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git.donarmstrong.com Git - biopieces.git/log
martinahansen [Wed, 5 Dec 2012 10:21:36 +0000 (10:21 +0000)]
refactorying PatternMatcher to Dynamic
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2032
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martinahansen [Wed, 5 Dec 2012 10:20:05 +0000 (10:20 +0000)]
renamed patternmatcher to dynamic
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2031
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martinahansen [Wed, 5 Dec 2012 10:19:39 +0000 (10:19 +0000)]
cleaned comments
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2030
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martinahansen [Wed, 5 Dec 2012 09:33:29 +0000 (09:33 +0000)]
refactor match->patmatch scan->patscan
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2029
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martinahansen [Wed, 5 Dec 2012 09:32:46 +0000 (09:32 +0000)]
refactor match->patmatch scan->patscan
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2028
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martinahansen [Tue, 4 Dec 2012 12:51:49 +0000 (12:51 +0000)]
added patmatch method to backtrack.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2027
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martinahansen [Tue, 4 Dec 2012 10:37:46 +0000 (10:37 +0000)]
added private to patternmatcher
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2026
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martinahansen [Tue, 4 Dec 2012 10:35:06 +0000 (10:35 +0000)]
fixed unit tests for patternmatcher
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2025
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martinahansen [Tue, 4 Dec 2012 07:03:41 +0000 (07:03 +0000)]
added some text
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2024
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martinahansen [Mon, 3 Dec 2012 21:45:58 +0000 (21:45 +0000)]
fixed constants for align.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2023
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martinahansen [Mon, 3 Dec 2012 21:45:03 +0000 (21:45 +0000)]
ported patternmatcher to C
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2022
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martinahansen [Fri, 30 Nov 2012 11:29:07 +0000 (11:29 +0000)]
finished backtrack drama
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2021
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martinahansen [Fri, 30 Nov 2012 11:21:41 +0000 (11:21 +0000)]
added state to backtrack.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2020
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martinahansen [Fri, 30 Nov 2012 11:21:06 +0000 (11:21 +0000)]
done revert of test_backtrack.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2019
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martinahansen [Fri, 30 Nov 2012 11:13:09 +0000 (11:13 +0000)]
reverted test_backtrack.rb to r1827
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2018
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martinahansen [Fri, 30 Nov 2012 11:05:08 +0000 (11:05 +0000)]
reverted backtrack.rb to 2006 prior to struct version
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2017
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martinahansen [Thu, 29 Nov 2012 20:12:34 +0000 (20:12 +0000)]
disabling backtrack which causes compile error
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2016
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martinahansen [Thu, 29 Nov 2012 13:12:46 +0000 (13:12 +0000)]
added 3 parameters to blast_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2009
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martinahansen [Wed, 28 Nov 2012 18:08:46 +0000 (18:08 +0000)]
fixing up backtrack code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2008
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martinahansen [Wed, 28 Nov 2012 10:35:46 +0000 (10:35 +0000)]
added output of mis ind and del to backtrack code
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2007
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martinahansen [Tue, 27 Nov 2012 20:52:44 +0000 (20:52 +0000)]
polished backtrack.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2006
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martinahansen [Tue, 27 Nov 2012 18:06:20 +0000 (18:06 +0000)]
backtrack.rb polish
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2005
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martinahansen [Tue, 27 Nov 2012 07:22:55 +0000 (07:22 +0000)]
added -c to nuc dist plot
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2004
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martinahansen [Tue, 27 Nov 2012 07:21:04 +0000 (07:21 +0000)]
added -c to plot_nuc_dist
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2003
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martinahansen [Tue, 27 Nov 2012 07:17:20 +0000 (07:17 +0000)]
added missing seq fix to plot_nucleotide_distribution
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2001
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martinahansen [Tue, 27 Nov 2012 07:03:54 +0000 (07:03 +0000)]
added relative count to plot_nucleotide_distribution
git-svn-id: http://biopieces.googlecode.com/svn/trunk@2000
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martinahansen [Tue, 27 Nov 2012 06:38:53 +0000 (06:38 +0000)]
more power to the QA
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1999
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martinahansen [Mon, 26 Nov 2012 22:16:58 +0000 (22:16 +0000)]
more power to the QA
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1998
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martinahansen [Mon, 26 Nov 2012 16:26:00 +0000 (16:26 +0000)]
added adaptor removal to QA
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1997
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martinahansen [Mon, 26 Nov 2012 08:35:58 +0000 (08:35 +0000)]
polish of QA_Illumina_report.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1995
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martinahansen [Fri, 23 Nov 2012 21:31:58 +0000 (21:31 +0000)]
small fix QA_Illumina_report.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1994
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martinahansen [Fri, 23 Nov 2012 20:46:50 +0000 (20:46 +0000)]
added QA_Illumina_report.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1993
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martinahansen [Wed, 21 Nov 2012 09:30:07 +0000 (09:30 +0000)]
added exception handling for missing SFF coordinates
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1992
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martinahansen [Tue, 20 Nov 2012 09:00:05 +0000 (09:00 +0000)]
added uchime to usearch
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1991
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martinahansen [Mon, 19 Nov 2012 14:20:46 +0000 (14:20 +0000)]
add uchime_seq biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1989
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martinahansen [Fri, 2 Nov 2012 13:33:34 +0000 (13:33 +0000)]
added tests for find_pairs
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1987
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martinahansen [Fri, 2 Nov 2012 13:07:33 +0000 (13:07 +0000)]
removing order_pairs2 and order_pairs3
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1985
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martinahansen [Fri, 2 Nov 2012 12:49:13 +0000 (12:49 +0000)]
find_pairs added
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1984
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martinahansen [Thu, 1 Nov 2012 17:45:33 +0000 (17:45 +0000)]
fixed but in order_pairs3
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1983
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martinahansen [Thu, 1 Nov 2012 14:32:27 +0000 (14:32 +0000)]
added verbose info to order_pairs3
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1982
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martinahansen [Thu, 1 Nov 2012 14:18:11 +0000 (14:18 +0000)]
added get_entry method to biopieces.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1981
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martinahansen [Thu, 1 Nov 2012 14:17:29 +0000 (14:17 +0000)]
adding order_pairs3
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1980
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martinahansen [Wed, 31 Oct 2012 21:23:55 +0000 (21:23 +0000)]
changed order_pairs2 to gdbm
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1979
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martinahansen [Wed, 31 Oct 2012 21:21:52 +0000 (21:21 +0000)]
changed order_pairs2 to gdbm
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1978
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martinahansen [Wed, 31 Oct 2012 21:07:35 +0000 (21:07 +0000)]
added order_pairs2
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1977
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martinahansen [Wed, 31 Oct 2012 20:50:00 +0000 (20:50 +0000)]
added order_pairs2
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1976
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martinahansen [Fri, 26 Oct 2012 05:20:30 +0000 (05:20 +0000)]
updated installer
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1975
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martinahansen [Thu, 25 Oct 2012 12:01:50 +0000 (12:01 +0000)]
updated installer
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1974
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martinahansen [Thu, 25 Oct 2012 11:42:00 +0000 (11:42 +0000)]
added debranch function to classify_taxonomy
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1972
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martinahansen [Wed, 24 Oct 2012 18:07:12 +0000 (18:07 +0000)]
updated classify_taxonomy to GG12-10
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1971
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martinahansen [Tue, 23 Oct 2012 17:06:30 +0000 (17:06 +0000)]
fixed nasty bug in classify_taxonomy
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1970
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martinahansen [Mon, 22 Oct 2012 13:07:55 +0000 (13:07 +0000)]
fixed nasty bug in classify_taxonomy
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1969
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martinahansen [Tue, 16 Oct 2012 14:12:34 +0000 (14:12 +0000)]
removed raise from classify_taxonomy
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1965
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martinahansen [Mon, 15 Oct 2012 17:11:42 +0000 (17:11 +0000)]
removed raise from classify_taxonomy
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1964
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martinahansen [Fri, 12 Oct 2012 08:49:09 +0000 (08:49 +0000)]
fixed classify_taxonomy
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1963
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martinahansen [Wed, 10 Oct 2012 13:20:55 +0000 (13:20 +0000)]
added some file locking to biopieces.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1962
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martinahansen [Wed, 10 Oct 2012 12:49:35 +0000 (12:49 +0000)]
added some file locking to Biopieces.pm
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1961
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martinahansen [Wed, 10 Oct 2012 12:36:09 +0000 (12:36 +0000)]
added flock to biostat
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1960
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martinahansen [Wed, 10 Oct 2012 12:28:52 +0000 (12:28 +0000)]
removed stale file crap from biostat
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1959
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martinahansen [Wed, 10 Oct 2012 12:21:21 +0000 (12:21 +0000)]
added dynamic mem allocation to findsim.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1958
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martinahansen [Wed, 10 Oct 2012 12:20:38 +0000 (12:20 +0000)]
added dynamic mem allocation to findsim.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1957
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martinahansen [Tue, 9 Oct 2012 09:22:51 +0000 (09:22 +0000)]
changed default values for findsim_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1954
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martinahansen [Tue, 9 Oct 2012 09:16:17 +0000 (09:16 +0000)]
cleanup of findsim.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1953
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martinahansen [Tue, 9 Oct 2012 08:56:00 +0000 (08:56 +0000)]
cleanup of findsim_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1952
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martinahansen [Tue, 9 Oct 2012 08:54:17 +0000 (08:54 +0000)]
cleanup of findsim.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1951
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martinahansen [Thu, 27 Sep 2012 13:10:04 +0000 (13:10 +0000)]
upgraded kmer_freq test
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1950
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martinahansen [Thu, 27 Sep 2012 13:08:48 +0000 (13:08 +0000)]
polished kmer_freq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1949
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martinahansen [Thu, 27 Sep 2012 13:02:11 +0000 (13:02 +0000)]
removed kmer_freq test files
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1947
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martinahansen [Thu, 27 Sep 2012 12:58:17 +0000 (12:58 +0000)]
clearning up kmer_stats and kmer_freq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1945
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martinahansen [Thu, 27 Sep 2012 12:40:13 +0000 (12:40 +0000)]
finishing work on match.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1943
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martinahansen [Tue, 25 Sep 2012 13:07:13 +0000 (13:07 +0000)]
work kmer_stats biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1941
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martinahansen [Tue, 25 Sep 2012 07:58:07 +0000 (07:58 +0000)]
added kmer_stats biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1938
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martinahansen [Fri, 21 Sep 2012 09:27:34 +0000 (09:27 +0000)]
added parser for phred qual to fasta.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1937
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martinahansen [Fri, 21 Sep 2012 09:10:48 +0000 (09:10 +0000)]
added qual_base(33|64)? methods to seq.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1936
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martinahansen [Fri, 21 Sep 2012 09:09:50 +0000 (09:09 +0000)]
slight polish of read_fastq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1935
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martinahansen [Thu, 20 Sep 2012 15:10:47 +0000 (15:10 +0000)]
added bases_per_file option to find_adaptor
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1933
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martinahansen [Wed, 19 Sep 2012 11:19:11 +0000 (11:19 +0000)]
fixed database type guess for blast_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1932
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martinahansen [Thu, 13 Sep 2012 13:19:26 +0000 (13:19 +0000)]
pair.rb now working correctly
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1930
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martinahansen [Wed, 12 Sep 2012 19:43:13 +0000 (19:43 +0000)]
worked on pair aligner
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1929
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martinahansen [Tue, 11 Sep 2012 10:04:45 +0000 (10:04 +0000)]
working on pair.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1921
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martinahansen [Tue, 11 Sep 2012 09:58:37 +0000 (09:58 +0000)]
added align/match.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1920
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martinahansen [Tue, 11 Sep 2012 09:54:08 +0000 (09:54 +0000)]
worked on pair.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1919
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martinahansen [Mon, 10 Sep 2012 09:50:07 +0000 (09:50 +0000)]
fixed unit tests for seq.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1916
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martinahansen [Tue, 4 Sep 2012 14:51:00 +0000 (14:51 +0000)]
added math_aux.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1913
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martinahansen [Tue, 4 Sep 2012 14:50:36 +0000 (14:50 +0000)]
added test_math_aux.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1912
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martinahansen [Tue, 4 Sep 2012 12:05:30 +0000 (12:05 +0000)]
fixed bug in clip_adaptor where LEFT_POS > RIGHT_POS
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1911
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martinahansen [Tue, 4 Sep 2012 12:04:21 +0000 (12:04 +0000)]
fixed bug in clip_adaptor where LEFT_POS > RIGHT_POS
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1910
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martinahansen [Mon, 3 Sep 2012 11:30:10 +0000 (11:30 +0000)]
revamped find_adaptor and clip_adaptor
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1909
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martinahansen [Mon, 3 Sep 2012 11:29:11 +0000 (11:29 +0000)]
updated testing files for find_adaptor and clip_adaptor
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1907
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martinahansen [Thu, 30 Aug 2012 12:10:27 +0000 (12:10 +0000)]
deleted old QA_454_report script
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1906
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martinahansen [Thu, 30 Aug 2012 12:09:53 +0000 (12:09 +0000)]
added nucleotide plot to QA_454_report
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1905
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martinahansen [Thu, 30 Aug 2012 11:18:48 +0000 (11:18 +0000)]
added plot_nucleotide_distribution biopiece
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1902
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martinahansen [Thu, 30 Aug 2012 08:23:27 +0000 (08:23 +0000)]
finally figured how to change plot color
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1900
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martinahansen [Thu, 16 Aug 2012 11:19:00 +0000 (11:19 +0000)]
did something to findsim.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1898
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martinahansen [Wed, 15 Aug 2012 13:34:14 +0000 (13:34 +0000)]
made find_orfs run on DNA or RNA
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1896
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martinahansen [Tue, 14 Aug 2012 13:24:45 +0000 (13:24 +0000)]
fixed mean_scores to deal with 0 length seqs
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1893
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martinahansen [Tue, 14 Aug 2012 13:23:10 +0000 (13:23 +0000)]
reverted trim_seq
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1892
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martinahansen [Tue, 14 Aug 2012 13:16:36 +0000 (13:16 +0000)]
changed trim_seq to omit outputting sequences with length 0
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1891
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martinahansen [Thu, 9 Aug 2012 11:15:37 +0000 (11:15 +0000)]
upgraded QA script to use new plot scores count feature
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1890
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martinahansen [Tue, 7 Aug 2012 17:50:02 +0000 (17:50 +0000)]
last fix on prodigal upgrade
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1888
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projects / biopieces.git / log