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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
2009-05-28	martinahansen	migrated patscan_seq	commit \| commitdiff \| tree
2009-05-28	martinahansen	migrated patscan_seq	commit \| commitdiff \| tree
2009-05-27	martinahansen	migrated oligo_freq	commit \| commitdiff \| tree
2009-05-27	martinahansen	migrated trans family	commit \| commitdiff \| tree
2009-05-27	martinahansen	migrated merge_records	commit \| commitdiff \| tree
2009-05-27	martinahansen	migrated max, min, mean, and median _vals	commit \| commitdiff \| tree
2009-05-27	martinahansen	migrated match_seq	commit \| commitdiff \| tree
2009-05-27	martinahansen	added 3 more	commit \| commitdiff \| tree
2009-05-26	martinahansen	migrated 3 biopieces	commit \| commitdiff \| tree
2009-05-26	martinahansen	migrated create_vmatch_index	commit \| commitdiff \| tree
2009-05-26	martinahansen	migrated create_weight_matrix	commit \| commitdiff \| tree
2009-05-26	martinahansen	migrated count_vals	commit \| commitdiff \| tree
2009-05-26	martinahansen	migrated count_records	commit \| commitdiff \| tree
2009-05-26	martinahansen	migrated and fixed calc_fixedstep	commit \| commitdiff \| tree
2009-05-25	martinahansen	migrated calc_bit_scores	commit \| commitdiff \| tree
2009-05-25	martinahansen	migrated blat_seq	commit \| commitdiff \| tree
2009-05-24	martinahansen	migrated assemble_tag_contigs	commit \| commitdiff \| tree
2009-05-24	martinahansen	migrated split biopieces	commit \| commitdiff \| tree
2009-05-24	martinahansen	migrated split biopieces	commit \| commitdiff \| tree
2009-05-24	martinahansen	migrated random_records	commit \| commitdiff \| tree
2009-05-24	martinahansen	magrated analyze biopieces	commit \| commitdiff \| tree
2009-05-24	martinahansen	magrated analyze biopieces	commit \| commitdiff \| tree
2009-05-24	martinahansen	migrated write_align	commit \| commitdiff \| tree
2009-05-24	martinahansen	migrated align_seq	commit \| commitdiff \| tree
2009-05-24	martinahansen	migrated add_ident	commit \| commitdiff \| tree
2009-05-24	martinahansen	migrated shuffle_seq	commit \| commitdiff \| tree
2009-05-24	martinahansen	migrated complement_seq and reverse_seq	commit \| commitdiff \| tree
2009-05-23	martinahansen	migrated extract_seq	commit \| commitdiff \| tree
2009-05-23	martinahansen	rewrite begin	commit \| commitdiff \| tree
2009-05-14	martinahansen	polishing split_vals	commit \| commitdiff \| tree
2009-05-13	martinahansen	added lowercase_seq symlink	commit \| commitdiff \| tree
2009-05-13	martinahansen	fixing lowercase_seq	commit \| commitdiff \| tree
2009-05-13	martinahansen	fixed symlink trouble	commit \| commitdiff \| tree
2009-05-13	martinahansen	git-svn-id: http://biopieces.googlecode.com/svn/trunk...	commit \| commitdiff \| tree
2009-05-13	martinahansen	git-svn-id: http://biopieces.googlecode.com/svn/trunk...	commit \| commitdiff \| tree
2009-05-13	martinahansen	moved all binaries and created symlinks instead	commit \| commitdiff \| tree
2009-05-12	martinahansen	split Biopieces.pm into BioRun.pm and Biopieces.pm	commit \| commitdiff \| tree
2009-05-12	martinahansen	changed wiki renderer	commit \| commitdiff \| tree
2008-12-17	martinahansen	fixed BED BUG	commit \| commitdiff \| tree
2008-12-11	martinahansen	lots of PSL related changes	commit \| commitdiff \| tree
2008-12-11	martinahansen	added exon capabilities to calc_fixedstep	commit \| commitdiff \| tree
2008-12-11	martinahansen	calc_fixedstep reverted to perl	commit \| commitdiff \| tree
2008-12-11	martinahansen	fixed carriage return bug in read_ucsc_config	commit \| commitdiff \| tree
2008-12-09	martinahansen	added splice to get_genome_seq	commit \| commitdiff \| tree
2008-12-09	martinahansen	fixed bug in remove_ucsc_tracks	commit \| commitdiff \| tree
2008-12-08	martinahansen	minor fixes	commit \| commitdiff \| tree
2008-12-08	martinahansen	added --check to a number of Biopieces	commit \| commitdiff \| tree
2008-12-08	martinahansen	reverting to BED lists	commit \| commitdiff \| tree
2008-12-08	martinahansen	changed BED.pm from list to hash	commit \| commitdiff \| tree
2008-12-08	martinahansen	made check_bed optional	commit \| commitdiff \| tree
2008-12-05	martinahansen	fixed CHR_BEG=0 bug	commit \| commitdiff \| tree
2008-12-05	martinahansen	changed barray from ushort to uint	commit \| commitdiff \| tree
2008-12-05	martinahansen	added bed2tag_contigs as backend to assemble_tag_contigs	commit \| commitdiff \| tree
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