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2012-07-13	martinahansen	fixed another bug in find orfs	commit \| commitdiff \| tree
2012-07-13	martinahansen	fixed bug in orf finder	commit \| commitdiff \| tree
2012-07-13	martinahansen	fixed grave bug in find_orfs	commit \| commitdiff \| tree
2012-07-13	martinahansen	made orf finder case insensitive	commit \| commitdiff \| tree
2012-07-13	martinahansen	added find_orfs	commit \| commitdiff \| tree
2012-07-13	martinahansen	added orf finder to seq.rb	commit \| commitdiff \| tree
2012-07-10	martinahansen	ported align_pair_seq to ruby	commit \| commitdiff \| tree
2012-07-10	martinahansen	added align/pair.rb to ruby trunk	commit \| commitdiff \| tree
2012-07-10	martinahansen	fixed align.rb up a bit	commit \| commitdiff \| tree
2012-07-10	martinahansen	minor fix to find_adaptor 2	commit \| commitdiff \| tree
2012-07-10	martinahansen	minor fix to find_adaptor	commit \| commitdiff \| tree
2012-07-10	martinahansen	added -m hardcoded option to prodigal.rb	commit \| commitdiff \| tree
2012-07-10	martinahansen	fixed bug for missing sequence in genbank parser	commit \| commitdiff \| tree
2012-07-02	martinahansen	added mum.rb	commit \| commitdiff \| tree
2012-07-02	martinahansen	updated order_pairs	commit \| commitdiff \| tree
2012-07-02	martinahansen	updated order_pairs	commit \| commitdiff \| tree
2012-06-29	martinahansen	clean-up of ruby code to remove rake warnings	commit \| commitdiff \| tree
2012-06-29	martinahansen	rewrote mean_scores to fix bug	commit \| commitdiff \| tree
2012-06-29	martinahansen	added scores_mean method to seq.rb	commit \| commitdiff \| tree
2012-06-28	martinahansen	cleanup of pair stuff in align.rb	commit \| commitdiff \| tree
2012-06-27	martinahansen	fixed inline code warning	commit \| commitdiff \| tree
2012-06-25	martinahansen	fixed bug in findsim.rb	commit \| commitdiff \| tree
2012-06-25	martinahansen	added max_diversity swith to findsim.rb	commit \| commitdiff \| tree
2012-06-25	martinahansen	added max_diversity swith to findsim.rb	commit \| commitdiff \| tree
2012-06-25	martinahansen	added max_diversity swith to findsim.rb	commit \| commitdiff \| tree
2012-06-20	martinahansen	classify_taxonomy work	commit \| commitdiff \| tree
2012-06-20	martinahansen	classify_taxonomy work	commit \| commitdiff \| tree
2012-06-13	martinahansen	added classify_taxonomy (unfinished biopiece)	commit \| commitdiff \| tree
2012-06-08	martinahansen	fixed raw intput bug in read_fasta and read_fastq	commit \| commitdiff \| tree
2012-06-08	martinahansen	refactoring biopieces.rb	commit \| commitdiff \| tree
2012-06-08	martinahansen	fixed unit tests for test_trim.rb	commit \| commitdiff \| tree
2012-06-01	martinahansen	added illumina 1.8 name scheme support to order pairs	commit \| commitdiff \| tree
2012-05-31	martinahansen	fixed bad error msg	commit \| commitdiff \| tree
2012-05-30	martinahansen	fixed bug in sff.rb clip and mask methods	commit \| commitdiff \| tree
2012-05-30	martinahansen	fixed bug in sff.rb to_seq method	commit \| commitdiff \| tree
2012-05-30	martinahansen	added to_seq method to sff.rb	commit \| commitdiff \| tree
2012-05-25	martinahansen	fixed trim_seq tests	commit \| commitdiff \| tree
2012-05-24	martinahansen	fixed ugly bug in trim.rb	commit \| commitdiff \| tree
2012-05-24	martinahansen	moved patscan.rb	commit \| commitdiff \| tree
2012-05-24	martinahansen	moved backtrack.rb	commit \| commitdiff \| tree
2012-05-24	martinahansen	moved patternmatcher.rb	commit \| commitdiff \| tree
2012-05-24	martinahansen	moving digest.rb	commit \| commitdiff \| tree
2012-05-24	martinahansen	upgraded trim_seq	commit \| commitdiff \| tree
2012-05-23	martinahansen	refactored SeqError/TrimError	commit \| commitdiff \| tree
2012-05-23	martinahansen	rewrite of seq.rb and addition of seq/trim.rb	commit \| commitdiff \| tree
2012-05-23	martinahansen	refactored argument precise to realign	commit \| commitdiff \| tree
2012-05-08	martinahansen	reverted findsim_seq and renamed precise switch to...	commit \| commitdiff \| tree
2012-05-02	martinahansen	finishing hmmer_seq	commit \| commitdiff \| tree
2012-05-02	martinahansen	added hmmer_seq biopiece	commit \| commitdiff \| tree
2012-04-30	martinahansen	upgraded write_fixedstep	commit \| commitdiff \| tree
2012-04-24	martinahansen	added split of quality scores to split_seq	commit \| commitdiff \| tree
2012-04-23	martinahansen	added precise switch to findsim	commit \| commitdiff \| tree
2012-04-23	martinahansen	workied on pair wise aligner	commit \| commitdiff \| tree
2012-04-19	martinahansen	added precise alignment option to findsim.rb	commit \| commitdiff \| tree
2012-04-19	martinahansen	fixed double insertion of indels in alignments (missing...	commit \| commitdiff \| tree
2012-04-18	martinahansen	added identity method to align.rb	commit \| commitdiff \| tree
2012-04-18	martinahansen	changed report_scores to max_hits in findsim.rb	commit \| commitdiff \| tree
2012-04-18	martinahansen	changed record_scores to max_hits refactoring	commit \| commitdiff \| tree
2012-04-18	martinahansen	added findsim_seq biopieces	commit \| commitdiff \| tree
2012-04-18	martinahansen	added to_bp method to findsim.rb	commit \| commitdiff \| tree
2012-04-18	martinahansen	fixed issue 32	commit \| commitdiff \| tree
2012-04-18	martinahansen	fixed x bug in compute	commit \| commitdiff \| tree
2012-04-18	martinahansen	added q_id and s_id options to findsim.rb	commit \| commitdiff \| tree
2012-04-17	martinahansen	added findsim.rb	commit \| commitdiff \| tree
2012-04-11	martinahansen	ported write_fastq to ruby and allowed different encoding...	commit \| commitdiff \| tree
2012-04-11	martinahansen	cleanup in read_fastq	commit \| commitdiff \| tree
2012-04-10	martinahansen	fixed comment	commit \| commitdiff \| tree
2012-04-10	martinahansen	upgraded read_fastq to handle illumina1.8 better	commit \| commitdiff \| tree
2012-04-10	martinahansen	upgraded tests for read_fastq	commit \| commitdiff \| tree
2012-04-10	martinahansen	removing stale test in files	commit \| commitdiff \| tree
2012-04-10	martinahansen	making changes to accomodate Illumina18 qual scores	commit \| commitdiff \| tree
2012-04-06	martinahansen	upgraded bitmap.rb to a 64bit version	commit \| commitdiff \| tree
2012-04-03	martinahansen	upgraded bitmap.rb	commit \| commitdiff \| tree
2012-03-26	martinahansen	fixed ugly 1-off bug in locator	commit \| commitdiff \| tree
2012-03-26	martinahansen	fixed ugly 1-off bug in locator.rb	commit \| commitdiff \| tree
2012-03-26	martinahansen	fixed ugly 1-off bug in locator.rb	commit \| commitdiff \| tree
2012-03-22	martinahansen	added bitmap.rb	commit \| commitdiff \| tree
2012-03-20	martinahansen	fixed issues in bwa_seq	commit \| commitdiff \| tree
2012-03-16	martinahansen	added closed? method to filesys.rb	commit \| commitdiff \| tree
2012-03-14	martinahansen	added check for empty files in usearch.rb	commit \| commitdiff \| tree
2012-03-13	martinahansen	fixed dir in bwa_seq	commit \| commitdiff \| tree
2012-03-13	martinahansen	fixed minor issue in align.rb tests	commit \| commitdiff \| tree
2012-03-13	martinahansen	addid missing S_END to sam.rb	commit \| commitdiff \| tree
2012-03-13	martinahansen	ported bwa_seq to ruby for better SAM support	commit \| commitdiff \| tree
2012-03-07	martinahansen	fixed overflow bug in align.rb	commit \| commitdiff \| tree
2012-03-05	martinahansen	changed align.to_s	commit \| commitdiff \| tree
2012-03-02	martinahansen	major upgrade of denoise_seq	commit \| commitdiff \| tree
2012-03-02	martinahansen	major upgrade of align.rb for denoising	commit \| commitdiff \| tree
2012-03-01	martinahansen	fixed bug in each_alignment	commit \| commitdiff \| tree
2012-02-23	martinahansen	added duplicate_record biopiece	commit \| commitdiff \| tree
2012-02-09	martinahansen	added force to rm of tmpdir	commit \| commitdiff \| tree
2012-02-07	martinahansen	added raw data reading to read_fasta and read_fastq	commit \| commitdiff \| tree
2012-02-07	martinahansen	fixed indentation in biopieces.rb	commit \| commitdiff \| tree
2012-02-03	martinahansen	rounding up work on denoise_seq	commit \| commitdiff \| tree
2012-02-03	martinahansen	added denoise_seq	commit \| commitdiff \| tree
2012-02-03	martinahansen	fixed attributes	commit \| commitdiff \| tree
2012-02-03	martinahansen	added FastqIndex to fastq.rb	commit \| commitdiff \| tree
2012-02-03	martinahansen	added ustar and each_alignment methods to usearch.rb	commit \| commitdiff \| tree
2012-02-03	martinahansen	added masks to align.rb	commit \| commitdiff \| tree
2012-01-31	martinahansen	major rewrite of align.rb	commit \| commitdiff \| tree
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