git.donarmstrong.com Git - biopieces.git/history

]> git.donarmstrong.com Git - biopieces.git/history - code_ruby

2014-03-18	martinahansen	removed debug message master	tree \| commitdiff
2014-03-18	martinahansen	fixed file bug	tree \| commitdiff
2014-03-18	martinahansen	added file check	tree \| commitdiff
2014-03-18	martinahansen	polish of fastq	tree \| commitdiff
2014-01-13	martinahansen	fixed each_orf	tree \| commitdiff
2014-01-13	martinahansen	removed subseq and subseq! methods in favor of []	tree \| commitdiff
2014-01-13	martinahansen	exchanged subseq with seq[]	tree \| commitdiff
2014-01-13	martinahansen	exchanged subseq with seq[]	tree \| commitdiff
2014-01-13	martinahansen	refactor foo to record	tree \| commitdiff
2013-12-13	martinahansen	changed fasta parse to allow leading empty lines	tree \| commitdiff
2013-12-11	martinahansen	fixed wrap bug in seq.rb	tree \| commitdiff
2013-12-05	martinahansen	fixed qual scores in sam.rb	tree \| commitdiff
2013-12-05	martinahansen	fixed qual scores in sam.rb	tree \| commitdiff
2013-12-02	martinahansen	fixed bug in assemble_pairs	tree \| commitdiff
2013-11-29	martinahansen	fixed another each_orf bug	tree \| commitdiff
2013-11-29	martinahansen	fixed bug in find_orfs	tree \| commitdiff
2013-10-30	martinahansen	fixed bug in pair assembler	tree \| commitdiff
2013-10-30	martinahansen	added patscan_trim method to Seq	tree \| commitdiff
2013-10-25	martinahansen	added -o and -x to analyze_vals	tree \| commitdiff
2013-10-24	martinahansen	refactored backtrack methods to use options hash in...	tree \| commitdiff
2013-10-24	martinahansen	fixed Seq object creation in sff.rb	tree \| commitdiff
2013-10-24	martinahansen	now using roche mid module for find_barcodes	tree \| commitdiff
2013-10-24	martinahansen	added roche mid module	tree \| commitdiff
2013-10-24	martinahansen	adding table.rb	tree \| commitdiff
2013-10-23	martinahansen	removed commented out stale code	tree \| commitdiff
2013-10-18	martinahansen	fixed method name change	tree \| commitdiff
2013-10-08	martinahansen	refactoring of assemble_pairs	tree \| commitdiff
2013-10-08	martinahansen	fixed seq qual length check	tree \| commitdiff
2013-10-07	martinahansen	DRY refactorying of backtrack code	tree \| commitdiff
2013-10-07	martinahansen	gzip fiddling	tree \| commitdiff
2013-10-07	martinahansen	exchanged zlib code with commandline gzip	tree \| commitdiff
2013-10-07	martinahansen	fixed symlink flaw in file type detection	tree \| commitdiff
2013-10-01	martinahansen	changed Seq.new argument to hash	tree \| commitdiff
2013-09-26	martinahansen	added test for length of seq/qual mismatch	tree \| commitdiff
2013-09-26	martinahansen	disabling buggy bzip2-ruby	tree \| commitdiff
2013-09-26	martinahansen	temporary fix of bzip2 read problem	tree \| commitdiff
2013-09-25	martinahansen	adding bzip2 support in ruby	tree \| commitdiff
2013-09-18	martinahansen	beautifing ambiguity.rb	tree \| commitdiff
2013-09-18	martinahansen	implemented hamming_dist in inline C	tree \| commitdiff
2013-09-18	martinahansen	add comments to ambiguity.rb	tree \| commitdiff
2013-09-18	martinahansen	fixed broken tests not workin with Ruby2	tree \| commitdiff
2013-09-18	martinahansen	added amiguity.rb	tree \| commitdiff
2013-09-18	martinahansen	added mem.rb	tree \| commitdiff
2013-09-18	martinahansen	added ambiguity to hamming_distance	tree \| commitdiff
2013-09-09	martinahansen	fixing usearch upgrade	tree \| commitdiff
2013-09-06	martinahansen	upgraded uclust_seq to support usearch7	tree \| commitdiff
2013-06-24	martinahansen	fixed genbank and embl parsing of 5'UTR and 3'UTR	tree \| commitdiff
2013-06-24	martinahansen	added \r remove hack to genbank/embl parsers	tree \| commitdiff
2013-06-23	martinahansen	moved inline C code to seperate file	tree \| commitdiff
2013-06-21	martinahansen	added edit_distance method to seq.rb	tree \| commitdiff
2013-06-21	martinahansen	fixed ambiguity in levenshtein.rb	tree \| commitdiff
2013-06-20	martinahansen	added levenshtein edit distance calculator	tree \| commitdiff
2013-06-20	martinahansen	added levenshtein edit distance calculator	tree \| commitdiff
2013-06-20	martinahansen	added levenshtein edit distance calculator	tree \| commitdiff
2013-06-04	martinahansen	added missing files	tree \| commitdiff
2013-06-04	martinahansen	revamped find_homopolymers	tree \| commitdiff
2013-04-29	martinahansen	fixed missing BP_TMP dir feature	tree \| commitdiff
2013-03-16	martinahansen	changed upper/lower case output in assemble_pairs	tree \| commitdiff
2013-03-13	martinahansen	fixed minor upcase bug in assemble.rb	tree \| commitdiff
2013-03-13	martinahansen	added comments to code	tree \| commitdiff
2013-03-13	martinahansen	upgraded assemble.rb to chose proper residue when mismatch	tree \| commitdiff
2013-03-13	martinahansen	added hacky thing to avoid warning from zlib	tree \| commitdiff
2013-03-12	martinahansen	added seq/assemble.rb	tree \| commitdiff
2013-03-12	martinahansen	fixed score base bug in sff.rb	tree \| commitdiff
2013-03-11	martinahansen	added [] og []= to seq.rb	tree \| commitdiff
2013-03-08	martinahansen	added split_pair_seq biopiece	tree \| commitdiff
2013-03-08	martinahansen	added new Biopiece merge_pair_seq	tree \| commitdiff
2013-03-08	martinahansen	added eof? method to filesys.rb	tree \| commitdiff
2013-03-08	martinahansen	refactoring of ruby code converting sequences types...	tree \| commitdiff
2013-03-08	martinahansen	added << method to Seq.rb	tree \| commitdiff
2013-03-08	martinahansen	rewrite of FASTQ internals	tree \| commitdiff
2013-02-28	martinahansen	finished refactoring s/has_key?/[]/	tree \| commitdiff
2013-02-28	martinahansen	refactoring of revcomp in seq.rb	tree \| commitdiff
2013-02-28	martinahansen	added Seq.shuffle method and tests	tree \| commitdiff
2013-02-25	martinahansen	fixed SCORE_BASE global var	tree \| commitdiff
2013-02-19	martinahansen	added provisional write sam support	tree \| commitdiff
2013-02-08	martinahansen	fixed quality score validity check	tree \| commitdiff
2013-02-04	martinahansen	added qual_valid? method to Seq.rb	tree \| commitdiff
2013-02-02	martinahansen	fixed minor bug in error handling	tree \| commitdiff
2013-01-16	martinahansen	fixed bad tests in match.rb	tree \| commitdiff
2013-01-03	martinahansen	polished pairwise alignment code	tree \| commitdiff
2013-01-02	martinahansen	added new match.rb and tests	tree \| commitdiff
2013-01-02	martinahansen	added new match.rb and tests	tree \| commitdiff
2013-01-02	martinahansen	added test for align dir	tree \| commitdiff
2013-01-02	martinahansen	renaming match.rb to matches.rb	tree \| commitdiff
2013-01-02	martinahansen	moved mum.rb	tree \| commitdiff
2012-12-20	martinahansen	clearnup of pair align code	tree \| commitdiff
2012-12-11	martinahansen	added unit test to backtrack code	tree \| commitdiff
2012-12-10	martinahansen	fixed bug in backtrack.rb	tree \| commitdiff
2012-12-10	martinahansen	fixed unit tests for backtrack.rb	tree \| commitdiff
2012-12-06	martinahansen	fixed unit tests	tree \| commitdiff
2012-12-05	martinahansen	renamed patternmatcher to dynamic	tree \| commitdiff
2012-12-05	martinahansen	renamed patternmatcher to dynamic	tree \| commitdiff
2012-12-05	martinahansen	fixing name space collision	tree \| commitdiff
2012-12-05	martinahansen	refactorying PatternMatcher to Dynamic	tree \| commitdiff
2012-12-05	martinahansen	renamed patternmatcher to dynamic	tree \| commitdiff
2012-12-05	martinahansen	cleaned comments	tree \| commitdiff
2012-12-05	martinahansen	refactor match->patmatch scan->patscan	tree \| commitdiff
2012-12-05	martinahansen	refactor match->patmatch scan->patscan	tree \| commitdiff
2012-12-04	martinahansen	added patmatch method to backtrack.rb	tree \| commitdiff
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