 14:23:35 +0000 (14:23 +0000)]
gzip fiddling

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2226 74ccb610-7750-0410-82ae-013aeee3265d

5 years agoexchanged zlib code with commandline gzip
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agofixed symlink flaw in file type detection
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agochanged Seq.new argument to hash
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agoadded test for length of seq/qual mismatch
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agodisabling buggy bzip2-ruby
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agotemporary fix of bzip2 read problem
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agoadded prefix option to write_fasta_files and write_fastq_files
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agoadded bzip2-ruby gem requirement
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agoadded bzip2-ruby gem requirement
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agoadded gzip/bzip2 output option to write_fastq_files
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agoadded support for gzip/bzip2 in write_fasta_files (and wrap)
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agoported write_fasta to ruby enabling bzip2 support
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agoadded bzip output test to write_fastq
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agoadding bzip2 support in ruby
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agofixed isseu in find_orphans
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agocreated find_orphans Biopiece
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agobeautifing ambiguity.rb
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agoimplemented hamming_dist in inline C
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agoadd comments to ambiguity.rb
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agofixed broken tests not workin with Ruby2
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agoadded amiguity.rb
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agoadded mem.rb
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agoadded ambiguity to hamming_distance
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agofixed overlap bug in patscan_seq
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agoadded missing cpus switch to uclust_seq
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agopolish usearch_seq
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agopolish uclust_seq
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agofixing usearch upgrade
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agoupgraded uclust_seq to support usearch7
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agofixed genbank and embl parsing of 5'UTR and 3'UTR
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agoadded \r remove hack to genbank/embl parsers
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 74ccb610-7750-0410-82ae-013aeee3265d

5 years agomoved inline C code to seperate file
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-013aeee3265d

5 years agoadded edit_distance method to seq.rb
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-013aeee3265d

5 years agofixed ambiguity in levenshtein.rb
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-013aeee3265d

5 years agoadded levenshtein edit distance calculator
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-013aeee3265d

5 years agoadded levenshtein edit distance calculator
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

5 years agoadded levenshtein edit distance calculator
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

5 years agoupdated patscan_seq
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-013aeee3265d

5 years agoupdated patscan_seq
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-013aeee3265d

5 years agoadded missing files
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-013aeee3265d

5 years agorevamped find_homopolymers
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-013aeee3265d