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2011-02-03	martinahansen	crude polish of shred_seq	commit \| commitdiff \| tree
2011-02-02	martinahansen	added echo_yellow to testing code	commit \| commitdiff \| tree
2011-02-01	martinahansen	added analyze_assembly biopiece	commit \| commitdiff \| tree
2011-02-01	martinahansen	added kmer_freq biopiece and tests	commit \| commitdiff \| tree
2011-02-01	martinahansen	added generate_oligos method to seq.rb	commit \| commitdiff \| tree
2011-01-31	martinahansen	python update?	commit \| commitdiff \| tree
2011-01-31	martinahansen	added tests of calc_N50	commit \| commitdiff \| tree
2011-01-31	martinahansen	fixed bug in calc_N50	commit \| commitdiff \| tree
2011-01-31	martinahansen	added calc_N50	commit \| commitdiff \| tree
2011-01-31	martinahansen	remove calc_n50	commit \| commitdiff \| tree
2011-01-31	martinahansen	removing calc_N50	commit \| commitdiff \| tree
2011-01-31	martinahansen	added calc_N50 biopiece	commit \| commitdiff \| tree
2011-01-31	martinahansen	add out accessor to Biopieces ruby code	commit \| commitdiff \| tree
2011-01-31	martinahansen	revoking data_out magic	commit \| commitdiff \| tree
2011-01-31	martinahansen	added :data_out magic to Biopeices ruby code	commit \| commitdiff \| tree
2011-01-30	martinahansen	polished shred_seq	commit \| commitdiff \| tree
2011-01-30	martinahansen	polished shred_seq	commit \| commitdiff \| tree
2011-01-29	martinahansen	fixed bug in shred_seq	commit \| commitdiff \| tree
2011-01-29	martinahansen	added shred_seq tests	commit \| commitdiff \| tree
2011-01-29	martinahansen	added shred_seq biopiece	commit \| commitdiff \| tree
2011-01-29	martinahansen	added version test of perl and ruby	commit \| commitdiff \| tree
2011-01-26	martinahansen	added warning in bashrc	commit \| commitdiff \| tree
2011-01-23	martinahansen	added Seq#to_key method	commit \| commitdiff \| tree
2011-01-22	martinahansen	changed seq names to 0 based in Digest#each	commit \| commitdiff \| tree
2011-01-22	martinahansen	updated tests for digest_seq	commit \| commitdiff \| tree
2011-01-22	martinahansen	added S_BEG and S_END keys to digest_seq	commit \| commitdiff \| tree
2011-01-22	martinahansen	fixed missing upcase bug in ruby Seq#Digest::each	commit \| commitdiff \| tree
2011-01-20	martinahansen	polish of bitarray.rb	commit \| commitdiff \| tree
2011-01-20	martinahansen	slight cleanup of find_gaps	commit \| commitdiff \| tree
2011-01-17	martinahansen	added tests for find_gaps	commit \| commitdiff \| tree
2011-01-17	martinahansen	fixed bug in Fasta.pm	commit \| commitdiff \| tree
2011-01-14	martinahansen	finishing unit tests for bitarray.rb	commit \| commitdiff \| tree
2011-01-14	martinahansen	fixed license text	commit \| commitdiff \| tree
2011-01-14	martinahansen	added S_LEN to find_gaps	commit \| commitdiff \| tree
2011-01-14	martinahansen	added bitarray ruby code	commit \| commitdiff \| tree
2011-01-12	martinahansen	posished Calc::standard_deviation	commit \| commitdiff \| tree
2011-01-10	martinahansen	fixed SEQ_LEN bug in transliterate_seq	commit \| commitdiff \| tree
2011-01-03	martinahansen	misq updates	commit \| commitdiff \| tree
2010-12-31	martinahansen	polishing find_mids	commit \| commitdiff \| tree
2010-12-21	martinahansen	fixed bug in bwa_seq	commit \| commitdiff \| tree
2010-12-17	martinahansen	added contributed biopieces calc_density	commit \| commitdiff \| tree
2010-12-16	martinahansen	added min option to find_homopolymers	commit \| commitdiff \| tree
2010-12-16	martinahansen	speedup fix of max_homopol again	commit \| commitdiff \| tree
2010-12-16	martinahansen	speedup fix of max_homopol	commit \| commitdiff \| tree
2010-12-16	martinahansen	added find_homopolymers biopiece	commit \| commitdiff \| tree
2010-12-13	martinahansen	added QA_Solexa_report.sh	commit \| commitdiff \| tree
2010-12-13	martinahansen	added QA_454_report.sh biopiece script	commit \| commitdiff \| tree
2010-12-10	martinahansen	added join_seq biopiece	commit \| commitdiff \| tree
2010-12-10	martinahansen	genbank.rb fixes	commit \| commitdiff \| tree
2010-12-10	martinahansen	added shuffle_records	commit \| commitdiff \| tree
2010-12-09	martinahansen	fixed get_seq in genbank.rb	commit \| commitdiff \| tree
2010-12-09	martinahansen	fixed another locator bug in genbank.rb	commit \| commitdiff \| tree
2010-12-09	martinahansen	fixed cryptic bug in genbank.rb	commit \| commitdiff \| tree
2010-12-09	martinahansen	fixed cryptic bug in genbank.rb	commit \| commitdiff \| tree
2010-12-09	martinahansen	small safety add in genbank.rb	commit \| commitdiff \| tree
2010-12-09	martinahansen	fixed read_genbank tests	commit \| commitdiff \| tree
2010-12-09	martinahansen	fixed genbank.rb	commit \| commitdiff \| tree
2010-12-09	martinahansen	fixed genbank.rb	commit \| commitdiff \| tree
2010-12-08	martinahansen	added read_genbank	commit \| commitdiff \| tree
2010-11-24	martinahansen	added tests for translate_seq	commit \| commitdiff \| tree
2010-11-24	martinahansen	added tests for uniq_seq	commit \| commitdiff \| tree
2010-11-18	martinahansen	fixed bug in uclust_seq	commit \| commitdiff \| tree
2010-11-18	martinahansen	added --comp switch to uclust_seq	commit \| commitdiff \| tree
2010-11-14	martinahansen	adding 00README file to code_ruby dir	commit \| commitdiff \| tree
2010-11-14	martinahansen	added 00README to bp_test directory	commit \| commitdiff \| tree
2010-11-10	martinahansen	fixed find_mids to locate even low q mids	commit \| commitdiff \| tree
2010-11-09	martinahansen	added roche MID tags to find_mids	commit \| commitdiff \| tree
2010-11-02	martinahansen	added find_mids biopiece tests	commit \| commitdiff \| tree
2010-11-02	martinahansen	fixed bug in find_mids	commit \| commitdiff \| tree
2010-11-02	martinahansen	added find_mids biopiece	commit \| commitdiff \| tree
2010-11-02	martinahansen	fixed bug in clip_seq	commit \| commitdiff \| tree
2010-11-02	martinahansen	added clip_seq biopiece	commit \| commitdiff \| tree
2010-11-01	martinahansen	removing patscan ruby crap	commit \| commitdiff \| tree
2010-11-01	martinahansen	added patfind.rb	commit \| commitdiff \| tree
2010-10-31	martinahansen	fixed aliases in bashrc	commit \| commitdiff \| tree
2010-10-20	martinahansen	added patscan.rb	commit \| commitdiff \| tree
2010-10-15	martinahansen	polishing min max sum etc	commit \| commitdiff \| tree
2010-10-15	martinahansen	polished sum_vals and added tests	commit \| commitdiff \| tree
2010-10-15	martinahansen	added tests for mean_vals	commit \| commitdiff \| tree
2010-10-15	martinahansen	add tests for analyze_seq	commit \| commitdiff \| tree
2010-10-15	martinahansen	trouble shooting buffering problem	commit \| commitdiff \| tree
2010-10-14	martinahansen	ported analyze_seq to ruby	commit \| commitdiff \| tree
2010-10-14	martinahansen	ported analyze_seq to ruby	commit \| commitdiff \| tree
2010-10-13	martinahansen	fixed scores in bwa_seq	commit \| commitdiff \| tree
2010-10-13	martinahansen	removed local logging causing trouble	commit \| commitdiff \| tree
2010-10-13	martinahansen	fixed SAM.pm qual scores from phred-33 to phred-64	commit \| commitdiff \| tree
2010-10-13	martinahansen	changed bowtie_seq to use phred64	commit \| commitdiff \| tree
2010-10-13	martinahansen	polished read_454 and added tests	commit \| commitdiff \| tree
2010-10-13	martinahansen	polished plot_scores	commit \| commitdiff \| tree
2010-10-12	martinahansen	added align ruby lib	commit \| commitdiff \| tree
2010-10-12	martinahansen	added fastq ruby lib	commit \| commitdiff \| tree
2010-10-12	martinahansen	polished write_fastq	commit \| commitdiff \| tree
2010-10-12	martinahansen	slight bug fix of write_fastq	commit \| commitdiff \| tree
2010-10-12	martinahansen	upgraded scores_to_dec	commit \| commitdiff \| tree
2010-10-12	martinahansen	upgraded mask_seq	commit \| commitdiff \| tree
2010-10-12	martinahansen	added solexa switch to read_fastq	commit \| commitdiff \| tree
2010-10-12	martinahansen	upgraded read_fastq and added tests	commit \| commitdiff \| tree
2010-10-11	martinahansen	upgraded find_genes	commit \| commitdiff \| tree
2010-09-28	martinahansen	AlignTwoSeq.pm briefly revisited	commit \| commitdiff \| tree
2010-09-28	martinahansen	fixed indentation in perl code	commit \| commitdiff \| tree
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