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2013-05-16	martinahansen	added verbose count to grab	commit \| commitdiff \| tree
2013-05-06	martinahansen	fixed QA_Illumina_report.rb encoding	commit \| commitdiff \| tree
2013-04-29	martinahansen	fixed missing BP_TMP dir feature	commit \| commitdiff \| tree
2013-04-18	martinahansen	fixed divide bug in compute	commit \| commitdiff \| tree
2013-04-11	martinahansen	fixed bug in index_vals	commit \| commitdiff \| tree
2013-04-11	martinahansen	added index_vals biopiece	commit \| commitdiff \| tree
2013-03-20	martinahansen	corrected pcr_seq revcomp of patterns	commit \| commitdiff \| tree
2013-03-16	martinahansen	changed upper/lower case output in assemble_pairs	commit \| commitdiff \| tree
2013-03-13	martinahansen	dropped pandaseq requirement	commit \| commitdiff \| tree
2013-03-13	martinahansen	fixed minor upcase bug in assemble.rb	commit \| commitdiff \| tree
2013-03-13	martinahansen	upgraded tests of read_sff	commit \| commitdiff \| tree
2013-03-13	martinahansen	finish assemble_pairs revamp	commit \| commitdiff \| tree
2013-03-13	martinahansen	assemble_pairs revamp	commit \| commitdiff \| tree
2013-03-13	martinahansen	added comments to code	commit \| commitdiff \| tree
2013-03-13	martinahansen	added name check to assemble_pairs2	commit \| commitdiff \| tree
2013-03-13	martinahansen	added check for minimum seq length	commit \| commitdiff \| tree
2013-03-13	martinahansen	added check for minimum seq length	commit \| commitdiff \| tree
2013-03-13	martinahansen	fixed defaults and key names	commit \| commitdiff \| tree
2013-03-13	martinahansen	upgraded assemble.rb to chose proper residue when mismatch	commit \| commitdiff \| tree
2013-03-13	martinahansen	added hacky thing to avoid warning from zlib	commit \| commitdiff \| tree
2013-03-12	martinahansen	added keys to assemble_pairs2	commit \| commitdiff \| tree
2013-03-12	martinahansen	added assemble_pairs2	commit \| commitdiff \| tree
2013-03-12	martinahansen	added seq/assemble.rb	commit \| commitdiff \| tree
2013-03-12	martinahansen	fixed score base bug in sff.rb	commit \| commitdiff \| tree
2013-03-11	martinahansen	added word_size switch to blast_seq_pair	commit \| commitdiff \| tree
2013-03-11	martinahansen	changed blast_seq_pair to do multiple pairs	commit \| commitdiff \| tree
2013-03-11	martinahansen	added [] og []= to seq.rb	commit \| commitdiff \| tree
2013-03-08	martinahansen	added split_pair_seq biopiece	commit \| commitdiff \| tree
2013-03-08	martinahansen	added new Biopiece merge_pair_seq	commit \| commitdiff \| tree
2013-03-08	martinahansen	added new Biopiece merge_pair_seq	commit \| commitdiff \| tree
2013-03-08	martinahansen	dropped cat_seq Biopieces since join_seq exists	commit \| commitdiff \| tree
2013-03-08	martinahansen	added pair-end power to read_fastq	commit \| commitdiff \| tree
2013-03-08	martinahansen	added eof? method to filesys.rb	commit \| commitdiff \| tree
2013-03-08	martinahansen	refactoring of ruby code converting sequences types...	commit \| commitdiff \| tree
2013-03-08	martinahansen	added << method to Seq.rb	commit \| commitdiff \| tree
2013-03-08	martinahansen	rewrite of FASTQ internals	commit \| commitdiff \| tree
2013-03-01	martinahansen	fixed bug in plot_scores	commit \| commitdiff \| tree
2013-02-28	martinahansen	finished refactoring s/has_key?/[]/	commit \| commitdiff \| tree
2013-02-28	martinahansen	refactoring of ruby code s/has_key?/[]/	commit \| commitdiff \| tree
2013-02-28	martinahansen	fixed global SCORE_BASE in mean_scores	commit \| commitdiff \| tree
2013-02-28	martinahansen	refactoring of revcomp in seq.rb	commit \| commitdiff \| tree
2013-02-28	martinahansen	added Seq.shuffle method and tests	commit \| commitdiff \| tree
2013-02-28	martinahansen	updated find_SNPs tests	commit \| commitdiff \| tree
2013-02-25	martinahansen	fixed SCORE_BASE global var	commit \| commitdiff \| tree
2013-02-21	martinahansen	added coverage to find_SNPs	commit \| commitdiff \| tree
2013-02-21	martinahansen	fixed nasty bug in grab where -E and pattern 0 failed	commit \| commitdiff \| tree
2013-02-21	martinahansen	fixed nasty bug in grab where -E and pattern 0 failed	commit \| commitdiff \| tree
2013-02-20	martinahansen	made find_adaptor ignore too short sequences	commit \| commitdiff \| tree
2013-02-19	martinahansen	added write_sam biopiece	commit \| commitdiff \| tree
2013-02-19	martinahansen	disabled encoding validity check	commit \| commitdiff \| tree
2013-02-19	martinahansen	added provisional write sam support	commit \| commitdiff \| tree
2013-02-19	martinahansen	polished read_sam	commit \| commitdiff \| tree
2013-02-08	martinahansen	fixed quality score validity check	commit \| commitdiff \| tree
2013-02-06	martinahansen	disable validity check	commit \| commitdiff \| tree
2013-02-04	martinahansen	added quality score check to read_fastq	commit \| commitdiff \| tree
2013-02-04	martinahansen	added qual_valid? method to Seq.rb	commit \| commitdiff \| tree
2013-02-02	martinahansen	fixed minor bug in error handling	commit \| commitdiff \| tree
2013-01-22	martinahansen	fixed axis titles	commit \| commitdiff \| tree
2013-01-22	martinahansen	added plot_stacked_histogram biopiece	commit \| commitdiff \| tree
2013-01-21	martinahansen	added pandaseq prerequisite	commit \| commitdiff \| tree
2013-01-21	martinahansen	added tests for assemble_pairs biopiece	commit \| commitdiff \| tree
2013-01-21	martinahansen	added assemble_pairs biopiece	commit \| commitdiff \| tree
2013-01-20	martinahansen	added substitute_vals biopiece	commit \| commitdiff \| tree
2013-01-16	martinahansen	fixed bad tests in match.rb	commit \| commitdiff \| tree
2013-01-15	martinahansen	added png term to plot_matches	commit \| commitdiff \| tree
2013-01-14	martinahansen	added tests for create_seq_index and get_seq	commit \| commitdiff \| tree
2013-01-14	martinahansen	fixed apparent change in Carp yielding an extra . after...	commit \| commitdiff \| tree
2013-01-14	martinahansen	removed error check	commit \| commitdiff \| tree
2013-01-11	martinahansen	added bowtie2 biopieces	commit \| commitdiff \| tree
2013-01-09	martinahansen	adding kmer to contigs	commit \| commitdiff \| tree
2013-01-09	martinahansen	fixed up assemble_seq_velvet	commit \| commitdiff \| tree
2013-01-09	martinahansen	rewrote assemble_seq_velvet	commit \| commitdiff \| tree
2013-01-09	martinahansen	fixed pair end issue	commit \| commitdiff \| tree
2013-01-09	martinahansen	set cutoff to auto in velvet	commit \| commitdiff \| tree
2013-01-09	martinahansen	renamed assemle_seq_idba assemble_seq_idba	commit \| commitdiff \| tree
2013-01-09	martinahansen	renamed assemble_seq_idba_ud assemle_seq_idba	commit \| commitdiff \| tree
2013-01-09	martinahansen	removed old assemle_seq_idba	commit \| commitdiff \| tree
2013-01-04	martinahansen	fixed to_i bug in pcr_seq	commit \| commitdiff \| tree
2013-01-04	martinahansen	updated report	commit \| commitdiff \| tree
2013-01-04	martinahansen	updated pcr_seq and added tests	commit \| commitdiff \| tree
2013-01-03	martinahansen	polished pairwise alignment code	commit \| commitdiff \| tree
2013-01-02	martinahansen	added new match.rb and tests	commit \| commitdiff \| tree
2013-01-02	martinahansen	added new match.rb and tests	commit \| commitdiff \| tree
2013-01-02	martinahansen	added test for align dir	commit \| commitdiff \| tree
2013-01-02	martinahansen	renaming match.rb to matches.rb	commit \| commitdiff \| tree
2013-01-02	martinahansen	moved mum.rb	commit \| commitdiff \| tree
2012-12-20	martinahansen	clearnup of pair align code	commit \| commitdiff \| tree
2012-12-13	martinahansen	fixed minor bug in grab for exact_in where no key would...	commit \| commitdiff \| tree
2012-12-12	martinahansen	fixed QA_Illumina_report.rb SEQ_LEN > 20	commit \| commitdiff \| tree
2012-12-12	martinahansen	changed to new find_adaptor	commit \| commitdiff \| tree
2012-12-11	martinahansen	added unit test to backtrack code	commit \| commitdiff \| tree
2012-12-10	martinahansen	removed debug code from find_adaptor	commit \| commitdiff \| tree
2012-12-10	martinahansen	unrolling new find_adaptor	commit \| commitdiff \| tree
2012-12-10	martinahansen	fixed bug in backtrack.rb	commit \| commitdiff \| tree
2012-12-10	martinahansen	fixed unit tests for backtrack.rb	commit \| commitdiff \| tree
2012-12-06	martinahansen	fixed unit tests	commit \| commitdiff \| tree
2012-12-05	martinahansen	renamed patternmatcher to dynamic	commit \| commitdiff \| tree
2012-12-05	martinahansen	renamed patternmatcher to dynamic	commit \| commitdiff \| tree
2012-12-05	martinahansen	fixing name space collision	commit \| commitdiff \| tree
2012-12-05	martinahansen	refactorying PatternMatcher to Dynamic	commit \| commitdiff \| tree
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