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[biopieces.git] / code_ruby / lib / maasha / seq.rb

2013-12-11	martinahansen	fixed wrap bug in seq.rb	blob \| commitdiff \| raw
2013-11-29	martinahansen	fixed another each_orf bug	blob \| commitdiff \| raw \| diff to current
2013-11-29	martinahansen	fixed bug in find_orfs	blob \| commitdiff \| raw \| diff to current
2013-10-08	martinahansen	fixed seq qual length check	blob \| commitdiff \| raw \| diff to current
2013-10-01	martinahansen	changed Seq.new argument to hash	blob \| commitdiff \| raw \| diff to current
2013-09-26	martinahansen	added test for length of seq/qual mismatch	blob \| commitdiff \| raw \| diff to current
2013-09-18	martinahansen	implemented hamming_dist in inline C	blob \| commitdiff \| raw \| diff to current
2013-09-18	martinahansen	added ambiguity to hamming_distance	blob \| commitdiff \| raw \| diff to current
2013-06-21	martinahansen	added edit_distance method to seq.rb	blob \| commitdiff \| raw \| diff to current
2013-06-04	martinahansen	revamped find_homopolymers	blob \| commitdiff \| raw \| diff to current
2013-03-12	martinahansen	fixed score base bug in sff.rb	blob \| commitdiff \| raw \| diff to current
2013-03-11	martinahansen	added [] og []= to seq.rb	blob \| commitdiff \| raw \| diff to current
2013-03-08	martinahansen	added split_pair_seq biopiece	blob \| commitdiff \| raw \| diff to current
2013-03-08	martinahansen	refactoring of ruby code converting sequences types...	blob \| commitdiff \| raw \| diff to current
2013-03-08	martinahansen	added << method to Seq.rb	blob \| commitdiff \| raw \| diff to current
2013-03-08	martinahansen	rewrite of FASTQ internals	blob \| commitdiff \| raw \| diff to current
2013-02-28	martinahansen	refactoring of revcomp in seq.rb	blob \| commitdiff \| raw \| diff to current
2013-02-28	martinahansen	added Seq.shuffle method and tests	blob \| commitdiff \| raw \| diff to current
2013-02-25	martinahansen	fixed SCORE_BASE global var	blob \| commitdiff \| raw \| diff to current
2013-02-08	martinahansen	fixed quality score validity check	blob \| commitdiff \| raw \| diff to current
2013-02-04	martinahansen	added qual_valid? method to Seq.rb	blob \| commitdiff \| raw \| diff to current
2013-02-02	martinahansen	fixed minor bug in error handling	blob \| commitdiff \| raw \| diff to current
2012-12-06	martinahansen	fixed unit tests	blob \| commitdiff \| raw \| diff to current
2012-12-03	martinahansen	ported patternmatcher to C	blob \| commitdiff \| raw \| diff to current
2012-11-29	martinahansen	disabling backtrack which causes compile error	blob \| commitdiff \| raw \| diff to current
2012-11-28	martinahansen	fixing up backtrack code	blob \| commitdiff \| raw \| diff to current
2012-09-21	martinahansen	added qual_base(33\|64)? methods to seq.rb	blob \| commitdiff \| raw \| diff to current
2012-09-10	martinahansen	fixed unit tests for seq.rb	blob \| commitdiff \| raw \| diff to current
2012-08-07	martinahansen	last fix on prodigal upgrade	blob \| commitdiff \| raw \| diff to current
2012-07-13	martinahansen	fixed another bug in find orfs	blob \| commitdiff \| raw \| diff to current
2012-07-13	martinahansen	fixed bug in orf finder	blob \| commitdiff \| raw \| diff to current
2012-07-13	martinahansen	made orf finder case insensitive	blob \| commitdiff \| raw \| diff to current
2012-07-13	martinahansen	added orf finder to seq.rb	blob \| commitdiff \| raw \| diff to current
2012-06-29	martinahansen	rewrote mean_scores to fix bug	blob \| commitdiff \| raw \| diff to current
2012-06-29	martinahansen	added scores_mean method to seq.rb	blob \| commitdiff \| raw \| diff to current
2012-05-24	martinahansen	moved patscan.rb	blob \| commitdiff \| raw \| diff to current
2012-05-24	martinahansen	moved backtrack.rb	blob \| commitdiff \| raw \| diff to current
2012-05-24	martinahansen	moved patternmatcher.rb	blob \| commitdiff \| raw \| diff to current
2012-05-24	martinahansen	moving digest.rb	blob \| commitdiff \| raw \| diff to current
2012-05-23	martinahansen	rewrite of seq.rb and addition of seq/trim.rb	blob \| commitdiff \| raw \| diff to current
2012-04-10	martinahansen	making changes to accomodate Illumina18 qual scores	blob \| commitdiff \| raw \| diff to current
2012-01-24	martinahansen	fixed indels in methods mask_seq_hard/soft	blob \| commitdiff \| raw \| diff to current
2012-01-23	martinahansen	polish seq.rb	blob \| commitdiff \| raw \| diff to current
2012-01-23	martinahansen	rewrote mask_seq_hard and mask_seq_soft methods to...	blob \| commitdiff \| raw \| diff to current
2012-01-11	martinahansen	added remove_indels method	blob \| commitdiff \| raw \| diff to current
2011-12-05	martinahansen	upgraded mask_seq	blob \| commitdiff \| raw \| diff to current
2011-11-17	martinahansen	added requirement of RubyInline	blob \| commitdiff \| raw \| diff to current
2011-11-16	martinahansen	disabled inline	blob \| commitdiff \| raw \| diff to current
2011-11-15	martinahansen	fixed digest.rb	blob \| commitdiff \| raw \| diff to current
2011-11-15	martinahansen	added backtrack.rb	blob \| commitdiff \| raw \| diff to current
2011-11-13	martinahansen	cleaning up digest.rb	blob \| commitdiff \| raw \| diff to current
2011-11-09	martinahansen	fixed bug in seq.to_fasta	blob \| commitdiff \| raw \| diff to current
2011-11-01	martinahansen	added quality_trim to seq.rb along with unit tests	blob \| commitdiff \| raw \| diff to current
2011-11-01	martinahansen	fixed unit tests for reverse and revcomp in seq.rb	blob \| commitdiff \| raw \| diff to current
2011-11-01	martinahansen	fixed return on reverse_complement in seq.rb	blob \| commitdiff \| raw \| diff to current
2011-10-28	martinahansen	added reversing of qual to reverse	blob \| commitdiff \| raw \| diff to current
2011-10-25	martinahansen	added find_barcodes biopiece	blob \| commitdiff \| raw \| diff to current
2011-10-21	martinahansen	added shuffle! method to seq.rb	blob \| commitdiff \| raw \| diff to current
2011-10-13	martinahansen	smoothed ruby code to get rid of warnings	blob \| commitdiff \| raw \| diff to current
2011-10-13	martinahansen	added Class method Seq.new_bp to seq.rb	blob \| commitdiff \| raw \| diff to current
2011-10-13	martinahansen	added to_fastq method seq.rb	blob \| commitdiff \| raw \| diff to current
2011-09-23	martinahansen	fixed newline to rec seperator in seq.rb	blob \| commitdiff \| raw \| diff to current
2011-09-05	martinahansen	added hamming_distance method to seq.rb	blob \| commitdiff \| raw \| diff to current
2011-08-31	martinahansen	worked on sam - added 1 to phred score check in seq.rb	blob \| commitdiff \| raw \| diff to current
2011-06-13	martinahansen	added Seq.type_guess to ruby code	blob \| commitdiff \| raw \| diff to current
2011-05-13	martinahansen	changed layout of ruby source	blob \| commitdiff \| raw \| diff to current

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