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2012-12-05	martinahansen	refactorying PatternMatcher to Dynamic	commit \| commitdiff \| tree
2012-12-05	martinahansen	renamed patternmatcher to dynamic	commit \| commitdiff \| tree
2012-12-05	martinahansen	cleaned comments	commit \| commitdiff \| tree
2012-12-05	martinahansen	refactor match->patmatch scan->patscan	commit \| commitdiff \| tree
2012-12-05	martinahansen	refactor match->patmatch scan->patscan	commit \| commitdiff \| tree
2012-12-04	martinahansen	added patmatch method to backtrack.rb	commit \| commitdiff \| tree
2012-12-04	martinahansen	added private to patternmatcher	commit \| commitdiff \| tree
2012-12-04	martinahansen	fixed unit tests for patternmatcher	commit \| commitdiff \| tree
2012-12-04	martinahansen	added some text	commit \| commitdiff \| tree
2012-12-03	martinahansen	fixed constants for align.rb	commit \| commitdiff \| tree
2012-12-03	martinahansen	ported patternmatcher to C	commit \| commitdiff \| tree
2012-11-30	martinahansen	finished backtrack drama	commit \| commitdiff \| tree
2012-11-30	martinahansen	added state to backtrack.rb	commit \| commitdiff \| tree
2012-11-30	martinahansen	done revert of test_backtrack.rb	commit \| commitdiff \| tree
2012-11-30	martinahansen	reverted test_backtrack.rb to r1827	commit \| commitdiff \| tree
2012-11-30	martinahansen	reverted backtrack.rb to 2006 prior to struct version	commit \| commitdiff \| tree
2012-11-29	martinahansen	disabling backtrack which causes compile error	commit \| commitdiff \| tree
2012-11-29	martinahansen	added 3 parameters to blast_seq	commit \| commitdiff \| tree
2012-11-28	martinahansen	fixing up backtrack code	commit \| commitdiff \| tree
2012-11-28	martinahansen	added output of mis ind and del to backtrack code	commit \| commitdiff \| tree
2012-11-27	martinahansen	polished backtrack.rb	commit \| commitdiff \| tree
2012-11-27	martinahansen	backtrack.rb polish	commit \| commitdiff \| tree
2012-11-27	martinahansen	added -c to nuc dist plot	commit \| commitdiff \| tree
2012-11-27	martinahansen	added -c to plot_nuc_dist	commit \| commitdiff \| tree
2012-11-27	martinahansen	added missing seq fix to plot_nucleotide_distribution	commit \| commitdiff \| tree
2012-11-27	martinahansen	added relative count to plot_nucleotide_distribution	commit \| commitdiff \| tree
2012-11-27	martinahansen	more power to the QA	commit \| commitdiff \| tree
2012-11-26	martinahansen	more power to the QA	commit \| commitdiff \| tree
2012-11-26	martinahansen	added adaptor removal to QA	commit \| commitdiff \| tree
2012-11-26	martinahansen	polish of QA_Illumina_report.rb	commit \| commitdiff \| tree
2012-11-23	martinahansen	small fix QA_Illumina_report.rb	commit \| commitdiff \| tree
2012-11-23	martinahansen	added QA_Illumina_report.rb	commit \| commitdiff \| tree
2012-11-21	martinahansen	added exception handling for missing SFF coordinates	commit \| commitdiff \| tree
2012-11-20	martinahansen	added uchime to usearch	commit \| commitdiff \| tree
2012-11-19	martinahansen	add uchime_seq biopiece	commit \| commitdiff \| tree
2012-11-02	martinahansen	added tests for find_pairs	commit \| commitdiff \| tree
2012-11-02	martinahansen	removing order_pairs2 and order_pairs3	commit \| commitdiff \| tree
2012-11-02	martinahansen	find_pairs added	commit \| commitdiff \| tree
2012-11-01	martinahansen	fixed but in order_pairs3	commit \| commitdiff \| tree
2012-11-01	martinahansen	added verbose info to order_pairs3	commit \| commitdiff \| tree
2012-11-01	martinahansen	added get_entry method to biopieces.rb	commit \| commitdiff \| tree
2012-11-01	martinahansen	adding order_pairs3	commit \| commitdiff \| tree
2012-10-31	martinahansen	changed order_pairs2 to gdbm	commit \| commitdiff \| tree
2012-10-31	martinahansen	changed order_pairs2 to gdbm	commit \| commitdiff \| tree
2012-10-31	martinahansen	added order_pairs2	commit \| commitdiff \| tree
2012-10-31	martinahansen	added order_pairs2	commit \| commitdiff \| tree
2012-10-26	martinahansen	updated installer	commit \| commitdiff \| tree
2012-10-25	martinahansen	updated installer	commit \| commitdiff \| tree
2012-10-25	martinahansen	added debranch function to classify_taxonomy	commit \| commitdiff \| tree
2012-10-24	martinahansen	updated classify_taxonomy to GG12-10	commit \| commitdiff \| tree
2012-10-23	martinahansen	fixed nasty bug in classify_taxonomy	commit \| commitdiff \| tree
2012-10-22	martinahansen	fixed nasty bug in classify_taxonomy	commit \| commitdiff \| tree
2012-10-16	martinahansen	removed raise from classify_taxonomy	commit \| commitdiff \| tree
2012-10-15	martinahansen	removed raise from classify_taxonomy	commit \| commitdiff \| tree
2012-10-12	martinahansen	fixed classify_taxonomy	commit \| commitdiff \| tree
2012-10-10	martinahansen	added some file locking to biopieces.rb	commit \| commitdiff \| tree
2012-10-10	martinahansen	added some file locking to Biopieces.pm	commit \| commitdiff \| tree
2012-10-10	martinahansen	added flock to biostat	commit \| commitdiff \| tree
2012-10-10	martinahansen	removed stale file crap from biostat	commit \| commitdiff \| tree
2012-10-10	martinahansen	added dynamic mem allocation to findsim.rb	commit \| commitdiff \| tree
2012-10-10	martinahansen	added dynamic mem allocation to findsim.rb	commit \| commitdiff \| tree
2012-10-09	martinahansen	changed default values for findsim_seq	commit \| commitdiff \| tree
2012-10-09	martinahansen	cleanup of findsim.rb	commit \| commitdiff \| tree
2012-10-09	martinahansen	cleanup of findsim_seq	commit \| commitdiff \| tree
2012-10-09	martinahansen	cleanup of findsim.rb	commit \| commitdiff \| tree
2012-09-27	martinahansen	upgraded kmer_freq test	commit \| commitdiff \| tree
2012-09-27	martinahansen	polished kmer_freq	commit \| commitdiff \| tree
2012-09-27	martinahansen	removed kmer_freq test files	commit \| commitdiff \| tree
2012-09-27	martinahansen	clearning up kmer_stats and kmer_freq	commit \| commitdiff \| tree
2012-09-27	martinahansen	finishing work on match.rb	commit \| commitdiff \| tree
2012-09-25	martinahansen	work kmer_stats biopiece	commit \| commitdiff \| tree
2012-09-25	martinahansen	added kmer_stats biopiece	commit \| commitdiff \| tree
2012-09-21	martinahansen	added parser for phred qual to fasta.rb	commit \| commitdiff \| tree
2012-09-21	martinahansen	added qual_base(33\|64)? methods to seq.rb	commit \| commitdiff \| tree
2012-09-21	martinahansen	slight polish of read_fastq	commit \| commitdiff \| tree
2012-09-20	martinahansen	added bases_per_file option to find_adaptor	commit \| commitdiff \| tree
2012-09-19	martinahansen	fixed database type guess for blast_seq	commit \| commitdiff \| tree
2012-09-13	martinahansen	pair.rb now working correctly	commit \| commitdiff \| tree
2012-09-12	martinahansen	worked on pair aligner	commit \| commitdiff \| tree
2012-09-11	martinahansen	working on pair.rb	commit \| commitdiff \| tree
2012-09-11	martinahansen	added align/match.rb	commit \| commitdiff \| tree
2012-09-11	martinahansen	worked on pair.rb	commit \| commitdiff \| tree
2012-09-10	martinahansen	fixed unit tests for seq.rb	commit \| commitdiff \| tree
2012-09-04	martinahansen	added math_aux.rb	commit \| commitdiff \| tree
2012-09-04	martinahansen	added test_math_aux.rb	commit \| commitdiff \| tree
2012-09-04	martinahansen	fixed bug in clip_adaptor where LEFT_POS > RIGHT_POS	commit \| commitdiff \| tree
2012-09-04	martinahansen	fixed bug in clip_adaptor where LEFT_POS > RIGHT_POS	commit \| commitdiff \| tree
2012-09-03	martinahansen	revamped find_adaptor and clip_adaptor	commit \| commitdiff \| tree
2012-09-03	martinahansen	updated testing files for find_adaptor and clip_adaptor	commit \| commitdiff \| tree
2012-08-30	martinahansen	deleted old QA_454_report script	commit \| commitdiff \| tree
2012-08-30	martinahansen	added nucleotide plot to QA_454_report	commit \| commitdiff \| tree
2012-08-30	martinahansen	added plot_nucleotide_distribution biopiece	commit \| commitdiff \| tree
2012-08-30	martinahansen	finally figured how to change plot color	commit \| commitdiff \| tree
2012-08-16	martinahansen	did something to findsim.rb	commit \| commitdiff \| tree
2012-08-15	martinahansen	made find_orfs run on DNA or RNA	commit \| commitdiff \| tree
2012-08-14	martinahansen	fixed mean_scores to deal with 0 length seqs	commit \| commitdiff \| tree
2012-08-14	martinahansen	reverted trim_seq	commit \| commitdiff \| tree
2012-08-14	martinahansen	changed trim_seq to omit outputting sequences with...	commit \| commitdiff \| tree
2012-08-09	martinahansen	upgraded QA script to use new plot scores count feature	commit \| commitdiff \| tree
2012-08-07	martinahansen	last fix on prodigal upgrade	commit \| commitdiff \| tree
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