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biopieces.git
2013-04-29 martinahansenfixed missing BP_TMP dir feature commit | commitdiff | tree | snapshot
2013-04-18 martinahansenfixed divide bug in compute commit | commitdiff | tree | snapshot
2013-04-11 martinahansenfixed bug in index_vals commit | commitdiff | tree | snapshot
2013-04-11 martinahansenadded index_vals biopiece commit | commitdiff | tree | snapshot
2013-03-20 martinahansencorrected pcr_seq revcomp of patterns commit | commitdiff | tree | snapshot
2013-03-16 martinahansenchanged upper/lower case output in assemble_pairs commit | commitdiff | tree | snapshot
2013-03-13 martinahansendropped pandaseq requirement commit | commitdiff | tree | snapshot
2013-03-13 martinahansenfixed minor upcase bug in assemble.rb commit | commitdiff | tree | snapshot
2013-03-13 martinahansenupgraded tests of read_sff commit | commitdiff | tree | snapshot
2013-03-13 martinahansenfinish assemble_pairs revamp commit | commitdiff | tree | snapshot
2013-03-13 martinahansenassemble_pairs revamp commit | commitdiff | tree | snapshot
2013-03-13 martinahansenadded comments to code commit | commitdiff | tree | snapshot
2013-03-13 martinahansenadded name check to assemble_pairs2 commit | commitdiff | tree | snapshot
2013-03-13 martinahansenadded check for minimum seq length commit | commitdiff | tree | snapshot
2013-03-13 martinahansenadded check for minimum seq length commit | commitdiff | tree | snapshot
2013-03-13 martinahansenfixed defaults and key names commit | commitdiff | tree | snapshot
2013-03-13 martinahansenupgraded assemble.rb to chose proper residue when mismatch commit | commitdiff | tree | snapshot
2013-03-13 martinahansenadded hacky thing to avoid warning from zlib commit | commitdiff | tree | snapshot
2013-03-12 martinahansenadded keys to assemble_pairs2 commit | commitdiff | tree | snapshot
2013-03-12 martinahansenadded assemble_pairs2 commit | commitdiff | tree | snapshot
2013-03-12 martinahansenadded seq/assemble.rb commit | commitdiff | tree | snapshot
2013-03-12 martinahansenfixed score base bug in sff.rb commit | commitdiff | tree | snapshot
2013-03-11 martinahansenadded word_size switch to blast_seq_pair commit | commitdiff | tree | snapshot
2013-03-11 martinahansenchanged blast_seq_pair to do multiple pairs commit | commitdiff | tree | snapshot
2013-03-11 martinahansenadded [] og []= to seq.rb commit | commitdiff | tree | snapshot
2013-03-08 martinahansenadded split_pair_seq biopiece commit | commitdiff | tree | snapshot
2013-03-08 martinahansenadded new Biopiece merge_pair_seq commit | commitdiff | tree | snapshot
2013-03-08 martinahansenadded new Biopiece merge_pair_seq commit | commitdiff | tree | snapshot
2013-03-08 martinahansendropped cat_seq Biopieces since join_seq exists commit | commitdiff | tree | snapshot
2013-03-08 martinahansenadded pair-end power to read_fastq commit | commitdiff | tree | snapshot
2013-03-08 martinahansenadded eof? method to filesys.rb commit | commitdiff | tree | snapshot
2013-03-08 martinahansenrefactoring of ruby code converting sequences types... commit | commitdiff | tree | snapshot
2013-03-08 martinahansenadded << method to Seq.rb commit | commitdiff | tree | snapshot
2013-03-08 martinahansenrewrite of FASTQ internals commit | commitdiff | tree | snapshot
2013-03-01 martinahansenfixed bug in plot_scores commit | commitdiff | tree | snapshot
2013-02-28 martinahansenfinished refactoring s/has_key?/[]/ commit | commitdiff | tree | snapshot
2013-02-28 martinahansenrefactoring of ruby code s/has_key?/[]/ commit | commitdiff | tree | snapshot
2013-02-28 martinahansenfixed global SCORE_BASE in mean_scores commit | commitdiff | tree | snapshot
2013-02-28 martinahansenrefactoring of revcomp in seq.rb commit | commitdiff | tree | snapshot
2013-02-28 martinahansenadded Seq.shuffle method and tests commit | commitdiff | tree | snapshot
2013-02-28 martinahansenupdated find_SNPs tests commit | commitdiff | tree | snapshot
2013-02-25 martinahansenfixed SCORE_BASE global var commit | commitdiff | tree | snapshot
2013-02-21 martinahansenadded coverage to find_SNPs commit | commitdiff | tree | snapshot
2013-02-21 martinahansenfixed nasty bug in grab where -E and pattern 0 failed commit | commitdiff | tree | snapshot
2013-02-21 martinahansenfixed nasty bug in grab where -E and pattern 0 failed commit | commitdiff | tree | snapshot
2013-02-20 martinahansenmade find_adaptor ignore too short sequences commit | commitdiff | tree | snapshot
2013-02-19 martinahansenadded write_sam biopiece commit | commitdiff | tree | snapshot
2013-02-19 martinahansendisabled encoding validity check commit | commitdiff | tree | snapshot
2013-02-19 martinahansenadded provisional write sam support commit | commitdiff | tree | snapshot
2013-02-19 martinahansenpolished read_sam commit | commitdiff | tree | snapshot
2013-02-08 martinahansenfixed quality score validity check commit | commitdiff | tree | snapshot
2013-02-06 martinahansendisable validity check commit | commitdiff | tree | snapshot
2013-02-04 martinahansenadded quality score check to read_fastq commit | commitdiff | tree | snapshot
2013-02-04 martinahansenadded qual_valid? method to Seq.rb commit | commitdiff | tree | snapshot
2013-02-02 martinahansenfixed minor bug in error handling commit | commitdiff | tree | snapshot
2013-01-22 martinahansenfixed axis titles commit | commitdiff | tree | snapshot
2013-01-22 martinahansenadded plot_stacked_histogram biopiece commit | commitdiff | tree | snapshot
2013-01-21 martinahansenadded pandaseq prerequisite commit | commitdiff | tree | snapshot
2013-01-21 martinahansenadded tests for assemble_pairs biopiece commit | commitdiff | tree | snapshot
2013-01-21 martinahansenadded assemble_pairs biopiece commit | commitdiff | tree | snapshot
2013-01-20 martinahansenadded substitute_vals biopiece commit | commitdiff | tree | snapshot
2013-01-16 martinahansenfixed bad tests in match.rb commit | commitdiff | tree | snapshot
2013-01-15 martinahansenadded png term to plot_matches commit | commitdiff | tree | snapshot
2013-01-14 martinahansenadded tests for create_seq_index and get_seq commit | commitdiff | tree | snapshot
2013-01-14 martinahansenfixed apparent change in Carp yielding an extra . after... commit | commitdiff | tree | snapshot
2013-01-14 martinahansenremoved error check commit | commitdiff | tree | snapshot
2013-01-11 martinahansenadded bowtie2 biopieces commit | commitdiff | tree | snapshot
2013-01-09 martinahansenadding kmer to contigs commit | commitdiff | tree | snapshot
2013-01-09 martinahansenfixed up assemble_seq_velvet commit | commitdiff | tree | snapshot
2013-01-09 martinahansenrewrote assemble_seq_velvet commit | commitdiff | tree | snapshot
2013-01-09 martinahansenfixed pair end issue commit | commitdiff | tree | snapshot
2013-01-09 martinahansenset cutoff to auto in velvet commit | commitdiff | tree | snapshot
2013-01-09 martinahansenrenamed assemle_seq_idba assemble_seq_idba commit | commitdiff | tree | snapshot
2013-01-09 martinahansenrenamed assemble_seq_idba_ud assemle_seq_idba commit | commitdiff | tree | snapshot
2013-01-09 martinahansenremoved old assemle_seq_idba commit | commitdiff | tree | snapshot
2013-01-04 martinahansenfixed to_i bug in pcr_seq commit | commitdiff | tree | snapshot
2013-01-04 martinahansenupdated report commit | commitdiff | tree | snapshot
2013-01-04 martinahansenupdated pcr_seq and added tests commit | commitdiff | tree | snapshot
2013-01-03 martinahansenpolished pairwise alignment code commit | commitdiff | tree | snapshot
2013-01-02 martinahansenadded new match.rb and tests commit | commitdiff | tree | snapshot
2013-01-02 martinahansenadded new match.rb and tests commit | commitdiff | tree | snapshot
2013-01-02 martinahansenadded test for align dir commit | commitdiff | tree | snapshot
2013-01-02 martinahansenrenaming match.rb to matches.rb commit | commitdiff | tree | snapshot
2013-01-02 martinahansenmoved mum.rb commit | commitdiff | tree | snapshot
2012-12-20 martinahansenclearnup of pair align code commit | commitdiff | tree | snapshot
2012-12-13 martinahansenfixed minor bug in grab for exact_in where no key would... commit | commitdiff | tree | snapshot
2012-12-12 martinahansenfixed QA_Illumina_report.rb SEQ_LEN > 20 commit | commitdiff | tree | snapshot
2012-12-12 martinahansenchanged to new find_adaptor commit | commitdiff | tree | snapshot
2012-12-11 martinahansenadded unit test to backtrack code commit | commitdiff | tree | snapshot
2012-12-10 martinahansenremoved debug code from find_adaptor commit | commitdiff | tree | snapshot
2012-12-10 martinahansenunrolling new find_adaptor commit | commitdiff | tree | snapshot
2012-12-10 martinahansenfixed bug in backtrack.rb commit | commitdiff | tree | snapshot
2012-12-10 martinahansenfixed unit tests for backtrack.rb commit | commitdiff | tree | snapshot
2012-12-06 martinahansenfixed unit tests commit | commitdiff | tree | snapshot
2012-12-05 martinahansenrenamed patternmatcher to dynamic commit | commitdiff | tree | snapshot
2012-12-05 martinahansenrenamed patternmatcher to dynamic commit | commitdiff | tree | snapshot
2012-12-05 martinahansenfixing name space collision commit | commitdiff | tree | snapshot
2012-12-05 martinahansenrefactorying PatternMatcher to Dynamic commit | commitdiff | tree | snapshot
2012-12-05 martinahansenrenamed patternmatcher to dynamic commit | commitdiff | tree | snapshot
2012-12-05 martinahansencleaned comments commit | commitdiff | tree | snapshot
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Mirror (and my branches) of biopieces http://www.biopieces.org/