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2011-05-28	martinahansen	added multithreading to find_adaptor	commit \| commitdiff \| tree
2011-05-26	martinahansen	added order_pairs	commit \| commitdiff \| tree
2011-05-26	martinahansen	fixed type in assemble_seq_idba	commit \| commitdiff \| tree
2011-05-26	martinahansen	fixed mate-pair name issue in assemble_seq_idba	commit \| commitdiff \| tree
2011-05-25	martinahansen	added plot_distribution biopiece	commit \| commitdiff \| tree
2011-05-25	martinahansen	polished plot_scores	commit \| commitdiff \| tree
2011-05-24	martinahansen	upgraded bp_update alias due to complaints	commit \| commitdiff \| tree
2011-05-24	martinahansen	fixed fence post bug in plot_lendist	commit \| commitdiff \| tree
2011-05-24	martinahansen	working on clean_reads scripts	commit \| commitdiff \| tree
2011-05-24	martinahansen	working on clean_reads scripts	commit \| commitdiff \| tree
2011-05-24	martinahansen	fixed strange bug in find_adaptor	commit \| commitdiff \| tree
2011-05-24	martinahansen	fixed asseble_seq_velvet	commit \| commitdiff \| tree
2011-05-24	martinahansen	fixed asseble_seq_idba	commit \| commitdiff \| tree
2011-05-24	martinahansen	polished bp_scripts	commit \| commitdiff \| tree
2011-05-23	martinahansen	fixed find_adaptor tests	commit \| commitdiff \| tree
2011-05-23	martinahansen	polishing find_adaptor	commit \| commitdiff \| tree
2011-05-23	martinahansen	fixed critical flaw in find_adaptor	commit \| commitdiff \| tree
2011-05-23	martinahansen	fixed critical bug in biopieces.rb and reworked find_adaptor	commit \| commitdiff \| tree
2011-05-23	martinahansen	committing major ruby overhaul	commit \| commitdiff \| tree
2011-05-19	martinahansen	fiddleling with biopieces.rb	commit \| commitdiff \| tree
2011-05-19	martinahansen	preparing biopieces.rb rewrite	commit \| commitdiff \| tree
2011-05-18	martinahansen	fixed a path in biopieces.rb	commit \| commitdiff \| tree
2011-05-18	martinahansen	fixed paths in assemble_seq_idba + velvet	commit \| commitdiff \| tree
2011-05-18	martinahansen	refactored patternmatcher	commit \| commitdiff \| tree
2011-05-13	martinahansen	updated 00README file in ruby dir	commit \| commitdiff \| tree
2011-05-13	martinahansen	cleaning up old ruby trunk	commit \| commitdiff \| tree
2011-05-13	martinahansen	changed layout of ruby source	commit \| commitdiff \| tree
2011-05-13	martinahansen	add dist option to find_adaptor	commit \| commitdiff \| tree
2011-05-12	martinahansen	upgraded add_ident tests	commit \| commitdiff \| tree
2011-05-12	martinahansen	added offset switch to add_ident	commit \| commitdiff \| tree
2011-05-11	martinahansen	1 vector only patternmatcher.rb now :o)	commit \| commitdiff \| tree
2011-05-10	martinahansen	fixed pipes for adaptor removal	commit \| commitdiff \| tree
2011-05-10	martinahansen	added fix for negative 454 decimal values	commit \| commitdiff \| tree
2011-05-10	martinahansen	fixed type cast bug	commit \| commitdiff \| tree
2011-05-10	martinahansen	added procedure switch to analyze_assembly	commit \| commitdiff \| tree
2011-05-10	martinahansen	added procedure switch to find_genes	commit \| commitdiff \| tree
2011-05-10	martinahansen	polished analyze_assembly	commit \| commitdiff \| tree
2011-05-09	martinahansen	polishing gene cov feature in analyze_assembly	commit \| commitdiff \| tree
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
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