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2011-05-09	martinahansen	added gene coverage to analyze_assembly	commit \| commitdiff \| tree
2011-05-09	martinahansen	added coverage method to prodigal.rb	commit \| commitdiff \| tree
2011-05-09	martinahansen	added fix to find_genes	commit \| commitdiff \| tree
2011-05-09	martinahansen	ported find_genes to ruby	commit \| commitdiff \| tree
2011-05-09	martinahansen	fixed indentation in uclust_seq	commit \| commitdiff \| tree
2011-05-09	martinahansen	added prodigal.rb	commit \| commitdiff \| tree
2011-05-09	martinahansen	updated genbank.rb to allow empty defaults	commit \| commitdiff \| tree
2011-05-06	martinahansen	added full switch to find_genes	commit \| commitdiff \| tree
2011-05-06	martinahansen	removing sequence file from assemble_seq*	commit \| commitdiff \| tree
2011-05-05	martinahansen	polished asseble_seq_velvet	commit \| commitdiff \| tree
2011-05-05	martinahansen	removed name option from asseble_seq_idba	commit \| commitdiff \| tree
2011-05-04	martinahansen	added assemble_seq_velvet draft biopiece	commit \| commitdiff \| tree
2011-05-04	martinahansen	fixed default cast for lists in biopieces.rb	commit \| commitdiff \| tree
2011-05-04	martinahansen	refactoring arg name in assemble_seq_idba	commit \| commitdiff \| tree
2011-05-04	martinahansen	added --clean to assemble_seq_idba	commit \| commitdiff \| tree
2011-05-03	martinahansen	polished assemble_seq_idba	commit \| commitdiff \| tree
2011-05-03	martinahansen	added assemble_seq_idba	commit \| commitdiff \| tree
2011-05-03	martinahansen	made plot_scores 1-based	commit \| commitdiff \| tree
2011-05-03	martinahansen	corrected plot_matches missing -persists switch	commit \| commitdiff \| tree
2011-05-03	martinahansen	added titles to plot_scores	commit \| commitdiff \| tree
2011-05-02	martinahansen	fixed typo in analyce_gc	commit \| commitdiff \| tree
2011-05-02	martinahansen	code update	commit \| commitdiff \| tree
2011-05-02	martinahansen	ported plot_scores to ruby	commit \| commitdiff \| tree
2011-05-02	martinahansen	removed redundant line from plot_scores	commit \| commitdiff \| tree
2011-05-02	martinahansen	testing unspecified features	commit \| commitdiff \| tree
2011-05-02	martinahansen	added tests to analyze_gc	commit \| commitdiff \| tree
2011-04-26	martinahansen	adaptor script posilished	commit \| commitdiff \| tree
2011-04-26	martinahansen	added useful biopiece scripts	commit \| commitdiff \| tree
2011-04-19	martinahansen	fixed bit fields in pattern matcher	commit \| commitdiff \| tree
2011-04-19	martinahansen	polishing find_adaptor	commit \| commitdiff \| tree
2011-04-19	martinahansen	added cache option to find_adaptor	commit \| commitdiff \| tree
2011-04-19	martinahansen	added cache option to find_adaptor	commit \| commitdiff \| tree
2011-04-18	martinahansen	added clip_adaptor biopiece	commit \| commitdiff \| tree
2011-04-18	martinahansen	added clip_adaptor biopiece	commit \| commitdiff \| tree
2011-04-18	martinahansen	added tests for find_adaptor	commit \| commitdiff \| tree
2011-04-18	martinahansen	fixed bug in find_adaptor	commit \| commitdiff \| tree
2011-04-18	martinahansen	fixed bug in find_adaptor	commit \| commitdiff \| tree
2011-04-18	martinahansen	added find_adaptor biopiece	commit \| commitdiff \| tree
2011-04-16	martinahansen	cleaned patternmatcher code	commit \| commitdiff \| tree
2011-04-15	martinahansen	pattern hell	commit \| commitdiff \| tree
2011-04-14	martinahansen	updated patternmatcher code	commit \| commitdiff \| tree
2011-04-14	martinahansen	added length check to read_454	commit \| commitdiff \| tree
2011-04-14	martinahansen	fixed missing qual trimming in remove_mids	commit \| commitdiff \| tree
2011-04-13	martinahansen	added remove_mids tests	commit \| commitdiff \| tree
2011-04-13	martinahansen	added remove_mids	commit \| commitdiff \| tree
2011-04-11	martinahansen	prettyfied gnuplots	commit \| commitdiff \| tree
2011-04-11	martinahansen	added persist to gnuplot commands	commit \| commitdiff \| tree
2011-03-30	martinahansen	reverted patternmatcher to original	commit \| commitdiff \| tree
2011-03-30	martinahansen	removing Args.pyc from svn	commit \| commitdiff \| tree
2011-03-30	martinahansen	updated find_mids	commit \| commitdiff \| tree
2011-03-30	martinahansen	updated tests for find_mids	commit \| commitdiff \| tree
2011-03-30	martinahansen	renamed find_mids.in file	commit \| commitdiff \| tree
2011-03-30	martinahansen	renamed find_mids.in file	commit \| commitdiff \| tree
2011-03-29	martinahansen	seq.rb update	commit \| commitdiff \| tree
2011-03-29	martinahansen	added final unit test to test_patternmatcher.rb	commit \| commitdiff \| tree
2011-03-29	martinahansen	fixed Rakefile	commit \| commitdiff \| tree
2011-03-29	martinahansen	removed amatch dependency in ruby code	commit \| commitdiff \| tree
2011-03-28	martinahansen	fixed patternmatcher.rb	commit \| commitdiff \| tree
2011-03-28	martinahansen	added PatternMatcher to ruby code	commit \| commitdiff \| tree
2011-03-20	martinahansen	plain and hd match in ruby Seq.rb now works	commit \| commitdiff \| tree
2011-03-19	martinahansen	worked on match code in Seq.rb	commit \| commitdiff \| tree
2011-03-19	martinahansen	added rdoc stuff	commit \| commitdiff \| tree
2011-03-19	martinahansen	worked on match code for ruby Seq class	commit \| commitdiff \| tree
2011-03-19	martinahansen	added test_digest.rb	commit \| commitdiff \| tree
2011-03-19	martinahansen	split digest.rb from seq.rb	commit \| commitdiff \| tree
2011-03-19	martinahansen	removing align.rb code	commit \| commitdiff \| tree
2011-03-19	martinahansen	removing align.rb code	commit \| commitdiff \| tree
2011-03-19	martinahansen	cleanup of Filsys in ruby code	commit \| commitdiff \| tree
2011-03-18	martinahansen	filesys now polished	commit \| commitdiff \| tree
2011-03-18	martinahansen	added filesys	commit \| commitdiff \| tree
2011-03-18	martinahansen	fixed stdin read for fastq and ruby code	commit \| commitdiff \| tree
2011-03-18	martinahansen	polishing stdin for ruby code	commit \| commitdiff \| tree
2011-03-17	martinahansen	ruby cleanup	commit \| commitdiff \| tree
2011-03-15	martinahansen	fixed bug in bwa_seq	commit \| commitdiff \| tree
2011-03-14	martinahansen	fixed missing license	commit \| commitdiff \| tree
2011-03-08	martinahansen	updated remove_illumina_adaptor	commit \| commitdiff \| tree
2011-03-07	martinahansen	updated remove_illumina_adaptor	commit \| commitdiff \| tree
2011-03-07	martinahansen	added hamming distance to adaptor location/clipping...	commit \| commitdiff \| tree
2011-03-07	martinahansen	added hamming_dist method to bits.rb	commit \| commitdiff \| tree
2011-03-07	martinahansen	added bits.rb and test_bits.rb	commit \| commitdiff \| tree
2011-02-20	martinahansen	polished seq.rb	commit \| commitdiff \| tree
2011-02-20	martinahansen	added remove_illumina_adaptor Biopiece	commit \| commitdiff \| tree
2011-02-19	martinahansen	added qual clipping to ruby code	commit \| commitdiff \| tree
2011-02-19	martinahansen	tried to fix unit testing errs in test_genbank.rb	commit \| commitdiff \| tree
2011-02-19	martinahansen	added Rakefile for unit testing of ruby code	commit \| commitdiff \| tree
2011-02-19	martinahansen	added adaptor_locate and adaptor_clip methods to ruby...	commit \| commitdiff \| tree
2011-02-11	martinahansen	fixed typo in sff.rb	commit \| commitdiff \| tree
2011-02-11	martinahansen	fixed typo in base36.rb	commit \| commitdiff \| tree
2011-02-11	martinahansen	updated tests for read_sff	commit \| commitdiff \| tree
2011-02-11	martinahansen	added xy-coord extraction code to sff.rb	commit \| commitdiff \| tree
2011-02-11	martinahansen	added xy-coord extraction code to sff.rb	commit \| commitdiff \| tree
2011-02-11	martinahansen	added base36.rb Ruby library	commit \| commitdiff \| tree
2011-02-08	martinahansen	removing stale test file	commit \| commitdiff \| tree
2011-02-08	martinahansen	added read_sff biopiece	commit \| commitdiff \| tree
2011-02-03	martinahansen	refactored shred_seq	commit \| commitdiff \| tree
2011-02-03	martinahansen	added subseq and subseq_rand methods to seq.rb	commit \| commitdiff \| tree
2011-02-03	martinahansen	crude polish of shred_seq	commit \| commitdiff \| tree
2011-02-02	martinahansen	added echo_yellow to testing code	commit \| commitdiff \| tree
2011-02-01	martinahansen	added analyze_assembly biopiece	commit \| commitdiff \| tree
2011-02-01	martinahansen	added kmer_freq biopiece and tests	commit \| commitdiff \| tree
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