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

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

2013-11-25	martinahansen	fixed encoding bug in read_454	tree \| commitdiff
2013-11-25	martinahansen	fixed encoding in write_454	tree \| commitdiff
2013-11-25	martinahansen	plot_scores max length set to 100K	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	now using roche mid module for find_barcodes	tree \| commitdiff
2013-10-16	martinahansen	cleanup of analyze_vals added analyze_scores	tree \| commitdiff
2013-10-15	martinahansen	rewrote analyze_vals	tree \| commitdiff
2013-10-15	martinahansen	rewrote write_tab	tree \| commitdiff
2013-10-08	martinahansen	refactoring of assemble_pairs	tree \| commitdiff
2013-10-01	martinahansen	changed Seq.new argument to hash	tree \| commitdiff
2013-09-26	martinahansen	added prefix option to write_fasta_files and write_fast...	tree \| commitdiff
2013-09-25	martinahansen	added gzip/bzip2 output option to write_fastq_files	tree \| commitdiff
2013-09-25	martinahansen	added support for gzip/bzip2 in write_fasta_files ...	tree \| commitdiff
2013-09-25	martinahansen	ported write_fasta to ruby enabling bzip2 support	tree \| commitdiff
2013-09-25	martinahansen	adding bzip2 support in ruby	tree \| commitdiff
2013-09-23	martinahansen	fixed isseu in find_orphans	tree \| commitdiff
2013-09-23	martinahansen	created find_orphans Biopiece	tree \| commitdiff
2013-09-16	martinahansen	fixed overlap bug in patscan_seq	tree \| commitdiff
2013-09-13	martinahansen	added missing cpus switch to uclust_seq	tree \| commitdiff
2013-09-09	martinahansen	polish usearch_seq	tree \| commitdiff
2013-09-09	martinahansen	polish uclust_seq	tree \| commitdiff
2013-09-09	martinahansen	fixing usearch upgrade	tree \| commitdiff
2013-09-06	martinahansen	upgraded uclust_seq to support usearch7	tree \| commitdiff
2013-06-17	martinahansen	updated patscan_seq	tree \| commitdiff
2013-06-17	martinahansen	updated patscan_seq	tree \| commitdiff
2013-06-04	martinahansen	revamped find_homopolymers	tree \| commitdiff
2013-05-16	martinahansen	more verbose grab output	tree \| commitdiff
2013-05-16	martinahansen	added verbose count to grab	tree \| commitdiff
2013-04-18	martinahansen	fixed divide bug in compute	tree \| commitdiff
2013-04-11	martinahansen	fixed bug in index_vals	tree \| commitdiff
2013-04-11	martinahansen	added index_vals biopiece	tree \| commitdiff
2013-03-20	martinahansen	corrected pcr_seq revcomp of patterns	tree \| commitdiff
2013-03-13	martinahansen	finish assemble_pairs revamp	tree \| commitdiff
2013-03-13	martinahansen	assemble_pairs revamp	tree \| commitdiff
2013-03-13	martinahansen	added name check to assemble_pairs2	tree \| commitdiff
2013-03-13	martinahansen	added check for minimum seq length	tree \| commitdiff
2013-03-13	martinahansen	added check for minimum seq length	tree \| commitdiff
2013-03-13	martinahansen	fixed defaults and key names	tree \| commitdiff
2013-03-12	martinahansen	added keys to assemble_pairs2	tree \| commitdiff
2013-03-12	martinahansen	added assemble_pairs2	tree \| commitdiff
2013-03-11	martinahansen	added word_size switch to blast_seq_pair	tree \| commitdiff
2013-03-11	martinahansen	changed blast_seq_pair to do multiple pairs	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	dropped cat_seq Biopieces since join_seq exists	tree \| commitdiff
2013-03-08	martinahansen	added pair-end power to read_fastq	tree \| commitdiff
2013-03-08	martinahansen	refactoring of ruby code converting sequences types...	tree \| commitdiff
2013-03-08	martinahansen	rewrite of FASTQ internals	tree \| commitdiff
2013-03-01	martinahansen	fixed bug in plot_scores	tree \| commitdiff
2013-02-28	martinahansen	refactoring of ruby code s/has_key?/[]/	tree \| commitdiff
2013-02-28	martinahansen	fixed global SCORE_BASE in mean_scores	tree \| commitdiff
2013-02-28	martinahansen	refactoring of revcomp in seq.rb	tree \| commitdiff
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
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