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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
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
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