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2012-06-08 martinahansenfixed unit tests for test_trim.rb tree | commitdiff
2012-05-31 martinahansenfixed bad error msg tree | commitdiff
2012-05-30 martinahansenfixed bug in sff.rb clip and mask methods tree | commitdiff
2012-05-30 martinahansenfixed bug in sff.rb to_seq method tree | commitdiff
2012-05-30 martinahansenadded to_seq method to sff.rb tree | commitdiff
2012-05-24 martinahansenfixed ugly bug in trim.rb tree | commitdiff
2012-05-24 martinahansenmoved patscan.rb tree | commitdiff
2012-05-24 martinahansenmoved backtrack.rb tree | commitdiff
2012-05-24 martinahansenmoved patternmatcher.rb tree | commitdiff
2012-05-24 martinahansenmoving digest.rb tree | commitdiff
2012-05-23 martinahansenrefactored SeqError/TrimError tree | commitdiff
2012-05-23 martinahansenrewrite of seq.rb and addition of seq/trim.rb tree | commitdiff
2012-05-23 martinahansenrefactored argument precise to realign tree | commitdiff
2012-04-23 martinahansenworkied on pair wise aligner tree | commitdiff
2012-04-19 martinahansenadded precise alignment option to findsim.rb tree | commitdiff
2012-04-19 martinahansenfixed double insertion of indels in alignments (missing... tree | commitdiff
2012-04-18 martinahansenadded identity method to align.rb tree | commitdiff
2012-04-18 martinahansenchanged report_scores to max_hits in findsim.rb tree | commitdiff
2012-04-18 martinahansenadded to_bp method to findsim.rb tree | commitdiff
2012-04-18 martinahansenadded q_id and s_id options to findsim.rb tree | commitdiff
2012-04-17 martinahansenadded findsim.rb tree | commitdiff
2012-04-11 martinahansenported write_fastq to ruby and allowed different encodi... tree | commitdiff
2012-04-10 martinahansenmaking changes to accomodate Illumina18 qual scores tree | commitdiff
2012-04-06 martinahansenupgraded bitmap.rb to a 64bit version tree | commitdiff
2012-04-03 martinahansenupgraded bitmap.rb tree | commitdiff
2012-03-26 martinahansenfixed ugly 1-off bug in locator.rb tree | commitdiff
2012-03-22 martinahansenadded bitmap.rb tree | commitdiff
2012-03-16 martinahansenadded closed? method to filesys.rb tree | commitdiff
2012-03-14 martinahansenadded check for empty files in usearch.rb tree | commitdiff
2012-03-13 martinahansenfixed minor issue in align.rb tests tree | commitdiff
2012-03-13 martinahansenaddid missing S_END to sam.rb tree | commitdiff
2012-03-07 martinahansenfixed overflow bug in align.rb tree | commitdiff
2012-03-05 martinahansenchanged align.to_s tree | commitdiff
2012-03-02 martinahansenmajor upgrade of align.rb for denoising tree | commitdiff
2012-03-01 martinahansenfixed bug in each_alignment tree | commitdiff
2012-02-23 martinahansenadded duplicate_record biopiece tree | commitdiff
2012-02-09 martinahansenadded force to rm of tmpdir tree | commitdiff
2012-02-07 martinahansenfixed indentation in biopieces.rb tree | commitdiff
2012-02-03 martinahansenrounding up work on denoise_seq tree | commitdiff
2012-02-03 martinahansenfixed attributes tree | commitdiff
2012-02-03 martinahansenadded FastqIndex to fastq.rb tree | commitdiff
2012-02-03 martinahansenadded ustar and each_alignment methods to usearch.rb tree | commitdiff
2012-02-03 martinahansenadded masks to align.rb tree | commitdiff
2012-01-31 martinahansenmajor rewrite of align.rb tree | commitdiff
2012-01-31 martinahansenadd ustar method to usearch.rb tree | commitdiff
2012-01-27 martinahansenfinal touches to align.rb tree | commitdiff
2012-01-24 martinahansenfixed indels in methods mask_seq_hard/soft tree | commitdiff
2012-01-23 martinahansenpolish seq.rb tree | commitdiff
2012-01-23 martinahansenrewrote mask_seq_hard and mask_seq_soft methods to... tree | commitdiff
2012-01-22 martinahansenfixed popen3 issue in align.rb tree | commitdiff
2012-01-20 martinahansenchanged Align.muscle to file based instead of popen3 tree | commitdiff
2012-01-12 martinahansenfixed typo tree | commitdiff
2012-01-12 martinahansenadded check for duplicate seq_names to align.rb tree | commitdiff
2012-01-12 martinahansenadded preservation of indels and case to align.rb tree | commitdiff
2012-01-12 martinahansenadded align.rb to ruby code tree | commitdiff
2012-01-11 martinahansenadded remove_indels method tree | commitdiff
2011-12-20 martinahansenfixed --rev swith in usearch.rb tree | commitdiff
2011-12-12 martinahansenadded embl.rb tree | commitdiff
2011-12-12 martinahansensplit off locator stuff from genbank.rb to locator.rb tree | commitdiff
2011-12-07 martinahansenminor tweak to genbank.rb tree | commitdiff
2011-12-06 martinahansenfixed count bug in sff.rb tree | commitdiff
2011-12-05 martinahansenupgraded mask_seq tree | commitdiff
2011-11-25 martinahansencleanup of usearch.rb tree | commitdiff
2011-11-25 martinahansenmoved usearch code to external file tree | commitdiff
2011-11-24 martinahansenfixed regex in backtrack.rb tree | commitdiff
2011-11-23 martinahansenremoved stale unit tests from test_biopieces.rb tree | commitdiff
2011-11-23 martinahansenfixed glob unit test in test_biopieces.rb tree | commitdiff
2011-11-22 martinahansengot rid of nasty to_sym in biopieces.rb tree | commitdiff
2011-11-22 martinahansengot rid of type in filesys.rb tree | commitdiff
2011-11-22 martinahansenbeautifying backtrack.rb tree | commitdiff
2011-11-22 martinahansenslight cleanup of backtrack code tree | commitdiff
2011-11-21 martinahansenadded tests for uclust_seq tree | commitdiff
2011-11-17 martinahansenadded requirement of RubyInline tree | commitdiff
2011-11-17 martinahansenfixed ins/del reverse tree | commitdiff
2011-11-16 martinahansenfixed FLAG bug in sam.rb tree | commitdiff
2011-11-16 martinahansendisabled inline tree | commitdiff
2011-11-16 martinahansenfixed bug in backtrack.rb tree | commitdiff
2011-11-15 martinahansenfixed digest.rb tree | commitdiff
2011-11-15 martinahansenadded backtrack.rb tree | commitdiff
2011-11-15 martinahansenadded backtrack.rb tree | commitdiff
2011-11-13 martinahansenadded backtrack.rb tree | commitdiff
2011-11-13 martinahansencleaning up digest.rb tree | commitdiff
2011-11-09 martinahansenfixed bug in seq.to_fasta tree | commitdiff
2011-11-01 martinahansenadded quality_trim to seq.rb along with unit tests tree | commitdiff
2011-11-01 martinahansenfixed unit tests for reverse and revcomp in seq.rb tree | commitdiff
2011-11-01 martinahansenfixed return on reverse_complement in seq.rb tree | commitdiff
2011-10-28 martinahansenadded reversing of qual to reverse tree | commitdiff
2011-10-25 martinahansenadded find_barcodes biopiece tree | commitdiff
2011-10-21 martinahansenadded shuffle! method to seq.rb tree | commitdiff
2011-10-19 martinahansenrevoked to old working version of each_interval in... tree | commitdiff
2011-10-19 martinahansenworked on each_interval, but still too slow tree | commitdiff
2011-10-19 martinahansenspeed optimized interval_set and interval_unset in... tree | commitdiff
2011-10-18 martinahansenrewrote interval_set in bitarray.rb = 20 x faster tree | commitdiff
2011-10-18 martinahansenmemory optimization on bitarray.rb tree | commitdiff
2011-10-17 martinahansenadded more methods to bitarray.rb tree | commitdiff
2011-10-17 martinahansenadded methods to bitarray.rb tree | commitdiff
2011-10-17 martinahansenbitarray.rb bits_on method speedup x 3 tree | commitdiff
2011-10-17 martinahansencleanup of bitarray.rb tree | commitdiff
2011-10-17 martinahansenchanged bitwise operators in bitarray to inline tree | commitdiff
2011-10-17 martinahansenupgraded bitarray to work with narray for speed tree | commitdiff
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