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2011-07-03	martinahansen	added warnings to bp_test	commit \| commitdiff \| tree
2011-07-03	martinahansen	added warnings to bp_test	commit \| commitdiff \| tree
2011-06-17	martinahansen	added sam.rb to ruby trunk	commit \| commitdiff \| tree
2011-06-17	martinahansen	added sam.rb to ruby trunk	commit \| commitdiff \| tree
2011-06-15	martinahansen	added tests for rename_keys	commit \| commitdiff \| tree
2011-06-15	martinahansen	changed testing log file name	commit \| commitdiff \| tree
2011-06-15	martinahansen	added tests for blast_seq_pair	commit \| commitdiff \| tree
2011-06-14	martinahansen	hackery changes to plot_matches to deal with blast...	commit \| commitdiff \| tree
2011-06-14	martinahansen	blast_seq_pair polish	commit \| commitdiff \| tree
2011-06-14	martinahansen	blast_seq_pair polish	commit \| commitdiff \| tree
2011-06-14	martinahansen	blast_seq_pair polish	commit \| commitdiff \| tree
2011-06-14	martinahansen	added blast_seq_pair	commit \| commitdiff \| tree
2011-06-13	martinahansen	added Seq.type_guess to ruby code	commit \| commitdiff \| tree
2011-06-08	martinahansen	added tests for remove_keys	commit \| commitdiff \| tree
2011-06-08	martinahansen	added tests for remove_indels	commit \| commitdiff \| tree
2011-06-08	martinahansen	added tests for reverse_seq	commit \| commitdiff \| tree
2011-06-08	martinahansen	added tests for complement_seq	commit \| commitdiff \| tree
2011-06-06	martinahansen	fixed cat_seq	commit \| commitdiff \| tree
2011-06-06	martinahansen	added cat_seq biopiece	commit \| commitdiff \| tree
2011-06-05	martinahansen	shortened messages in test suite	commit \| commitdiff \| tree
2011-06-05	martinahansen	added tests for uniq_vals	commit \| commitdiff \| tree
2011-06-05	martinahansen	added tests for sort_records	commit \| commitdiff \| tree
2011-06-04	martinahansen	added tests for transliterate_vals	commit \| commitdiff \| tree
2011-06-04	martinahansen	added tests for transliterate_seq	commit \| commitdiff \| tree
2011-06-03	martinahansen	added tests for length_vals	commit \| commitdiff \| tree
2011-06-03	martinahansen	added test for calc_bit_scores	commit \| commitdiff \| tree
2011-05-31	martinahansen	added assemble_seq_ray	commit \| commitdiff \| tree
2011-05-30	martinahansen	upgraded mean_scores	commit \| commitdiff \| tree
2011-05-30	martinahansen	rename switch to something more appropriate	commit \| commitdiff \| tree
2011-05-30	martinahansen	removed unused code from find_adaptor	commit \| commitdiff \| tree
2011-05-30	martinahansen	added perl module and ruby gem test to bp_test	commit \| commitdiff \| tree
2011-05-29	martinahansen	squashing bugs in find_adaptor	commit \| commitdiff \| tree
2011-05-29	martinahansen	working on find_adaptor	commit \| commitdiff \| tree
2011-05-28	martinahansen	added multithreading to find_adaptor	commit \| commitdiff \| tree
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
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