]> git.donarmstrong.com Git - biopieces.git/shortlog
biopieces.git
2013-03-13 martinahansendropped pandaseq requirement
2013-03-13 martinahansenfixed minor upcase bug in assemble.rb
2013-03-13 martinahansenupgraded tests of read_sff
2013-03-13 martinahansenfinish assemble_pairs revamp
2013-03-13 martinahansenassemble_pairs revamp
2013-03-13 martinahansenadded comments to code
2013-03-13 martinahansenadded name check to assemble_pairs2
2013-03-13 martinahansenadded check for minimum seq length
2013-03-13 martinahansenadded check for minimum seq length
2013-03-13 martinahansenfixed defaults and key names
2013-03-13 martinahansenupgraded assemble.rb to chose proper residue when mismatch
2013-03-13 martinahansenadded hacky thing to avoid warning from zlib
2013-03-12 martinahansenadded keys to assemble_pairs2
2013-03-12 martinahansenadded assemble_pairs2
2013-03-12 martinahansenadded seq/assemble.rb
2013-03-12 martinahansenfixed score base bug in sff.rb
2013-03-11 martinahansenadded word_size switch to blast_seq_pair
2013-03-11 martinahansenchanged blast_seq_pair to do multiple pairs
2013-03-11 martinahansenadded [] og []= to seq.rb
2013-03-08 martinahansenadded split_pair_seq biopiece
2013-03-08 martinahansenadded new Biopiece merge_pair_seq
2013-03-08 martinahansenadded new Biopiece merge_pair_seq
2013-03-08 martinahansendropped cat_seq Biopieces since join_seq exists
2013-03-08 martinahansenadded pair-end power to read_fastq
2013-03-08 martinahansenadded eof? method to filesys.rb
2013-03-08 martinahansenrefactoring of ruby code converting sequences types...
2013-03-08 martinahansenadded << method to Seq.rb
2013-03-08 martinahansenrewrite of FASTQ internals
2013-03-01 martinahansenfixed bug in plot_scores
2013-02-28 martinahansenfinished refactoring s/has_key?/[]/
2013-02-28 martinahansenrefactoring of ruby code s/has_key?/[]/
2013-02-28 martinahansenfixed global SCORE_BASE in mean_scores
2013-02-28 martinahansenrefactoring of revcomp in seq.rb
2013-02-28 martinahansenadded Seq.shuffle method and tests
2013-02-28 martinahansenupdated find_SNPs tests
2013-02-25 martinahansenfixed SCORE_BASE global var
2013-02-21 martinahansenadded coverage to find_SNPs
2013-02-21 martinahansenfixed nasty bug in grab where -E and pattern 0 failed
2013-02-21 martinahansenfixed nasty bug in grab where -E and pattern 0 failed
2013-02-20 martinahansenmade find_adaptor ignore too short sequences
2013-02-19 martinahansenadded write_sam biopiece
2013-02-19 martinahansendisabled encoding validity check
2013-02-19 martinahansenadded provisional write sam support
2013-02-19 martinahansenpolished read_sam
2013-02-08 martinahansenfixed quality score validity check
2013-02-06 martinahansendisable validity check
2013-02-04 martinahansenadded quality score check to read_fastq
2013-02-04 martinahansenadded qual_valid? method to Seq.rb
2013-02-02 martinahansenfixed minor bug in error handling
2013-01-22 martinahansenfixed axis titles
2013-01-22 martinahansenadded plot_stacked_histogram biopiece
2013-01-21 martinahansenadded pandaseq prerequisite
2013-01-21 martinahansenadded tests for assemble_pairs biopiece
2013-01-21 martinahansenadded assemble_pairs biopiece
2013-01-20 martinahansenadded substitute_vals biopiece
2013-01-16 martinahansenfixed bad tests in match.rb
2013-01-15 martinahansenadded png term to plot_matches
2013-01-14 martinahansenadded tests for create_seq_index and get_seq
2013-01-14 martinahansenfixed apparent change in Carp yielding an extra . after...
2013-01-14 martinahansenremoved error check
2013-01-11 martinahansenadded bowtie2 biopieces
2013-01-09 martinahansenadding kmer to contigs
2013-01-09 martinahansenfixed up assemble_seq_velvet
2013-01-09 martinahansenrewrote assemble_seq_velvet
2013-01-09 martinahansenfixed pair end issue
2013-01-09 martinahansenset cutoff to auto in velvet
2013-01-09 martinahansenrenamed assemle_seq_idba assemble_seq_idba
2013-01-09 martinahansenrenamed assemble_seq_idba_ud assemle_seq_idba
2013-01-09 martinahansenremoved old assemle_seq_idba
2013-01-04 martinahansenfixed to_i bug in pcr_seq
2013-01-04 martinahansenupdated report
2013-01-04 martinahansenupdated pcr_seq and added tests
2013-01-03 martinahansenpolished pairwise alignment code
2013-01-02 martinahansenadded new match.rb and tests
2013-01-02 martinahansenadded new match.rb and tests
2013-01-02 martinahansenadded test for align dir
2013-01-02 martinahansenrenaming match.rb to matches.rb
2013-01-02 martinahansenmoved mum.rb
2012-12-20 martinahansenclearnup of pair align code
2012-12-13 martinahansenfixed minor bug in grab for exact_in where no key would...
2012-12-12 martinahansenfixed QA_Illumina_report.rb SEQ_LEN > 20
2012-12-12 martinahansenchanged to new find_adaptor
2012-12-11 martinahansenadded unit test to backtrack code
2012-12-10 martinahansenremoved debug code from find_adaptor
2012-12-10 martinahansenunrolling new find_adaptor
2012-12-10 martinahansenfixed bug in backtrack.rb
2012-12-10 martinahansenfixed unit tests for backtrack.rb
2012-12-06 martinahansenfixed unit tests
2012-12-05 martinahansenrenamed patternmatcher to dynamic
2012-12-05 martinahansenrenamed patternmatcher to dynamic
2012-12-05 martinahansenfixing name space collision
2012-12-05 martinahansenrefactorying PatternMatcher to Dynamic
2012-12-05 martinahansenrenamed patternmatcher to dynamic
2012-12-05 martinahansencleaned comments
2012-12-05 martinahansenrefactor match->patmatch scan->patscan
2012-12-05 martinahansenrefactor match->patmatch scan->patscan
2012-12-04 martinahansenadded patmatch method to backtrack.rb
2012-12-04 martinahansenadded private to patternmatcher
2012-12-04 martinahansenfixed unit tests for patternmatcher
2012-12-04 martinahansenadded some text
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