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2013-11-29	martinahansen	added tests to find_orfs	commit \| commitdiff \| tree
2013-11-29	martinahansen	fixed another each_orf bug	commit \| commitdiff \| tree
2013-11-29	martinahansen	fixed bug in find_orfs	commit \| commitdiff \| tree
2013-11-29	martinahansen	added slice_align biopiece	commit \| commitdiff \| tree
2013-11-25	martinahansen	fixed encoding bug in read_454	commit \| commitdiff \| tree
2013-11-25	martinahansen	fixed encoding in write_454	commit \| commitdiff \| tree
2013-11-25	martinahansen	plot_scores max length set to 100K	commit \| commitdiff \| tree
2013-11-07	martinahansen	fixed installer issue	commit \| commitdiff \| tree
2013-10-30	martinahansen	fixed bug in pair assembler	commit \| commitdiff \| tree
2013-10-30	martinahansen	added patscan_trim method to Seq	commit \| commitdiff \| tree
2013-10-25	martinahansen	fixed analyze_vals issue	commit \| commitdiff \| tree
2013-10-25	martinahansen	added -o and -x to analyze_vals	commit \| commitdiff \| tree
2013-10-24	martinahansen	refactored backtrack methods to use options hash in...	commit \| commitdiff \| tree
2013-10-24	martinahansen	fixed Seq object creation in sff.rb	commit \| commitdiff \| tree
2013-10-24	martinahansen	now using roche mid module for find_barcodes	commit \| commitdiff \| tree
2013-10-24	martinahansen	added roche mid module	commit \| commitdiff \| tree
2013-10-24	martinahansen	adding table.rb	commit \| commitdiff \| tree
2013-10-23	martinahansen	removed commented out stale code	commit \| commitdiff \| tree
2013-10-18	martinahansen	fixed method name change	commit \| commitdiff \| tree
2013-10-17	martinahansen	fixed QA_454_report.rb to work with new analyze_vals	commit \| commitdiff \| tree
2013-10-17	martinahansen	fixed QA_454_report.rb to work with new analyze_vals	commit \| commitdiff \| tree
2013-10-17	martinahansen	fixed QA_454_report.rb to work with new analyze_vals	commit \| commitdiff \| tree
2013-10-17	martinahansen	fixed QA_454_report.rb to work with new analyze_vals	commit \| commitdiff \| tree
2013-10-16	martinahansen	cleanup of analyze_vals added analyze_scores	commit \| commitdiff \| tree
2013-10-15	martinahansen	rewrote analyze_vals	commit \| commitdiff \| tree
2013-10-15	martinahansen	rewrote write_tab	commit \| commitdiff \| tree
2013-10-15	martinahansen	rewrote write_tab	commit \| commitdiff \| tree
2013-10-08	martinahansen	refactoring of assemble_pairs	commit \| commitdiff \| tree
2013-10-08	martinahansen	fixed seq qual length check	commit \| commitdiff \| tree
2013-10-07	martinahansen	DRY refactorying of backtrack code	commit \| commitdiff \| tree
2013-10-07	martinahansen	gzip fiddling	commit \| commitdiff \| tree
2013-10-07	martinahansen	exchanged zlib code with commandline gzip	commit \| commitdiff \| tree
2013-10-07	martinahansen	fixed symlink flaw in file type detection	commit \| commitdiff \| tree
2013-10-01	martinahansen	changed Seq.new argument to hash	commit \| commitdiff \| tree
2013-09-26	martinahansen	added test for length of seq/qual mismatch	commit \| commitdiff \| tree
2013-09-26	martinahansen	disabling buggy bzip2-ruby	commit \| commitdiff \| tree
2013-09-26	martinahansen	temporary fix of bzip2 read problem	commit \| commitdiff \| tree
2013-09-26	martinahansen	added prefix option to write_fasta_files and write_fastq_files	commit \| commitdiff \| tree
2013-09-25	martinahansen	added bzip2-ruby gem requirement	commit \| commitdiff \| tree
2013-09-25	martinahansen	added bzip2-ruby gem requirement	commit \| commitdiff \| tree
2013-09-25	martinahansen	added gzip/bzip2 output option to write_fastq_files	commit \| commitdiff \| tree
2013-09-25	martinahansen	added support for gzip/bzip2 in write_fasta_files ...	commit \| commitdiff \| tree
2013-09-25	martinahansen	ported write_fasta to ruby enabling bzip2 support	commit \| commitdiff \| tree
2013-09-25	martinahansen	added bzip output test to write_fastq	commit \| commitdiff \| tree
2013-09-25	martinahansen	adding bzip2 support in ruby	commit \| commitdiff \| tree
2013-09-23	martinahansen	fixed isseu in find_orphans	commit \| commitdiff \| tree
2013-09-23	martinahansen	created find_orphans Biopiece	commit \| commitdiff \| tree
2013-09-18	martinahansen	beautifing ambiguity.rb	commit \| commitdiff \| tree
2013-09-18	martinahansen	implemented hamming_dist in inline C	commit \| commitdiff \| tree
2013-09-18	martinahansen	add comments to ambiguity.rb	commit \| commitdiff \| tree
2013-09-18	martinahansen	fixed broken tests not workin with Ruby2	commit \| commitdiff \| tree
2013-09-18	martinahansen	added amiguity.rb	commit \| commitdiff \| tree
2013-09-18	martinahansen	added mem.rb	commit \| commitdiff \| tree
2013-09-18	martinahansen	added ambiguity to hamming_distance	commit \| commitdiff \| tree
2013-09-16	martinahansen	fixed overlap bug in patscan_seq	commit \| commitdiff \| tree
2013-09-13	martinahansen	added missing cpus switch to uclust_seq	commit \| commitdiff \| tree
2013-09-09	martinahansen	polish usearch_seq	commit \| commitdiff \| tree
2013-09-09	martinahansen	polish uclust_seq	commit \| commitdiff \| tree
2013-09-09	martinahansen	fixing usearch upgrade	commit \| commitdiff \| tree
2013-09-06	martinahansen	upgraded uclust_seq to support usearch7	commit \| commitdiff \| tree
2013-06-24	martinahansen	fixed genbank and embl parsing of 5'UTR and 3'UTR	commit \| commitdiff \| tree
2013-06-24	martinahansen	added \r remove hack to genbank/embl parsers	commit \| commitdiff \| tree
2013-06-23	martinahansen	moved inline C code to seperate file	commit \| commitdiff \| tree
2013-06-21	martinahansen	added edit_distance method to seq.rb	commit \| commitdiff \| tree
2013-06-21	martinahansen	fixed ambiguity in levenshtein.rb	commit \| commitdiff \| tree
2013-06-20	martinahansen	added levenshtein edit distance calculator	commit \| commitdiff \| tree
2013-06-20	martinahansen	added levenshtein edit distance calculator	commit \| commitdiff \| tree
2013-06-20	martinahansen	added levenshtein edit distance calculator	commit \| commitdiff \| tree
2013-06-17	martinahansen	updated patscan_seq	commit \| commitdiff \| tree
2013-06-17	martinahansen	updated patscan_seq	commit \| commitdiff \| tree
2013-06-04	martinahansen	added missing files	commit \| commitdiff \| tree
2013-06-04	martinahansen	revamped find_homopolymers	commit \| commitdiff \| tree
2013-05-16	martinahansen	more verbose grab output	commit \| commitdiff \| tree
2013-05-16	martinahansen	added verbose count to grab	commit \| commitdiff \| tree
2013-05-06	martinahansen	fixed QA_Illumina_report.rb encoding	commit \| commitdiff \| tree
2013-04-29	martinahansen	fixed missing BP_TMP dir feature	commit \| commitdiff \| tree
2013-04-18	martinahansen	fixed divide bug in compute	commit \| commitdiff \| tree
2013-04-11	martinahansen	fixed bug in index_vals	commit \| commitdiff \| tree
2013-04-11	martinahansen	added index_vals biopiece	commit \| commitdiff \| tree
2013-03-20	martinahansen	corrected pcr_seq revcomp of patterns	commit \| commitdiff \| tree
2013-03-16	martinahansen	changed upper/lower case output in assemble_pairs	commit \| commitdiff \| tree
2013-03-13	martinahansen	dropped pandaseq requirement	commit \| commitdiff \| tree
2013-03-13	martinahansen	fixed minor upcase bug in assemble.rb	commit \| commitdiff \| tree
2013-03-13	martinahansen	upgraded tests of read_sff	commit \| commitdiff \| tree
2013-03-13	martinahansen	finish assemble_pairs revamp	commit \| commitdiff \| tree
2013-03-13	martinahansen	assemble_pairs revamp	commit \| commitdiff \| tree
2013-03-13	martinahansen	added comments to code	commit \| commitdiff \| tree
2013-03-13	martinahansen	added name check to assemble_pairs2	commit \| commitdiff \| tree
2013-03-13	martinahansen	added check for minimum seq length	commit \| commitdiff \| tree
2013-03-13	martinahansen	added check for minimum seq length	commit \| commitdiff \| tree
2013-03-13	martinahansen	fixed defaults and key names	commit \| commitdiff \| tree
2013-03-13	martinahansen	upgraded assemble.rb to chose proper residue when mismatch	commit \| commitdiff \| tree
2013-03-13	martinahansen	added hacky thing to avoid warning from zlib	commit \| commitdiff \| tree
2013-03-12	martinahansen	added keys to assemble_pairs2	commit \| commitdiff \| tree
2013-03-12	martinahansen	added assemble_pairs2	commit \| commitdiff \| tree
2013-03-12	martinahansen	added seq/assemble.rb	commit \| commitdiff \| tree
2013-03-12	martinahansen	fixed score base bug in sff.rb	commit \| commitdiff \| tree
2013-03-11	martinahansen	added word_size switch to blast_seq_pair	commit \| commitdiff \| tree
2013-03-11	martinahansen	changed blast_seq_pair to do multiple pairs	commit \| commitdiff \| tree
2013-03-11	martinahansen	added [] og []= to seq.rb	commit \| commitdiff \| tree
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