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git.donarmstrong.com Git - biopieces.git/log
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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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martinahansen [Wed, 11 Aug 2010 12:38:34 +0000 (12:38 +0000)]
ruby code cleanup
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1054
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martinahansen [Mon, 9 Aug 2010 10:09:04 +0000 (10:09 +0000)]
added lisence to ruby code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1053
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martinahansen [Fri, 6 Aug 2010 13:50:06 +0000 (13:50 +0000)]
added rdoc
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1045
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martinahansen [Fri, 6 Aug 2010 13:18:08 +0000 (13:18 +0000)]
fixed ruby test code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1044
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martinahansen [Fri, 6 Aug 2010 12:05:43 +0000 (12:05 +0000)]
added swapcase_seq written in RUBY
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1042
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martinahansen [Fri, 6 Aug 2010 11:53:35 +0000 (11:53 +0000)]
dropping swapcase_seq tobereplaced
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1041
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martinahansen [Fri, 6 Aug 2010 10:06:43 +0000 (10:06 +0000)]
added test for analyze_gc
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1039
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martinahansen [Fri, 6 Aug 2010 09:33:05 +0000 (09:33 +0000)]
ruby exit status battle part #
12312423
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1038
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martinahansen [Fri, 6 Aug 2010 08:59:16 +0000 (08:59 +0000)]
added -o option and tests to analyze_vals
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1037
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martinahansen [Thu, 5 Aug 2010 13:37:18 +0000 (13:37 +0000)]
added test for add_ident
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1035
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martinahansen [Thu, 5 Aug 2010 08:54:11 +0000 (08:54 +0000)]
added test_read_solexa to tests
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1034
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martinahansen [Wed, 4 Aug 2010 14:01:26 +0000 (14:01 +0000)]
asdfasdr
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1033
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martinahansen [Wed, 4 Aug 2010 13:24:43 +0000 (13:24 +0000)]
polishing ruby code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1032
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martinahansen [Wed, 4 Aug 2010 12:10:19 +0000 (12:10 +0000)]
added write_tab tests
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1031
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martinahansen [Wed, 4 Aug 2010 09:12:10 +0000 (09:12 +0000)]
more polishing of testing suite
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1029
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martinahansen [Wed, 4 Aug 2010 09:09:35 +0000 (09:09 +0000)]
removing binary crap
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1028
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martinahansen [Wed, 4 Aug 2010 09:06:24 +0000 (09:06 +0000)]
polishing on testing suite
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1027
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martinahansen [Tue, 3 Aug 2010 15:11:07 +0000 (15:11 +0000)]
added more tests
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1026
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martinahansen [Tue, 3 Aug 2010 14:36:33 +0000 (14:36 +0000)]
had to fix shebang in testing env
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1024
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martinahansen [Tue, 3 Aug 2010 14:17:34 +0000 (14:17 +0000)]
testing suite paths upgraded
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1023
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martinahansen [Tue, 3 Aug 2010 13:07:53 +0000 (13:07 +0000)]
fixed first bug in testing suite
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1018
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martinahansen [Tue, 3 Aug 2010 13:06:04 +0000 (13:06 +0000)]
added testing suite
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1017
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martinahansen [Tue, 3 Aug 2010 12:34:58 +0000 (12:34 +0000)]
corrected slight bug in grab
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1015
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martinahansen [Wed, 30 Jun 2010 14:29:50 +0000 (14:29 +0000)]
added trim_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1006
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martinahansen [Tue, 29 Jun 2010 12:34:24 +0000 (12:34 +0000)]
added biopieces mean_scores
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1002
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martinahansen [Mon, 28 Jun 2010 08:27:47 +0000 (08:27 +0000)]
added ID to SCORE alias in KISS.pm
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1000
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martinahansen [Mon, 28 Jun 2010 08:18:36 +0000 (08:18 +0000)]
added usearch_seq biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@998
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martinahansen [Sat, 26 Jun 2010 09:47:45 +0000 (09:47 +0000)]
corrected typo
git-svn-id: http://biopieces.googlecode.com/svn/trunk@995
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martinahansen [Tue, 22 Jun 2010 14:49:53 +0000 (14:49 +0000)]
messing with exit in ruby - still
git-svn-id: http://biopieces.googlecode.com/svn/trunk@994
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martinahansen [Tue, 22 Jun 2010 09:42:25 +0000 (09:42 +0000)]
corrected type in log messages
git-svn-id: http://biopieces.googlecode.com/svn/trunk@993
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martinahansen [Mon, 21 Jun 2010 12:26:25 +0000 (12:26 +0000)]
polishing exit in ruby code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@992
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martinahansen [Thu, 17 Jun 2010 12:22:58 +0000 (12:22 +0000)]
added list switch to *_vals biopieces
git-svn-id: http://biopieces.googlecode.com/svn/trunk@990
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martinahansen [Thu, 17 Jun 2010 12:05:54 +0000 (12:05 +0000)]
added list switch to mean_vals
git-svn-id: http://biopieces.googlecode.com/svn/trunk@989
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martinahansen [Thu, 17 Jun 2010 11:36:00 +0000 (11:36 +0000)]
added fixedstep biopieces
git-svn-id: http://biopieces.googlecode.com/svn/trunk@987
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martinahansen [Wed, 16 Jun 2010 14:05:19 +0000 (14:05 +0000)]
schrubbing UCSC.pm code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@985
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martinahansen [Wed, 16 Jun 2010 13:01:14 +0000 (13:01 +0000)]
fixed s/Common/Filesys/ renaming in UCSC.pm
git-svn-id: http://biopieces.googlecode.com/svn/trunk@984
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martinahansen [Wed, 16 Jun 2010 12:41:28 +0000 (12:41 +0000)]
ruby code fixing exit
git-svn-id: http://biopieces.googlecode.com/svn/trunk@983
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martinahansen [Wed, 16 Jun 2010 11:55:16 +0000 (11:55 +0000)]
ruby code fixing exit
git-svn-id: http://biopieces.googlecode.com/svn/trunk@982
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martinahansen [Tue, 15 Jun 2010 11:55:05 +0000 (11:55 +0000)]
ruby code schrubbing
git-svn-id: http://biopieces.googlecode.com/svn/trunk@981
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martinahansen [Mon, 14 Jun 2010 13:57:21 +0000 (13:57 +0000)]
fixed unit tests for biopieces.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@980
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martinahansen [Fri, 28 May 2010 15:11:44 +0000 (15:11 +0000)]
trouble with list of list and class Cast
git-svn-id: http://biopieces.googlecode.com/svn/trunk@979
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martinahansen [Fri, 28 May 2010 14:07:11 +0000 (14:07 +0000)]
splitting class Biopieces
git-svn-id: http://biopieces.googlecode.com/svn/trunk@978
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martinahansen [Fri, 28 May 2010 13:49:25 +0000 (13:49 +0000)]
splitting class Biopieces
git-svn-id: http://biopieces.googlecode.com/svn/trunk@977
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martinahansen [Fri, 28 May 2010 10:43:23 +0000 (10:43 +0000)]
updating ruby code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@976
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martinahansen [Fri, 28 May 2010 08:49:13 +0000 (08:49 +0000)]
cleaned up ruby dir
git-svn-id: http://biopieces.googlecode.com/svn/trunk@975
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martinahansen [Thu, 27 May 2010 15:33:44 +0000 (15:33 +0000)]
ruby unit tests refactored
git-svn-id: http://biopieces.googlecode.com/svn/trunk@974
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martinahansen [Thu, 27 May 2010 10:09:40 +0000 (10:09 +0000)]
updated biopieces code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@973
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martinahansen [Tue, 25 May 2010 11:15:29 +0000 (11:15 +0000)]
added plot_scores fix
git-svn-id: http://biopieces.googlecode.com/svn/trunk@969
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martinahansen [Tue, 25 May 2010 10:07:32 +0000 (10:07 +0000)]
added plot_scores
git-svn-id: http://biopieces.googlecode.com/svn/trunk@968
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martinahansen [Thu, 20 May 2010 10:15:21 +0000 (10:15 +0000)]
fixed missing SEQ_LEN in read_454
git-svn-id: http://biopieces.googlecode.com/svn/trunk@967
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martinahansen [Thu, 20 May 2010 10:02:22 +0000 (10:02 +0000)]
added solexa_str_mean to read_454
git-svn-id: http://biopieces.googlecode.com/svn/trunk@964
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martinahansen [Thu, 20 May 2010 09:31:05 +0000 (09:31 +0000)]
added bp_scripts directory and stats scripts
git-svn-id: http://biopieces.googlecode.com/svn/trunk@963
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martinahansen [Wed, 19 May 2010 07:01:33 +0000 (07:01 +0000)]
added read_454 and write_454 (and ruby stuff)
git-svn-id: http://biopieces.googlecode.com/svn/trunk@961
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martinahansen [Tue, 18 May 2010 14:46:41 +0000 (14:46 +0000)]
extract seq now also extract SCORES if present
git-svn-id: http://biopieces.googlecode.com/svn/trunk@958
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martinahansen [Tue, 18 May 2010 09:47:36 +0000 (09:47 +0000)]
fixed harmless bug in remove_adaptor
git-svn-id: http://biopieces.googlecode.com/svn/trunk@957
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martinahansen [Fri, 14 May 2010 13:09:25 +0000 (13:09 +0000)]
cleaning up ruby code dir
git-svn-id: http://biopieces.googlecode.com/svn/trunk@952
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martinahansen [Tue, 11 May 2010 07:48:16 +0000 (07:48 +0000)]
fixed bug in write_fixedstep
git-svn-id: http://biopieces.googlecode.com/svn/trunk@951
74ccb610-7750-0410-82ae-
013aeee3265d
martinahansen [Tue, 27 Apr 2010 06:46:10 +0000 (06:46 +0000)]
fixed speed issue with track_ruler in BGB
git-svn-id: http://biopieces.googlecode.com/svn/trunk@950
74ccb610-7750-0410-82ae-
013aeee3265d
martinahansen [Mon, 26 Apr 2010 11:37:59 +0000 (11:37 +0000)]
optimized track_ruler in BGB
git-svn-id: http://biopieces.googlecode.com/svn/trunk@949
74ccb610-7750-0410-82ae-
013aeee3265d
martinahansen [Tue, 20 Apr 2010 15:21:55 +0000 (15:21 +0000)]
added trimming of scores to remove_adaptor
git-svn-id: http://biopieces.googlecode.com/svn/trunk@947
74ccb610-7750-0410-82ae-
013aeee3265d
martinahansen [Tue, 6 Apr 2010 06:41:18 +0000 (06:41 +0000)]
fixing undef $clade bug in BGB
git-svn-id: http://biopieces.googlecode.com/svn/trunk@946
74ccb610-7750-0410-82ae-
013aeee3265d
martinahansen [Wed, 31 Mar 2010 07:48:19 +0000 (07:48 +0000)]
dna page session export bug in BGB
git-svn-id: http://biopieces.googlecode.com/svn/trunk@945
74ccb610-7750-0410-82ae-
013aeee3265d
martinahansen [Tue, 30 Mar 2010 18:56:06 +0000 (18:56 +0000)]
fixed 0 defined bug in BGB
git-svn-id: http://biopieces.googlecode.com/svn/trunk@944
74ccb610-7750-0410-82ae-
013aeee3265d
martinahansen [Mon, 22 Mar 2010 08:28:47 +0000 (08:28 +0000)]
ugly fix of BGB ladder problem
git-svn-id: http://biopieces.googlecode.com/svn/trunk@938
74ccb610-7750-0410-82ae-
013aeee3265d
martinahansen [Mon, 22 Mar 2010 08:11:37 +0000 (08:11 +0000)]
fixing ladder bug in BGB
git-svn-id: http://biopieces.googlecode.com/svn/trunk@937
74ccb610-7750-0410-82ae-
013aeee3265d
projects / biopieces.git / log