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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
2012-01-31	martinahansen	add ustar method to usearch.rb	commit \| commitdiff \| tree
2012-01-27	martinahansen	final touches to align.rb	commit \| commitdiff \| tree
2012-01-24	martinahansen	fixed indels in methods mask_seq_hard/soft	commit \| commitdiff \| tree
2012-01-23	martinahansen	fixed broken pcr_seq	commit \| commitdiff \| tree
2012-01-23	martinahansen	polish seq.rb	commit \| commitdiff \| tree
2012-01-23	martinahansen	rewrote mask_seq_hard and mask_seq_soft methods to...	commit \| commitdiff \| tree
2012-01-22	martinahansen	fixed popen3 issue in align.rb	commit \| commitdiff \| tree
2012-01-20	martinahansen	changed Align.muscle to file based instead of popen3	commit \| commitdiff \| tree
2012-01-18	martinahansen	added additional prerequisite check for RubyInline	commit \| commitdiff \| tree
2012-01-12	martinahansen	fixed typo	commit \| commitdiff \| tree
2012-01-12	martinahansen	added check for duplicate seq_names to align.rb	commit \| commitdiff \| tree
2012-01-12	martinahansen	added preservation of indels and case to align.rb	commit \| commitdiff \| tree
2012-01-12	martinahansen	added align.rb to ruby code	commit \| commitdiff \| tree
2012-01-11	martinahansen	added remove_indels method	commit \| commitdiff \| tree
2012-01-03	martinahansen	fixed issue in compute	commit \| commitdiff \| tree
2012-01-03	martinahansen	fixed issue in compute	commit \| commitdiff \| tree
2012-01-02	martinahansen	fixed missing ; in create_blast_index	commit \| commitdiff \| tree
2011-12-29	martinahansen	added extra RL tags to find_barcodes	commit \| commitdiff \| tree
2011-12-22	martinahansen	increaded database size for blast	commit \| commitdiff \| tree
2011-12-20	martinahansen	fixed --rev swith in usearch.rb	commit \| commitdiff \| tree
2011-12-15	martinahansen	fixed typo in replace_vals	commit \| commitdiff \| tree
2011-12-15	martinahansen	fixed typo in replace_vals	commit \| commitdiff \| tree
2011-12-12	martinahansen	add tests for read_embl	commit \| commitdiff \| tree
2011-12-12	martinahansen	added new read_embl (ruby)	commit \| commitdiff \| tree
2011-12-12	martinahansen	removed old read_embl (perl)	commit \| commitdiff \| tree
2011-12-12	martinahansen	added embl.rb	commit \| commitdiff \| tree
2011-12-12	martinahansen	split off locator stuff from genbank.rb to locator.rb	commit \| commitdiff \| tree
2011-12-08	martinahansen	added check for duplicate keys in replace_vals	commit \| commitdiff \| tree
2011-12-08	martinahansen	added replace_vals biopiece	commit \| commitdiff \| tree
2011-12-07	martinahansen	added new biopeice remove_indel_columns	commit \| commitdiff \| tree
2011-12-07	martinahansen	minor tweak to genbank.rb	commit \| commitdiff \| tree
2011-12-06	martinahansen	fixed count bug in sff.rb	commit \| commitdiff \| tree
2011-12-06	martinahansen	minor tweaks added to installer	commit \| commitdiff \| tree
2011-12-05	martinahansen	upgraded mask_seq	commit \| commitdiff \| tree
2011-11-25	martinahansen	cleanup of usearch.rb	commit \| commitdiff \| tree
2011-11-25	martinahansen	moved usearch code to external file	commit \| commitdiff \| tree
2011-11-24	martinahansen	removed bp_doc/ and content	commit \| commitdiff \| tree
2011-11-24	martinahansen	fixed regex in backtrack.rb	commit \| commitdiff \| tree
2011-11-23	martinahansen	removed stale unit tests from test_biopieces.rb	commit \| commitdiff \| tree
2011-11-23	martinahansen	fixed glob unit test in test_biopieces.rb	commit \| commitdiff \| tree
2011-11-23	martinahansen	removed comma	commit \| commitdiff \| tree
2011-11-22	martinahansen	got rid of nasty to_sym in biopieces.rb	commit \| commitdiff \| tree
2011-11-22	martinahansen	got rid of nasty to_sym in biopieces.rb	commit \| commitdiff \| tree
2011-11-22	martinahansen	got rid of type in filesys.rb	commit \| commitdiff \| tree
2011-11-22	martinahansen	beautifying backtrack.rb	commit \| commitdiff \| tree
2011-11-22	martinahansen	slight cleanup of backtrack code	commit \| commitdiff \| tree
2011-11-21	martinahansen	made --rev defacto in useach_seq	commit \| commitdiff \| tree
2011-11-21	martinahansen	upgraded usearch_seq	commit \| commitdiff \| tree
2011-11-21	martinahansen	added tests for uclust_seq	commit \| commitdiff \| tree
2011-11-19	martinahansen	fixed bug in uniq_vals causing clusters named 0 to...	commit \| commitdiff \| tree
2011-11-18	martinahansen	rewriting uclust_seq	commit \| commitdiff \| tree
2011-11-17	martinahansen	fixed bug in grab	commit \| commitdiff \| tree
2011-11-17	martinahansen	added tests to remove_primers	commit \| commitdiff \| tree
2011-11-17	martinahansen	fixed remove_primers	commit \| commitdiff \| tree
2011-11-17	martinahansen	fixed bug in remove_primers	commit \| commitdiff \| tree
2011-11-17	martinahansen	added remove_primers biopiece	commit \| commitdiff \| tree
2011-11-17	martinahansen	fixed stupid windows \r bug in Patscan::read_patterns	commit \| commitdiff \| tree
2011-11-17	martinahansen	added requirement of RubyInline	commit \| commitdiff \| tree
2011-11-17	martinahansen	fixed ins/del reverse	commit \| commitdiff \| tree
2011-11-16	martinahansen	fixed FLAG bug in sam.rb	commit \| commitdiff \| tree
2011-11-16	martinahansen	disabled inline	commit \| commitdiff \| tree
2011-11-16	martinahansen	fixed bug in backtrack.rb	commit \| commitdiff \| tree
2011-11-15	martinahansen	fixed digest.rb	commit \| commitdiff \| tree
2011-11-15	martinahansen	added backtrack.rb	commit \| commitdiff \| tree
2011-11-15	martinahansen	added backtrack.rb	commit \| commitdiff \| tree
2011-11-14	martinahansen	upgraded uclust_seq to work with useach 5.1.221	commit \| commitdiff \| tree
2011-11-13	martinahansen	added backtrack.rb	commit \| commitdiff \| tree
2011-11-13	martinahansen	fixed digest_seq	commit \| commitdiff \| tree
2011-11-13	martinahansen	cleaning up digest.rb	commit \| commitdiff \| tree
2011-11-09	martinahansen	added Backtrack.pm	commit \| commitdiff \| tree
2011-11-09	martinahansen	fixed bug in seq.to_fasta	commit \| commitdiff \| tree
2011-11-09	martinahansen	fixed bugs in installer	commit \| commitdiff \| tree
2011-11-08	martinahansen	fixed bug in QA_454_report.rb	commit \| commitdiff \| tree
2011-11-07	martinahansen	added ruby version of read_sam	commit \| commitdiff \| tree
2011-11-07	martinahansen	removed perl version of read_sam	commit \| commitdiff \| tree
2011-11-02	martinahansen	added length check to bowtie_seq	commit \| commitdiff \| tree
2011-11-02	martinahansen	added length check to bowtie_seq	commit \| commitdiff \| tree
2011-11-02	martinahansen	fixed qual argument for bowtie on fasta only	commit \| commitdiff \| tree
2011-11-01	martinahansen	added quality_trim to seq.rb along with unit tests	commit \| commitdiff \| tree
2011-11-01	martinahansen	fixed unit tests for reverse and revcomp in seq.rb	commit \| commitdiff \| tree
2011-11-01	martinahansen	fixed return on reverse_complement in seq.rb	commit \| commitdiff \| tree
2011-10-31	martinahansen	added metagenome flag to assemble_seq_idba	commit \| commitdiff \| tree
2011-10-28	martinahansen	added reversing of qual to reverse	commit \| commitdiff \| tree
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