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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
2010-09-23	martinahansen	cleanup of uclust_seq	commit \| commitdiff \| tree
2010-09-22	martinahansen	polishing on uclust_seq	commit \| commitdiff \| tree
2010-09-21	martinahansen	added uclust_seq Biopiece - Work in progress!	commit \| commitdiff \| tree
2010-09-20	martinahansen	fixed typo in text in digest_seq	commit \| commitdiff \| tree
2010-09-20	martinahansen	fixes and test for digest_seq	commit \| commitdiff \| tree
2010-09-20	martinahansen	added digest_seq Biopiece	commit \| commitdiff \| tree
2010-09-17	martinahansen	added Digest class to ruby code	commit \| commitdiff \| tree
2010-09-16	martinahansen	added pcr_seq Biopiece	commit \| commitdiff \| tree
2010-09-16	martinahansen	added reverse method to ruby Seq class	commit \| commitdiff \| tree
2010-09-13	martinahansen	added bin_vals biopiece and tests	commit \| commitdiff \| tree
2010-09-09	martinahansen	ported length_seq to ruby	commit \| commitdiff \| tree
2010-09-09	martinahansen	fixing length_seq	commit \| commitdiff \| tree
2010-09-09	martinahansen	added Ruby version check	commit \| commitdiff \| tree
2010-09-09	martinahansen	slight fix of trailing newline in progress_meter	commit \| commitdiff \| tree
2010-09-09	martinahansen	slight fix of trailing newline in progress_meter	commit \| commitdiff \| tree
2010-09-09	martinahansen	slight fix of trailing newline in progress_meter	commit \| commitdiff \| tree
2010-09-09	martinahansen	slight fix of printf in progress_meter	commit \| commitdiff \| tree
2010-09-09	martinahansen	added progress_meter biopiece	commit \| commitdiff \| tree
2010-09-08	martinahansen	fixed minor bug in write_align of pairwise protein...	commit \| commitdiff \| tree
2010-09-02	martinahansen	added scores_to_dec biopiece, wiki, and tests	commit \| commitdiff \| tree
2010-09-01	martinahansen	reverting ruby unit test to old school	commit \| commitdiff \| tree
2010-09-01	martinahansen	added tests for mask_seq	commit \| commitdiff \| tree
2010-09-01	martinahansen	added mask_seq biopiece	commit \| commitdiff \| tree
2010-09-01	martinahansen	replaced option keys from strings to symbols in ruby...	commit \| commitdiff \| tree
2010-08-20	martinahansen	shifted ruby biopiece records to use symbols instead...	commit \| commitdiff \| tree
2010-08-18	martinahansen	added zip reading to read_fasta	commit \| commitdiff \| tree
2010-08-18	martinahansen	read_fasta now reads zipped fasta fails again	commit \| commitdiff \| tree
2010-08-17	martinahansen	updating test_read_fasta	commit \| commitdiff \| tree
2010-08-17	martinahansen	replacing read_fasta with ruby version	commit \| commitdiff \| tree
2010-08-17	martinahansen	replacing read_fasta with ruby version	commit \| commitdiff \| tree
2010-08-17	martinahansen	replacing read_fasta with ruby version	commit \| commitdiff \| tree
2010-08-17	martinahansen	replacing read_fasta with ruby version	commit \| commitdiff \| tree
2010-08-16	martinahansen	updating seq.rb	commit \| commitdiff \| tree
2010-08-16	martinahansen	updateing seq.rb	commit \| commitdiff \| tree
2010-08-13	martinahansen	fixed type bug in ruby code	commit \| commitdiff \| tree
2010-08-12	martinahansen	polishing testing suite	commit \| commitdiff \| tree
2010-08-12	martinahansen	added test for blast biopieces	commit \| commitdiff \| tree
2010-08-11	martinahansen	ruby code cleanup	commit \| commitdiff \| tree
2010-08-09	martinahansen	added lisence to ruby code	commit \| commitdiff \| tree
2010-08-06	martinahansen	added rdoc	commit \| commitdiff \| tree
2010-08-06	martinahansen	fixed ruby test code	commit \| commitdiff \| tree
2010-08-06	martinahansen	added swapcase_seq written in RUBY	commit \| commitdiff \| tree
2010-08-06	martinahansen	dropping swapcase_seq tobereplaced	commit \| commitdiff \| tree
2010-08-06	martinahansen	added test for analyze_gc	commit \| commitdiff \| tree
2010-08-06	martinahansen	ruby exit status battle part #12312423	commit \| commitdiff \| tree
2010-08-06	martinahansen	added -o option and tests to analyze_vals	commit \| commitdiff \| tree
2010-08-05	martinahansen	added test for add_ident	commit \| commitdiff \| tree
2010-08-05	martinahansen	added test_read_solexa to tests	commit \| commitdiff \| tree
2010-08-04	martinahansen	asdfasdr	commit \| commitdiff \| tree
2010-08-04	martinahansen	polishing ruby code	commit \| commitdiff \| tree
2010-08-04	martinahansen	added write_tab tests	commit \| commitdiff \| tree
2010-08-04	martinahansen	more polishing of testing suite	commit \| commitdiff \| tree
2010-08-04	martinahansen	removing binary crap	commit \| commitdiff \| tree
2010-08-04	martinahansen	polishing on testing suite	commit \| commitdiff \| tree
2010-08-03	martinahansen	added more tests	commit \| commitdiff \| tree
2010-08-03	martinahansen	had to fix shebang in testing env	commit \| commitdiff \| tree
2010-08-03	martinahansen	testing suite paths upgraded	commit \| commitdiff \| tree
2010-08-03	martinahansen	fixed first bug in testing suite	commit \| commitdiff \| tree
2010-08-03	martinahansen	added testing suite	commit \| commitdiff \| tree
2010-08-03	martinahansen	corrected slight bug in grab	commit \| commitdiff \| tree
2010-06-30	martinahansen	added trim_seq	commit \| commitdiff \| tree
2010-06-29	martinahansen	added biopieces mean_scores	commit \| commitdiff \| tree
2010-06-28	martinahansen	added ID to SCORE alias in KISS.pm	commit \| commitdiff \| tree
2010-06-28	martinahansen	added usearch_seq biopiece	commit \| commitdiff \| tree
2010-06-26	martinahansen	corrected typo	commit \| commitdiff \| tree
2010-06-22	martinahansen	messing with exit in ruby - still	commit \| commitdiff \| tree
2010-06-22	martinahansen	corrected type in log messages	commit \| commitdiff \| tree
2010-06-21	martinahansen	polishing exit in ruby code	commit \| commitdiff \| tree
2010-06-17	martinahansen	added list switch to *_vals biopieces	commit \| commitdiff \| tree
2010-06-17	martinahansen	added list switch to mean_vals	commit \| commitdiff \| tree
2010-06-17	martinahansen	added fixedstep biopieces	commit \| commitdiff \| tree
2010-06-16	martinahansen	schrubbing UCSC.pm code	commit \| commitdiff \| tree
2010-06-16	martinahansen	fixed s/Common/Filesys/ renaming in UCSC.pm	commit \| commitdiff \| tree
2010-06-16	martinahansen	ruby code fixing exit	commit \| commitdiff \| tree
2010-06-16	martinahansen	ruby code fixing exit	commit \| commitdiff \| tree
2010-06-15	martinahansen	ruby code schrubbing	commit \| commitdiff \| tree
2010-06-14	martinahansen	fixed unit tests for biopieces.rb	commit \| commitdiff \| tree
2010-05-28	martinahansen	trouble with list of list and class Cast	commit \| commitdiff \| tree
2010-05-28	martinahansen	splitting class Biopieces	commit \| commitdiff \| tree
2010-05-28	martinahansen	splitting class Biopieces	commit \| commitdiff \| tree
2010-05-28	martinahansen	updating ruby code	commit \| commitdiff \| tree
2010-05-28	martinahansen	cleaned up ruby dir	commit \| commitdiff \| tree
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