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2012-12-04 martinahansenadded private to patternmatcher tree | commitdiff
2012-12-04 martinahansenfixed unit tests for patternmatcher tree | commitdiff
2012-12-04 martinahansenadded some text tree | commitdiff
2012-12-03 martinahansenfixed constants for align.rb tree | commitdiff
2012-12-03 martinahansenported patternmatcher to C tree | commitdiff
2012-11-30 martinahansenfinished backtrack drama tree | commitdiff
2012-11-30 martinahansenadded state to backtrack.rb tree | commitdiff
2012-11-30 martinahansendone revert of test_backtrack.rb tree | commitdiff
2012-11-30 martinahansenreverted test_backtrack.rb to r1827 tree | commitdiff
2012-11-30 martinahansenreverted backtrack.rb to 2006 prior to struct version tree | commitdiff
2012-11-29 martinahansendisabling backtrack which causes compile error tree | commitdiff
2012-11-28 martinahansenfixing up backtrack code tree | commitdiff
2012-11-28 martinahansenadded output of mis ind and del to backtrack code tree | commitdiff
2012-11-27 martinahansenpolished backtrack.rb tree | commitdiff
2012-11-27 martinahansenbacktrack.rb polish tree | commitdiff
2012-11-21 martinahansenadded exception handling for missing SFF coordinates tree | commitdiff
2012-11-20 martinahansenadded uchime to usearch tree | commitdiff
2012-11-01 martinahansenadded get_entry method to biopieces.rb tree | commitdiff
2012-10-10 martinahansenadded some file locking to biopieces.rb tree | commitdiff
2012-10-10 martinahansenadded dynamic mem allocation to findsim.rb tree | commitdiff
2012-10-10 martinahansenadded dynamic mem allocation to findsim.rb tree | commitdiff
2012-10-09 martinahansencleanup of findsim.rb tree | commitdiff
2012-10-09 martinahansencleanup of findsim.rb tree | commitdiff
2012-09-27 martinahansenfinishing work on match.rb tree | commitdiff
2012-09-21 martinahansenadded parser for phred qual to fasta.rb tree | commitdiff
2012-09-21 martinahansenadded qual_base(33|64)? methods to seq.rb tree | commitdiff
2012-09-13 martinahansenpair.rb now working correctly tree | commitdiff
2012-09-12 martinahansenworked on pair aligner tree | commitdiff
2012-09-11 martinahansenworking on pair.rb tree | commitdiff
2012-09-11 martinahansenadded align/match.rb tree | commitdiff
2012-09-11 martinahansenworked on pair.rb tree | commitdiff
2012-09-10 martinahansenfixed unit tests for seq.rb tree | commitdiff
2012-09-04 martinahansenadded math_aux.rb tree | commitdiff
2012-09-04 martinahansenadded test_math_aux.rb tree | commitdiff
2012-08-16 martinahansendid something to findsim.rb tree | commitdiff
2012-08-07 martinahansenlast fix on prodigal upgrade tree | commitdiff
2012-08-07 martinahansenupgraded prodigal tree | commitdiff
2012-07-13 martinahansenfixed another bug in find orfs tree | commitdiff
2012-07-13 martinahansenfixed bug in orf finder tree | commitdiff
2012-07-13 martinahansenmade orf finder case insensitive tree | commitdiff
2012-07-13 martinahansenadded orf finder to seq.rb tree | commitdiff
2012-07-10 martinahansenadded align/pair.rb to ruby trunk tree | commitdiff
2012-07-10 martinahansenfixed align.rb up a bit tree | commitdiff
2012-07-10 martinahansenadded -m hardcoded option to prodigal.rb tree | commitdiff
2012-07-10 martinahansenfixed bug for missing sequence in genbank parser tree | commitdiff
2012-07-02 martinahansenadded mum.rb tree | commitdiff
2012-06-29 martinahansenclean-up of ruby code to remove rake warnings tree | commitdiff
2012-06-29 martinahansenrewrote mean_scores to fix bug tree | commitdiff
2012-06-29 martinahansenadded scores_mean method to seq.rb tree | commitdiff
2012-06-28 martinahansencleanup of pair stuff in align.rb tree | commitdiff
2012-06-27 martinahansenfixed inline code warning tree | commitdiff
2012-06-25 martinahansenfixed bug in findsim.rb tree | commitdiff
2012-06-25 martinahansenadded max_diversity swith to findsim.rb tree | commitdiff
2012-06-08 martinahansenrefactoring biopieces.rb tree | commitdiff
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
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