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

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
2012-04-11	martinahansen	ported write_fastq to ruby and allowed different encodi...	tree \| commitdiff
2012-04-11	martinahansen	cleanup in read_fastq	tree \| commitdiff
2012-04-10	martinahansen	fixed comment	tree \| commitdiff
2012-04-10	martinahansen	upgraded read_fastq to handle illumina1.8 better	tree \| commitdiff
2012-03-20	martinahansen	fixed issues in bwa_seq	tree \| commitdiff
2012-03-13	martinahansen	fixed dir in bwa_seq	tree \| commitdiff
2012-03-13	martinahansen	ported bwa_seq to ruby for better SAM support	tree \| commitdiff
2012-03-02	martinahansen	major upgrade of denoise_seq	tree \| commitdiff
2012-02-23	martinahansen	added duplicate_record biopiece	tree \| commitdiff
2012-02-07	martinahansen	added raw data reading to read_fasta and read_fastq	tree \| commitdiff
2012-02-03	martinahansen	added denoise_seq	tree \| commitdiff
2012-01-23	martinahansen	fixed broken pcr_seq	tree \| commitdiff
2012-01-03	martinahansen	fixed issue in compute	tree \| commitdiff
2012-01-03	martinahansen	fixed issue in compute	tree \| commitdiff
2012-01-02	martinahansen	fixed missing ; in create_blast_index	tree \| commitdiff
2011-12-29	martinahansen	added extra RL tags to find_barcodes	tree \| commitdiff
2011-12-22	martinahansen	increaded database size for blast	tree \| commitdiff
2011-12-15	martinahansen	fixed typo in replace_vals	tree \| commitdiff
2011-12-15	martinahansen	fixed typo in replace_vals	tree \| commitdiff
2011-12-12	martinahansen	added new read_embl (ruby)	tree \| commitdiff
2011-12-12	martinahansen	removed old read_embl (perl)	tree \| commitdiff
2011-12-08	martinahansen	added check for duplicate keys in replace_vals	tree \| commitdiff
2011-12-08	martinahansen	added replace_vals biopiece	tree \| commitdiff
2011-12-07	martinahansen	added new biopeice remove_indel_columns	tree \| commitdiff
2011-12-05	martinahansen	upgraded mask_seq	tree \| commitdiff
2011-11-25	martinahansen	moved usearch code to external file	tree \| commitdiff
2011-11-23	martinahansen	removed comma	tree \| commitdiff
2011-11-22	martinahansen	got rid of nasty to_sym in biopieces.rb	tree \| commitdiff
2011-11-21	martinahansen	made --rev defacto in useach_seq	tree \| commitdiff
2011-11-21	martinahansen	upgraded usearch_seq	tree \| commitdiff
2011-11-19	martinahansen	fixed bug in uniq_vals causing clusters named 0 to...	tree \| commitdiff
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
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