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biopieces.git
2012-07-10 martinahansenported align_pair_seq to ruby commit | commitdiff | tree | snapshot
2012-07-10 martinahansenadded align/pair.rb to ruby trunk commit | commitdiff | tree | snapshot
2012-07-10 martinahansenfixed align.rb up a bit commit | commitdiff | tree | snapshot
2012-07-10 martinahansenminor fix to find_adaptor 2 commit | commitdiff | tree | snapshot
2012-07-10 martinahansenminor fix to find_adaptor commit | commitdiff | tree | snapshot
2012-07-10 martinahansenadded -m hardcoded option to prodigal.rb commit | commitdiff | tree | snapshot
2012-07-10 martinahansenfixed bug for missing sequence in genbank parser commit | commitdiff | tree | snapshot
2012-07-02 martinahansenadded mum.rb commit | commitdiff | tree | snapshot
2012-07-02 martinahansenupdated order_pairs commit | commitdiff | tree | snapshot
2012-07-02 martinahansenupdated order_pairs commit | commitdiff | tree | snapshot
2012-06-29 martinahansenclean-up of ruby code to remove rake warnings commit | commitdiff | tree | snapshot
2012-06-29 martinahansenrewrote mean_scores to fix bug commit | commitdiff | tree | snapshot
2012-06-29 martinahansenadded scores_mean method to seq.rb commit | commitdiff | tree | snapshot
2012-06-28 martinahansencleanup of pair stuff in align.rb commit | commitdiff | tree | snapshot
2012-06-27 martinahansenfixed inline code warning commit | commitdiff | tree | snapshot
2012-06-25 martinahansenfixed bug in findsim.rb commit | commitdiff | tree | snapshot
2012-06-25 martinahansenadded max_diversity swith to findsim.rb commit | commitdiff | tree | snapshot
2012-06-25 martinahansenadded max_diversity swith to findsim.rb commit | commitdiff | tree | snapshot
2012-06-25 martinahansenadded max_diversity swith to findsim.rb commit | commitdiff | tree | snapshot
2012-06-20 martinahansenclassify_taxonomy work commit | commitdiff | tree | snapshot
2012-06-20 martinahansenclassify_taxonomy work commit | commitdiff | tree | snapshot
2012-06-13 martinahansenadded classify_taxonomy (unfinished biopiece) commit | commitdiff | tree | snapshot
2012-06-08 martinahansenfixed raw intput bug in read_fasta and read_fastq commit | commitdiff | tree | snapshot
2012-06-08 martinahansenrefactoring biopieces.rb commit | commitdiff | tree | snapshot
2012-06-08 martinahansenfixed unit tests for test_trim.rb commit | commitdiff | tree | snapshot
2012-06-01 martinahansenadded illumina 1.8 name scheme support to order pairs commit | commitdiff | tree | snapshot
2012-05-31 martinahansenfixed bad error msg commit | commitdiff | tree | snapshot
2012-05-30 martinahansenfixed bug in sff.rb clip and mask methods commit | commitdiff | tree | snapshot
2012-05-30 martinahansenfixed bug in sff.rb to_seq method commit | commitdiff | tree | snapshot
2012-05-30 martinahansenadded to_seq method to sff.rb commit | commitdiff | tree | snapshot
2012-05-25 martinahansenfixed trim_seq tests commit | commitdiff | tree | snapshot
2012-05-24 martinahansenfixed ugly bug in trim.rb commit | commitdiff | tree | snapshot
2012-05-24 martinahansenmoved patscan.rb commit | commitdiff | tree | snapshot
2012-05-24 martinahansenmoved backtrack.rb commit | commitdiff | tree | snapshot
2012-05-24 martinahansenmoved patternmatcher.rb commit | commitdiff | tree | snapshot
2012-05-24 martinahansenmoving digest.rb commit | commitdiff | tree | snapshot
2012-05-24 martinahansenupgraded trim_seq commit | commitdiff | tree | snapshot
2012-05-23 martinahansenrefactored SeqError/TrimError commit | commitdiff | tree | snapshot
2012-05-23 martinahansenrewrite of seq.rb and addition of seq/trim.rb commit | commitdiff | tree | snapshot
2012-05-23 martinahansenrefactored argument precise to realign commit | commitdiff | tree | snapshot
2012-05-08 martinahansenreverted findsim_seq and renamed precise switch to... commit | commitdiff | tree | snapshot
2012-05-02 martinahansenfinishing hmmer_seq commit | commitdiff | tree | snapshot
2012-05-02 martinahansenadded hmmer_seq biopiece commit | commitdiff | tree | snapshot
2012-04-30 martinahansenupgraded write_fixedstep commit | commitdiff | tree | snapshot
2012-04-24 martinahansenadded split of quality scores to split_seq commit | commitdiff | tree | snapshot
2012-04-23 martinahansenadded precise switch to findsim commit | commitdiff | tree | snapshot
2012-04-23 martinahansenworkied on pair wise aligner commit | commitdiff | tree | snapshot
2012-04-19 martinahansenadded precise alignment option to findsim.rb commit | commitdiff | tree | snapshot
2012-04-19 martinahansenfixed double insertion of indels in alignments (missing... commit | commitdiff | tree | snapshot
2012-04-18 martinahansenadded identity method to align.rb commit | commitdiff | tree | snapshot
2012-04-18 martinahansenchanged report_scores to max_hits in findsim.rb commit | commitdiff | tree | snapshot
2012-04-18 martinahansenchanged record_scores to max_hits refactoring commit | commitdiff | tree | snapshot
2012-04-18 martinahansenadded findsim_seq biopieces commit | commitdiff | tree | snapshot
2012-04-18 martinahansenadded to_bp method to findsim.rb commit | commitdiff | tree | snapshot
2012-04-18 martinahansenfixed issue 32 commit | commitdiff | tree | snapshot
2012-04-18 martinahansenfixed x bug in compute commit | commitdiff | tree | snapshot
2012-04-18 martinahansenadded q_id and s_id options to findsim.rb commit | commitdiff | tree | snapshot
2012-04-17 martinahansenadded findsim.rb commit | commitdiff | tree | snapshot
2012-04-11 martinahansenported write_fastq to ruby and allowed different encodi... commit | commitdiff | tree | snapshot
2012-04-11 martinahansencleanup in read_fastq commit | commitdiff | tree | snapshot
2012-04-10 martinahansenfixed comment commit | commitdiff | tree | snapshot
2012-04-10 martinahansenupgraded read_fastq to handle illumina1.8 better commit | commitdiff | tree | snapshot
2012-04-10 martinahansenupgraded tests for read_fastq commit | commitdiff | tree | snapshot
2012-04-10 martinahansenremoving stale test in files commit | commitdiff | tree | snapshot
2012-04-10 martinahansenmaking changes to accomodate Illumina18 qual scores commit | commitdiff | tree | snapshot
2012-04-06 martinahansenupgraded bitmap.rb to a 64bit version commit | commitdiff | tree | snapshot
2012-04-03 martinahansenupgraded bitmap.rb commit | commitdiff | tree | snapshot
2012-03-26 martinahansenfixed ugly 1-off bug in locator commit | commitdiff | tree | snapshot
2012-03-26 martinahansenfixed ugly 1-off bug in locator.rb commit | commitdiff | tree | snapshot
2012-03-26 martinahansenfixed ugly 1-off bug in locator.rb commit | commitdiff | tree | snapshot
2012-03-22 martinahansenadded bitmap.rb commit | commitdiff | tree | snapshot
2012-03-20 martinahansenfixed issues in bwa_seq commit | commitdiff | tree | snapshot
2012-03-16 martinahansenadded closed? method to filesys.rb commit | commitdiff | tree | snapshot
2012-03-14 martinahansenadded check for empty files in usearch.rb commit | commitdiff | tree | snapshot
2012-03-13 martinahansenfixed dir in bwa_seq commit | commitdiff | tree | snapshot
2012-03-13 martinahansenfixed minor issue in align.rb tests commit | commitdiff | tree | snapshot
2012-03-13 martinahansenaddid missing S_END to sam.rb commit | commitdiff | tree | snapshot
2012-03-13 martinahansenported bwa_seq to ruby for better SAM support commit | commitdiff | tree | snapshot
2012-03-07 martinahansenfixed overflow bug in align.rb commit | commitdiff | tree | snapshot
2012-03-05 martinahansenchanged align.to_s commit | commitdiff | tree | snapshot
2012-03-02 martinahansenmajor upgrade of denoise_seq commit | commitdiff | tree | snapshot
2012-03-02 martinahansenmajor upgrade of align.rb for denoising commit | commitdiff | tree | snapshot
2012-03-01 martinahansenfixed bug in each_alignment commit | commitdiff | tree | snapshot
2012-02-23 martinahansenadded duplicate_record biopiece commit | commitdiff | tree | snapshot
2012-02-09 martinahansenadded force to rm of tmpdir commit | commitdiff | tree | snapshot
2012-02-07 martinahansenadded raw data reading to read_fasta and read_fastq commit | commitdiff | tree | snapshot
2012-02-07 martinahansenfixed indentation in biopieces.rb commit | commitdiff | tree | snapshot
2012-02-03 martinahansenrounding up work on denoise_seq commit | commitdiff | tree | snapshot
2012-02-03 martinahansenadded denoise_seq commit | commitdiff | tree | snapshot
2012-02-03 martinahansenfixed attributes commit | commitdiff | tree | snapshot
2012-02-03 martinahansenadded FastqIndex to fastq.rb commit | commitdiff | tree | snapshot
2012-02-03 martinahansenadded ustar and each_alignment methods to usearch.rb commit | commitdiff | tree | snapshot
2012-02-03 martinahansenadded masks to align.rb commit | commitdiff | tree | snapshot
2012-01-31 martinahansenmajor rewrite of align.rb commit | commitdiff | tree | snapshot
2012-01-31 martinahansenadd ustar method to usearch.rb commit | commitdiff | tree | snapshot
2012-01-27 martinahansenfinal touches to align.rb commit | commitdiff | tree | snapshot
2012-01-24 martinahansenfixed indels in methods mask_seq_hard/soft commit | commitdiff | tree | snapshot
2012-01-23 martinahansenfixed broken pcr_seq commit | commitdiff | tree | snapshot
2012-01-23 martinahansenpolish seq.rb commit | commitdiff | tree | snapshot
2012-01-23 martinahansenrewrote mask_seq_hard and mask_seq_soft methods to... commit | commitdiff | tree | snapshot
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