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

2013-02-25	martinahansen	fixed SCORE_BASE global var	tree \| commitdiff
2013-02-21	martinahansen	added coverage to find_SNPs	tree \| commitdiff
2013-02-21	martinahansen	fixed nasty bug in grab where -E and pattern 0 failed	tree \| commitdiff
2013-02-21	martinahansen	fixed nasty bug in grab where -E and pattern 0 failed	tree \| commitdiff
2013-02-20	martinahansen	made find_adaptor ignore too short sequences	tree \| commitdiff
2013-02-19	martinahansen	added write_sam biopiece	tree \| commitdiff
2013-02-19	martinahansen	disabled encoding validity check	tree \| commitdiff
2013-02-19	martinahansen	polished read_sam	tree \| commitdiff
2013-02-08	martinahansen	fixed quality score validity check	tree \| commitdiff
2013-02-06	martinahansen	disable validity check	tree \| commitdiff
2013-02-04	martinahansen	added quality score check to read_fastq	tree \| commitdiff
2013-01-22	martinahansen	fixed axis titles	tree \| commitdiff
2013-01-22	martinahansen	added plot_stacked_histogram biopiece	tree \| commitdiff
2013-01-21	martinahansen	added assemble_pairs biopiece	tree \| commitdiff
2013-01-20	martinahansen	added substitute_vals biopiece	tree \| commitdiff
2013-01-15	martinahansen	added png term to plot_matches	tree \| commitdiff
2013-01-14	martinahansen	removed error check	tree \| commitdiff
2013-01-11	martinahansen	added bowtie2 biopieces	tree \| commitdiff
2013-01-09	martinahansen	adding kmer to contigs	tree \| commitdiff
2013-01-09	martinahansen	fixed up assemble_seq_velvet	tree \| commitdiff
2013-01-09	martinahansen	rewrote assemble_seq_velvet	tree \| commitdiff
2013-01-09	martinahansen	fixed pair end issue	tree \| commitdiff
2013-01-09	martinahansen	set cutoff to auto in velvet	tree \| commitdiff
2013-01-09	martinahansen	renamed assemle_seq_idba assemble_seq_idba	tree \| commitdiff
2013-01-09	martinahansen	renamed assemble_seq_idba_ud assemle_seq_idba	tree \| commitdiff
2013-01-09	martinahansen	removed old assemle_seq_idba	tree \| commitdiff
2013-01-04	martinahansen	fixed to_i bug in pcr_seq	tree \| commitdiff
2013-01-04	martinahansen	updated pcr_seq and added tests	tree \| commitdiff
2012-12-13	martinahansen	fixed minor bug in grab for exact_in where no key would...	tree \| commitdiff
2012-12-10	martinahansen	removed debug code from find_adaptor	tree \| commitdiff
2012-12-10	martinahansen	unrolling new find_adaptor	tree \| commitdiff
2012-11-30	martinahansen	finished backtrack drama	tree \| commitdiff
2012-11-29	martinahansen	added 3 parameters to blast_seq	tree \| commitdiff
2012-11-28	martinahansen	fixing up backtrack code	tree \| commitdiff
2012-11-27	martinahansen	added missing seq fix to plot_nucleotide_distribution	tree \| commitdiff
2012-11-27	martinahansen	added relative count to plot_nucleotide_distribution	tree \| commitdiff
2012-11-19	martinahansen	add uchime_seq biopiece	tree \| commitdiff
2012-11-02	martinahansen	removing order_pairs2 and order_pairs3	tree \| commitdiff
2012-11-02	martinahansen	find_pairs added	tree \| commitdiff
2012-11-01	martinahansen	fixed but in order_pairs3	tree \| commitdiff
2012-11-01	martinahansen	added verbose info to order_pairs3	tree \| commitdiff
2012-11-01	martinahansen	adding order_pairs3	tree \| commitdiff
2012-10-31	martinahansen	changed order_pairs2 to gdbm	tree \| commitdiff
2012-10-31	martinahansen	changed order_pairs2 to gdbm	tree \| commitdiff
2012-10-31	martinahansen	added order_pairs2	tree \| commitdiff
2012-10-31	martinahansen	added order_pairs2	tree \| commitdiff
2012-10-25	martinahansen	added debranch function to classify_taxonomy	tree \| commitdiff
2012-10-24	martinahansen	updated classify_taxonomy to GG12-10	tree \| commitdiff
2012-10-23	martinahansen	fixed nasty bug in classify_taxonomy	tree \| commitdiff
2012-10-22	martinahansen	fixed nasty bug in classify_taxonomy	tree \| commitdiff
2012-10-16	martinahansen	removed raise from classify_taxonomy	tree \| commitdiff
2012-10-15	martinahansen	removed raise from classify_taxonomy	tree \| commitdiff
2012-10-12	martinahansen	fixed classify_taxonomy	tree \| commitdiff
2012-10-10	martinahansen	added flock to biostat	tree \| commitdiff
2012-10-10	martinahansen	removed stale file crap from biostat	tree \| commitdiff
2012-10-09	martinahansen	changed default values for findsim_seq	tree \| commitdiff
2012-10-09	martinahansen	cleanup of findsim_seq	tree \| commitdiff
2012-09-27	martinahansen	polished kmer_freq	tree \| commitdiff
2012-09-27	martinahansen	clearning up kmer_stats and kmer_freq	tree \| commitdiff
2012-09-25	martinahansen	work kmer_stats biopiece	tree \| commitdiff
2012-09-25	martinahansen	added kmer_stats biopiece	tree \| commitdiff
2012-09-21	martinahansen	slight polish of read_fastq	tree \| commitdiff
2012-09-20	martinahansen	added bases_per_file option to find_adaptor	tree \| commitdiff
2012-09-19	martinahansen	fixed database type guess for blast_seq	tree \| commitdiff
2012-09-04	martinahansen	fixed bug in clip_adaptor where LEFT_POS > RIGHT_POS	tree \| commitdiff
2012-09-03	martinahansen	revamped find_adaptor and clip_adaptor	tree \| commitdiff
2012-08-30	martinahansen	added plot_nucleotide_distribution biopiece	tree \| commitdiff
2012-08-30	martinahansen	finally figured how to change plot color	tree \| commitdiff
2012-08-15	martinahansen	made find_orfs run on DNA or RNA	tree \| commitdiff
2012-08-14	martinahansen	fixed mean_scores to deal with 0 length seqs	tree \| commitdiff
2012-08-14	martinahansen	reverted trim_seq	tree \| commitdiff
2012-08-14	martinahansen	changed trim_seq to omit outputting sequences with...	tree \| commitdiff
2012-08-07	martinahansen	fixed typo	tree \| commitdiff
2012-08-07	martinahansen	added assemble_seq_idba_ud	tree \| commitdiff
2012-08-07	martinahansen	added relative count to plot_scores + rewrite for speed	tree \| commitdiff
2012-07-13	martinahansen	fixed grave bug in find_orfs	tree \| commitdiff
2012-07-13	martinahansen	added find_orfs	tree \| commitdiff
2012-07-10	martinahansen	ported align_pair_seq to ruby	tree \| commitdiff
2012-07-10	martinahansen	minor fix to find_adaptor 2	tree \| commitdiff
2012-07-10	martinahansen	minor fix to find_adaptor	tree \| commitdiff
2012-07-02	martinahansen	updated order_pairs	tree \| commitdiff
2012-06-29	martinahansen	rewrote mean_scores to fix bug	tree \| commitdiff
2012-06-25	martinahansen	added max_diversity swith to findsim.rb	tree \| commitdiff
2012-06-25	martinahansen	added max_diversity swith to findsim.rb	tree \| commitdiff
2012-06-20	martinahansen	classify_taxonomy work	tree \| commitdiff
2012-06-20	martinahansen	classify_taxonomy work	tree \| commitdiff
2012-06-13	martinahansen	added classify_taxonomy (unfinished biopiece)	tree \| commitdiff
2012-06-08	martinahansen	fixed raw intput bug in read_fasta and read_fastq	tree \| commitdiff
2012-06-01	martinahansen	added illumina 1.8 name scheme support to order pairs	tree \| commitdiff
2012-05-24	martinahansen	upgraded trim_seq	tree \| commitdiff
2012-05-08	martinahansen	reverted findsim_seq and renamed precise switch to...	tree \| commitdiff
2012-05-02	martinahansen	finishing hmmer_seq	tree \| commitdiff
2012-05-02	martinahansen	added hmmer_seq biopiece	tree \| commitdiff
2012-04-30	martinahansen	upgraded write_fixedstep	tree \| commitdiff
2012-04-24	martinahansen	added split of quality scores to split_seq	tree \| commitdiff
2012-04-23	martinahansen	added precise switch to findsim	tree \| commitdiff
2012-04-18	martinahansen	changed record_scores to max_hits refactoring	tree \| commitdiff
2012-04-18	martinahansen	added findsim_seq biopieces	tree \| commitdiff
2012-04-18	martinahansen	fixed issue 32	tree \| commitdiff
2012-04-18	martinahansen	fixed x bug in compute	tree \| commitdiff
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