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2011-12-12	martinahansen	added new read_embl (ruby)	commit \| commitdiff \| tree
2011-12-12	martinahansen	removed old read_embl (perl)	commit \| commitdiff \| tree
2011-12-12	martinahansen	added embl.rb	commit \| commitdiff \| tree
2011-12-12	martinahansen	split off locator stuff from genbank.rb to locator.rb	commit \| commitdiff \| tree
2011-12-08	martinahansen	added check for duplicate keys in replace_vals	commit \| commitdiff \| tree
2011-12-08	martinahansen	added replace_vals biopiece	commit \| commitdiff \| tree
2011-12-07	martinahansen	added new biopeice remove_indel_columns	commit \| commitdiff \| tree
2011-12-07	martinahansen	minor tweak to genbank.rb	commit \| commitdiff \| tree
2011-12-06	martinahansen	fixed count bug in sff.rb	commit \| commitdiff \| tree
2011-12-06	martinahansen	minor tweaks added to installer	commit \| commitdiff \| tree
2011-12-05	martinahansen	upgraded mask_seq	commit \| commitdiff \| tree
2011-11-25	martinahansen	cleanup of usearch.rb	commit \| commitdiff \| tree
2011-11-25	martinahansen	moved usearch code to external file	commit \| commitdiff \| tree
2011-11-24	martinahansen	removed bp_doc/ and content	commit \| commitdiff \| tree
2011-11-24	martinahansen	fixed regex in backtrack.rb	commit \| commitdiff \| tree
2011-11-23	martinahansen	removed stale unit tests from test_biopieces.rb	commit \| commitdiff \| tree
2011-11-23	martinahansen	fixed glob unit test in test_biopieces.rb	commit \| commitdiff \| tree
2011-11-23	martinahansen	removed comma	commit \| commitdiff \| tree
2011-11-22	martinahansen	got rid of nasty to_sym in biopieces.rb	commit \| commitdiff \| tree
2011-11-22	martinahansen	got rid of nasty to_sym in biopieces.rb	commit \| commitdiff \| tree
2011-11-22	martinahansen	got rid of type in filesys.rb	commit \| commitdiff \| tree
2011-11-22	martinahansen	beautifying backtrack.rb	commit \| commitdiff \| tree
2011-11-22	martinahansen	slight cleanup of backtrack code	commit \| commitdiff \| tree
2011-11-21	martinahansen	made --rev defacto in useach_seq	commit \| commitdiff \| tree
2011-11-21	martinahansen	upgraded usearch_seq	commit \| commitdiff \| tree
2011-11-21	martinahansen	added tests for uclust_seq	commit \| commitdiff \| tree
2011-11-19	martinahansen	fixed bug in uniq_vals causing clusters named 0 to...	commit \| commitdiff \| tree
2011-11-18	martinahansen	rewriting uclust_seq	commit \| commitdiff \| tree
2011-11-17	martinahansen	fixed bug in grab	commit \| commitdiff \| tree
2011-11-17	martinahansen	added tests to remove_primers	commit \| commitdiff \| tree
2011-11-17	martinahansen	fixed remove_primers	commit \| commitdiff \| tree
2011-11-17	martinahansen	fixed bug in remove_primers	commit \| commitdiff \| tree
2011-11-17	martinahansen	added remove_primers biopiece	commit \| commitdiff \| tree
2011-11-17	martinahansen	fixed stupid windows \r bug in Patscan::read_patterns	commit \| commitdiff \| tree
2011-11-17	martinahansen	added requirement of RubyInline	commit \| commitdiff \| tree
2011-11-17	martinahansen	fixed ins/del reverse	commit \| commitdiff \| tree
2011-11-16	martinahansen	fixed FLAG bug in sam.rb	commit \| commitdiff \| tree
2011-11-16	martinahansen	disabled inline	commit \| commitdiff \| tree
2011-11-16	martinahansen	fixed bug in backtrack.rb	commit \| commitdiff \| tree
2011-11-15	martinahansen	fixed digest.rb	commit \| commitdiff \| tree
2011-11-15	martinahansen	added backtrack.rb	commit \| commitdiff \| tree
2011-11-15	martinahansen	added backtrack.rb	commit \| commitdiff \| tree
2011-11-14	martinahansen	upgraded uclust_seq to work with useach 5.1.221	commit \| commitdiff \| tree
2011-11-13	martinahansen	added backtrack.rb	commit \| commitdiff \| tree
2011-11-13	martinahansen	fixed digest_seq	commit \| commitdiff \| tree
2011-11-13	martinahansen	cleaning up digest.rb	commit \| commitdiff \| tree
2011-11-09	martinahansen	added Backtrack.pm	commit \| commitdiff \| tree
2011-11-09	martinahansen	fixed bug in seq.to_fasta	commit \| commitdiff \| tree
2011-11-09	martinahansen	fixed bugs in installer	commit \| commitdiff \| tree
2011-11-08	martinahansen	fixed bug in QA_454_report.rb	commit \| commitdiff \| tree
2011-11-07	martinahansen	added ruby version of read_sam	commit \| commitdiff \| tree
2011-11-07	martinahansen	removed perl version of read_sam	commit \| commitdiff \| tree
2011-11-02	martinahansen	added length check to bowtie_seq	commit \| commitdiff \| tree
2011-11-02	martinahansen	added length check to bowtie_seq	commit \| commitdiff \| tree
2011-11-02	martinahansen	fixed qual argument for bowtie on fasta only	commit \| commitdiff \| tree
2011-11-01	martinahansen	added quality_trim to seq.rb along with unit tests	commit \| commitdiff \| tree
2011-11-01	martinahansen	fixed unit tests for reverse and revcomp in seq.rb	commit \| commitdiff \| tree
2011-11-01	martinahansen	fixed return on reverse_complement in seq.rb	commit \| commitdiff \| tree
2011-10-31	martinahansen	added metagenome flag to assemble_seq_idba	commit \| commitdiff \| tree
2011-10-28	martinahansen	added reversing of qual to reverse	commit \| commitdiff \| tree
2011-10-27	martinahansen	removed biopieces find_mids remove_mids read_solexa	commit \| commitdiff \| tree
2011-10-27	martinahansen	added QA_454_report ruby script	commit \| commitdiff \| tree
2011-10-25	martinahansen	added find_barcodes biopiece	commit \| commitdiff \| tree
2011-10-25	martinahansen	added png terminal to plot_histogram	commit \| commitdiff \| tree
2011-10-23	martinahansen	updated biopieces_installer - adding bash check	commit \| commitdiff \| tree
2011-10-22	martinahansen	added version number to biopieces_installer	commit \| commitdiff \| tree
2011-10-22	martinahansen	added more control to appending of .bashrc in biopieces_inst...	commit \| commitdiff \| tree
2011-10-21	martinahansen	added shuffle! method to seq.rb	commit \| commitdiff \| tree
2011-10-20	martinahansen	ported trim_seq to ruby and added tests	commit \| commitdiff \| tree
2011-10-19	martinahansen	updated biopieces_installer.sh	commit \| commitdiff \| tree
2011-10-19	martinahansen	revoked to old working version of each_interval in...	commit \| commitdiff \| tree
2011-10-19	martinahansen	worked on each_interval, but still too slow	commit \| commitdiff \| tree
2011-10-19	martinahansen	speed optimized interval_set and interval_unset in...	commit \| commitdiff \| tree
2011-10-18	martinahansen	rewrote interval_set in bitarray.rb = 20 x faster	commit \| commitdiff \| tree
2011-10-18	martinahansen	memory optimization on bitarray.rb	commit \| commitdiff \| tree
2011-10-17	martinahansen	added more methods to bitarray.rb	commit \| commitdiff \| tree
2011-10-17	martinahansen	added methods to bitarray.rb	commit \| commitdiff \| tree
2011-10-17	martinahansen	bitarray.rb bits_on method speedup x 3	commit \| commitdiff \| tree
2011-10-17	martinahansen	cleanup of bitarray.rb	commit \| commitdiff \| tree
2011-10-17	martinahansen	changed bitwise operators in bitarray to inline	commit \| commitdiff \| tree
2011-10-17	martinahansen	upgraded bitarray to work with narray for speed	commit \| commitdiff \| tree
2011-10-17	martinahansen	added comment to bitarray.rb	commit \| commitdiff \| tree
2011-10-14	martinahansen	fixed biopieces installer	commit \| commitdiff \| tree
2011-10-14	martinahansen	slight change to installer	commit \| commitdiff \| tree
2011-10-14	martinahansen	added biopieces installer	commit \| commitdiff \| tree
2011-10-14	martinahansen	fixed critical missing uc bug in uniq_seq	commit \| commitdiff \| tree
2011-10-13	martinahansen	fixed fastq issue	commit \| commitdiff \| tree
2011-10-13	martinahansen	fixed last of fasta problems	commit \| commitdiff \| tree
2011-10-13	martinahansen	fixed assemblers	commit \| commitdiff \| tree
2011-10-13	martinahansen	fixing broken biopieces	commit \| commitdiff \| tree
2011-10-13	martinahansen	smoothed ruby code to get rid of warnings	commit \| commitdiff \| tree
2011-10-13	martinahansen	beautifying fasta.rb	commit \| commitdiff \| tree
2011-10-13	martinahansen	added Class method Seq.new_bp to seq.rb	commit \| commitdiff \| tree
2011-10-13	martinahansen	added to_fastq method seq.rb	commit \| commitdiff \| tree
2011-10-12	martinahansen	adding tests for write_fastq_files	commit \| commitdiff \| tree
2011-10-12	martinahansen	added write_fastq_files	commit \| commitdiff \| tree
2011-10-12	martinahansen	added crufty puts method to fastq.rb	commit \| commitdiff \| tree
2011-10-12	martinahansen	variable rename	commit \| commitdiff \| tree
2011-10-12	martinahansen	evil sort fix needed for assert_no_diff_dir	commit \| commitdiff \| tree
2011-10-12	martinahansen	fixed .svn dir issue with assert_no_diff_dir	commit \| commitdiff \| tree
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