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

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

2011-11-18	martinahansen	rewriting uclust_seq	tree \| commitdiff
2011-11-17	martinahansen	added tests to remove_primers	tree \| commitdiff
2011-11-17	martinahansen	fixed remove_primers	tree \| commitdiff
2011-11-17	martinahansen	fixed bug in remove_primers	tree \| commitdiff
2011-11-17	martinahansen	added remove_primers biopiece	tree \| commitdiff
2011-11-17	martinahansen	added requirement of RubyInline	tree \| commitdiff
2011-11-15	martinahansen	fixed digest.rb	tree \| commitdiff
2011-11-14	martinahansen	upgraded uclust_seq to work with useach 5.1.221	tree \| commitdiff
2011-11-13	martinahansen	fixed digest_seq	tree \| commitdiff
2011-11-13	martinahansen	cleaning up digest.rb	tree \| commitdiff
2011-11-07	martinahansen	added ruby version of read_sam	tree \| commitdiff
2011-11-07	martinahansen	removed perl version of read_sam	tree \| commitdiff
2011-11-02	martinahansen	added length check to bowtie_seq	tree \| commitdiff
2011-11-02	martinahansen	added length check to bowtie_seq	tree \| commitdiff
2011-11-02	martinahansen	fixed qual argument for bowtie on fasta only	tree \| commitdiff
2011-10-31	martinahansen	added metagenome flag to assemble_seq_idba	tree \| commitdiff
2011-10-27	martinahansen	removed biopieces find_mids remove_mids read_solexa	tree \| commitdiff
2011-10-25	martinahansen	added find_barcodes biopiece	tree \| commitdiff
2011-10-25	martinahansen	added png terminal to plot_histogram	tree \| commitdiff
2011-10-20	martinahansen	ported trim_seq to ruby and added tests	tree \| commitdiff
2011-10-14	martinahansen	fixed critical missing uc bug in uniq_seq	tree \| commitdiff
2011-10-13	martinahansen	fixed fastq issue	tree \| commitdiff
2011-10-13	martinahansen	fixed last of fasta problems	tree \| commitdiff
2011-10-13	martinahansen	fixed assemblers	tree \| commitdiff
2011-10-13	martinahansen	fixing broken biopieces	tree \| commitdiff
2011-10-13	martinahansen	beautifying fasta.rb	tree \| commitdiff
2011-10-12	martinahansen	added write_fastq_files	tree \| commitdiff
2011-10-12	martinahansen	variable rename	tree \| commitdiff
2011-10-12	martinahansen	added biopieces write_fasta_files	tree \| commitdiff
2011-09-29	martinahansen	added delimiter to join_seq	tree \| commitdiff
2011-09-26	martinahansen	fixed bug in patscan_seq arguments	tree \| commitdiff
2011-09-23	martinahansen	fixed patscan_seq	tree \| commitdiff
2011-09-20	martinahansen	updated patscan_seq	tree \| commitdiff
2011-09-06	martinahansen	rewrote remove_mids again	tree \| commitdiff
2011-09-06	martinahansen	fixed bug in remove_mids	tree \| commitdiff
2011-09-05	martinahansen	updated remove_mids	tree \| commitdiff
2011-09-01	martinahansen	fixed bug in find_SNPs	tree \| commitdiff
2011-09-01	martinahansen	added find_SNPs biopiece	tree \| commitdiff
2011-08-31	martinahansen	sam update	tree \| commitdiff
2011-06-14	martinahansen	hackery changes to plot_matches to deal with blast...	tree \| commitdiff
2011-06-14	martinahansen	blast_seq_pair polish	tree \| commitdiff
2011-06-14	martinahansen	blast_seq_pair polish	tree \| commitdiff
2011-06-14	martinahansen	blast_seq_pair polish	tree \| commitdiff
2011-06-14	martinahansen	added blast_seq_pair	tree \| commitdiff
2011-06-06	martinahansen	fixed cat_seq	tree \| commitdiff
2011-06-06	martinahansen	added cat_seq biopiece	tree \| commitdiff
2011-05-31	martinahansen	added assemble_seq_ray	tree \| commitdiff
2011-05-30	martinahansen	upgraded mean_scores	tree \| commitdiff
2011-05-30	martinahansen	rename switch to something more appropriate	tree \| commitdiff
2011-05-30	martinahansen	removed unused code from find_adaptor	tree \| commitdiff
2011-05-29	martinahansen	squashing bugs in find_adaptor	tree \| commitdiff
2011-05-29	martinahansen	working on find_adaptor	tree \| commitdiff
2011-05-28	martinahansen	added multithreading to find_adaptor	tree \| commitdiff
2011-05-28	martinahansen	added multithreading to find_adaptor	tree \| commitdiff
2011-05-26	martinahansen	added order_pairs	tree \| commitdiff
2011-05-26	martinahansen	fixed type in assemble_seq_idba	tree \| commitdiff
2011-05-26	martinahansen	fixed mate-pair name issue in assemble_seq_idba	tree \| commitdiff
2011-05-25	martinahansen	added plot_distribution biopiece	tree \| commitdiff
2011-05-25	martinahansen	polished plot_scores	tree \| commitdiff
2011-05-24	martinahansen	fixed fence post bug in plot_lendist	tree \| commitdiff
2011-05-24	martinahansen	fixed strange bug in find_adaptor	tree \| commitdiff
2011-05-24	martinahansen	fixed asseble_seq_velvet	tree \| commitdiff
2011-05-24	martinahansen	fixed asseble_seq_idba	tree \| commitdiff
2011-05-23	martinahansen	polishing find_adaptor	tree \| commitdiff
2011-05-23	martinahansen	fixed critical flaw in find_adaptor	tree \| commitdiff
2011-05-23	martinahansen	fixed critical bug in biopieces.rb and reworked find_ad...	tree \| commitdiff
2011-05-23	martinahansen	committing major ruby overhaul	tree \| commitdiff
2011-05-18	martinahansen	fixed paths in assemble_seq_idba + velvet	tree \| commitdiff
2011-05-13	martinahansen	changed layout of ruby source	tree \| commitdiff
2011-05-13	martinahansen	add dist option to find_adaptor	tree \| commitdiff
2011-05-12	martinahansen	added offset switch to add_ident	tree \| commitdiff
2011-05-10	martinahansen	fixed type cast bug	tree \| commitdiff
2011-05-10	martinahansen	added procedure switch to analyze_assembly	tree \| commitdiff
2011-05-10	martinahansen	added procedure switch to find_genes	tree \| commitdiff
2011-05-10	martinahansen	polished analyze_assembly	tree \| commitdiff
2011-05-09	martinahansen	polishing gene cov feature in analyze_assembly	tree \| commitdiff
2011-05-09	martinahansen	added gene coverage to analyze_assembly	tree \| commitdiff
2011-05-09	martinahansen	added fix to find_genes	tree \| commitdiff
2011-05-09	martinahansen	ported find_genes to ruby	tree \| commitdiff
2011-05-09	martinahansen	fixed indentation in uclust_seq	tree \| commitdiff
2011-05-06	martinahansen	added full switch to find_genes	tree \| commitdiff
2011-05-06	martinahansen	removing sequence file from assemble_seq*	tree \| commitdiff
2011-05-05	martinahansen	polished asseble_seq_velvet	tree \| commitdiff
2011-05-05	martinahansen	removed name option from asseble_seq_idba	tree \| commitdiff
2011-05-04	martinahansen	added assemble_seq_velvet draft biopiece	tree \| commitdiff
2011-05-04	martinahansen	refactoring arg name in assemble_seq_idba	tree \| commitdiff
2011-05-04	martinahansen	added --clean to assemble_seq_idba	tree \| commitdiff
2011-05-03	martinahansen	polished assemble_seq_idba	tree \| commitdiff
2011-05-03	martinahansen	added assemble_seq_idba	tree \| commitdiff
2011-05-03	martinahansen	made plot_scores 1-based	tree \| commitdiff
2011-05-03	martinahansen	corrected plot_matches missing -persists switch	tree \| commitdiff
2011-05-03	martinahansen	added titles to plot_scores	tree \| commitdiff
2011-05-02	martinahansen	fixed typo in analyce_gc	tree \| commitdiff
2011-05-02	martinahansen	code update	tree \| commitdiff
2011-05-02	martinahansen	ported plot_scores to ruby	tree \| commitdiff
2011-05-02	martinahansen	removed redundant line from plot_scores	tree \| commitdiff
2011-05-02	martinahansen	testing unspecified features	tree \| commitdiff
2011-04-19	martinahansen	polishing find_adaptor	tree \| commitdiff
2011-04-19	martinahansen	added cache option to find_adaptor	tree \| commitdiff
2011-04-19	martinahansen	added cache option to find_adaptor	tree \| commitdiff
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