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2009-08-10	martinahansen	added --no_gaps switch in blast_seq	commit \| commitdiff \| tree
2009-08-04	martinahansen	added a skip_scores switch to read_solexa and read_fastq	commit \| commitdiff \| tree
2009-08-02	martinahansen	fix embl parser	commit \| commitdiff \| tree
2009-08-02	martinahansen	finishing read_embl	commit \| commitdiff \| tree
2009-08-02	martinahansen	added get_embl_entry	commit \| commitdiff \| tree
2009-07-29	martinahansen	added embl_index	commit \| commitdiff \| tree
2009-07-29	martinahansen	added .biopiecesrc	commit \| commitdiff \| tree
2009-07-28	martinahansen	finished write_mysql	commit \| commitdiff \| tree
2009-07-28	martinahansen	changed read_solexa	commit \| commitdiff \| tree
2009-07-28	martinahansen	added quality threshold to read_fastq	commit \| commitdiff \| tree
2009-07-27	martinahansen	added write_mysql	commit \| commitdiff \| tree
2009-07-27	martinahansen	fixed list_mysql_databases	commit \| commitdiff \| tree
2009-07-27	martinahansen	added list_mysql_databases	commit \| commitdiff \| tree
2009-07-25	martinahansen	fixed feature in analyze_vals, issue 3	commit \| commitdiff \| tree
2009-07-24	martinahansen	fixed Gwiki colors	commit \| commitdiff \| tree
2009-07-23	martinahansen	fixed bowtie_seq	commit \| commitdiff \| tree
2009-07-23	martinahansen	fixed bowtie_seq	commit \| commitdiff \| tree
2009-07-23	martinahansen	added Bowtie.pm	commit \| commitdiff \| tree
2009-07-23	martinahansen	added create_bowtie_index	commit \| commitdiff \| tree
2009-07-23	martinahansen	added verbose stuff to bowtie_seq	commit \| commitdiff \| tree
2009-07-23	martinahansen	added verbose stuff to format_genome	commit \| commitdiff \| tree
2009-07-23	martinahansen	addid term colors to list_genomes	commit \| commitdiff \| tree
2009-07-23	martinahansen	added options to bowtie_seq	commit \| commitdiff \| tree
2009-07-22	martinahansen	added some args to bowtie_seq	commit \| commitdiff \| tree
2009-07-21	martinahansen	added test_common.c	commit \| commitdiff \| tree
2009-07-21	martinahansen	fixed bowtie_seq	commit \| commitdiff \| tree
2009-07-21	martinahansen	added read_fastq biopiece	commit \| commitdiff \| tree
2009-07-20	martinahansen	added bowtie_seq biopiece	commit \| commitdiff \| tree
2009-07-20	martinahansen	added bowtie to format_genome	commit \| commitdiff \| tree
2009-07-19	martinahansen	adding to ruby source	commit \| commitdiff \| tree
2009-07-12	martinahansen	more ruby stuff	commit \| commitdiff \| tree
2009-07-11	martinahansen	fixed bug in read_embl	commit \| commitdiff \| tree
2009-07-10	martinahansen	speedup of analyze_seq 3 fold	commit \| commitdiff \| tree
2009-07-10	martinahansen	added str_analyze to Common.pm	commit \| commitdiff \| tree
2009-07-10	martinahansen	fixed bug in create_vmatch_index	commit \| commitdiff \| tree
2009-07-10	martinahansen	fixed bug in remove_indels	commit \| commitdiff \| tree
2009-07-10	martinahansen	mucking with c and makefiles	commit \| commitdiff \| tree
2009-07-08	martinahansen	use warnings added to perl modules	commit \| commitdiff \| tree
2009-07-08	martinahansen	added use strict to all biopieces	commit \| commitdiff \| tree
2009-07-08	martinahansen	changed shebang	commit \| commitdiff \| tree
2009-07-07	martinahansen	minor changes	commit \| commitdiff \| tree
2009-07-04	martinahansen	updated seq.rb	commit \| commitdiff \| tree
2009-07-03	martinahansen	last cleanups	commit \| commitdiff \| tree
2009-07-03	martinahansen	clearning ruby dir	commit \| commitdiff \| tree
2009-07-01	martinahansen	changed seq_type from string to symbols in ruby	commit \| commitdiff \| tree
2009-07-01	martinahansen	changed seq_type from string to symbols in ruby	commit \| commitdiff \| tree
2009-06-30	martinahansen	updated ruby code	commit \| commitdiff \| tree
2009-06-30	martinahansen	cleanded up test_seq.rb	commit \| commitdiff \| tree
2009-06-30	martinahansen	added unit testing for ruby	commit \| commitdiff \| tree
2009-06-30	martinahansen	added unit testing for ruby	commit \| commitdiff \| tree
2009-06-30	martinahansen	added unit testing for ruby	commit \| commitdiff \| tree
2009-06-29	martinahansen	added seq.rb	commit \| commitdiff \| tree
2009-06-23	martinahansen	fixes and stuff	commit \| commitdiff \| tree
2009-06-17	martinahansen	fixed a number of bugs in PSL	commit \| commitdiff \| tree
2009-06-16	martinahansen	fixed perl5.10 issue for soft parser	commit \| commitdiff \| tree
2009-06-16	martinahansen	added VMATCH support to get_genome_seq	commit \| commitdiff \| tree
2009-06-16	martinahansen	fixed bug in time_stamp_diff	commit \| commitdiff \| tree
2009-06-15	martinahansen	added indel_seq	commit \| commitdiff \| tree
2009-06-15	martinahansen	added mutate_seq	commit \| commitdiff \| tree
2009-06-15	martinahansen	added non-overlapping feature to split_seq	commit \| commitdiff \| tree
2009-06-15	martinahansen	fixed bug in Fasta.pm	commit \| commitdiff \| tree
2009-06-11	martinahansen	added Data::Dumper support to bioscript	commit \| commitdiff \| tree
2009-06-09	martinahansen	fixed bug in plot_histogram	commit \| commitdiff \| tree
2009-06-09	martinahansen	fixed bug in read_tab	commit \| commitdiff \| tree
2009-06-08	martinahansen	rewrote bioscript	commit \| commitdiff \| tree
2009-06-08	martinahansen	rewrote bioscript	commit \| commitdiff \| tree
2009-06-08	martinahansen	fixed minor bugs	commit \| commitdiff \| tree
2009-06-06	martinahansen	fixed bug in format_genome	commit \| commitdiff \| tree
2009-06-06	martinahansen	fixes but in removal of tmp_dir	commit \| commitdiff \| tree
2009-06-06	martinahansen	fixes done to tmp_dir	commit \| commitdiff \| tree
2009-06-06	martinahansen	implementing status solution	commit \| commitdiff \| tree
2009-06-06	martinahansen	removed variables bulk type	commit \| commitdiff \| tree
2009-06-06	martinahansen	fixing status	commit \| commitdiff \| tree
2009-06-05	martinahansen	added align_pair_seq	commit \| commitdiff \| tree
2009-06-05	martinahansen	migration done	commit \| commitdiff \| tree
2009-06-05	martinahansen	almost done	commit \| commitdiff \| tree
2009-06-05	martinahansen	migrated removers	commit \| commitdiff \| tree
2009-06-05	martinahansen	migrated upload_to_ucsc	commit \| commitdiff \| tree
2009-06-04	martinahansen	almost there	commit \| commitdiff \| tree
2009-06-04	martinahansen	fixed a couple of bugs - good	commit \| commitdiff \| tree
2009-06-04	martinahansen	fixed bug in sort_records	commit \| commitdiff \| tree
2009-06-02	martinahansen	bleh blah	commit \| commitdiff \| tree
2009-06-02	martinahansen	deleting read_phastcons	commit \| commitdiff \| tree
2009-06-02	martinahansen	remove bin dir	commit \| commitdiff \| tree
2009-06-02	martinahansen	3 more again	commit \| commitdiff \| tree
2009-06-02	martinahansen	3 more	commit \| commitdiff \| tree
2009-06-02	martinahansen	more read_ tools migrated	commit \| commitdiff \| tree
2009-06-02	martinahansen	migrating read_ tools	commit \| commitdiff \| tree
2009-06-02	martinahansen	migration of all write tools done	commit \| commitdiff \| tree
2009-06-02	martinahansen	migrated 3 write tools	commit \| commitdiff \| tree
2009-05-29	martinahansen	migrated final plotters	commit \| commitdiff \| tree
2009-05-29	martinahansen	migrated plot_lendist	commit \| commitdiff \| tree
2009-05-29	martinahansen	migrated plot_karyogram	commit \| commitdiff \| tree
2009-05-29	martinahansen	migrated plot_histogram	commit \| commitdiff \| tree
2009-05-29	martinahansen	migrated plot_chrdist	commit \| commitdiff \| tree
2009-05-28	martinahansen	migrated remove_adaptor	commit \| commitdiff \| tree
2009-05-28	martinahansen	migrated 4 more	commit \| commitdiff \| tree
2009-05-28	martinahansen	migrated tile_seq	commit \| commitdiff \| tree
2009-05-28	martinahansen	migrated sort_records	commit \| commitdiff \| tree
2009-05-28	martinahansen	migrated sum_vals	commit \| commitdiff \| tree
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