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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
2012-12-05	martinahansen	renamed patternmatcher to dynamic	commit \| commitdiff \| tree
2012-12-05	martinahansen	cleaned comments	commit \| commitdiff \| tree
2012-12-05	martinahansen	refactor match->patmatch scan->patscan	commit \| commitdiff \| tree
2012-12-05	martinahansen	refactor match->patmatch scan->patscan	commit \| commitdiff \| tree
2012-12-04	martinahansen	added patmatch method to backtrack.rb	commit \| commitdiff \| tree
2012-12-04	martinahansen	added private to patternmatcher	commit \| commitdiff \| tree
2012-12-04	martinahansen	fixed unit tests for patternmatcher	commit \| commitdiff \| tree
2012-12-04	martinahansen	added some text	commit \| commitdiff \| tree
2012-12-03	martinahansen	fixed constants for align.rb	commit \| commitdiff \| tree
2012-12-03	martinahansen	ported patternmatcher to C	commit \| commitdiff \| tree
2012-11-30	martinahansen	finished backtrack drama	commit \| commitdiff \| tree
2012-11-30	martinahansen	added state to backtrack.rb	commit \| commitdiff \| tree
2012-11-30	martinahansen	done revert of test_backtrack.rb	commit \| commitdiff \| tree
2012-11-30	martinahansen	reverted test_backtrack.rb to r1827	commit \| commitdiff \| tree
2012-11-30	martinahansen	reverted backtrack.rb to 2006 prior to struct version	commit \| commitdiff \| tree
2012-11-29	martinahansen	disabling backtrack which causes compile error	commit \| commitdiff \| tree
2012-11-29	martinahansen	added 3 parameters to blast_seq	commit \| commitdiff \| tree
2012-11-28	martinahansen	fixing up backtrack code	commit \| commitdiff \| tree
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