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2008-09-24	martinahansen	adding rescan to bipartite_scan	commit \| commitdiff \| tree
2008-09-23	martinahansen	fixed STDERR and verbose	commit \| commitdiff \| tree
2008-09-23	martinahansen	add bipartite_decode	commit \| commitdiff \| tree
2008-09-23	martinahansen	add bipartite_decode	commit \| commitdiff \| tree
2008-09-23	martinahansen	backup time	commit \| commitdiff \| tree
2008-09-17	martinahansen	added SPAN to read_psl	commit \| commitdiff \| tree
2008-09-17	martinahansen	fixed tmp dir cleaner in Biopieces.pm	commit \| commitdiff \| tree
2008-09-16	martinahansen	added 5prime adaptor feature to remove_adaptor	commit \| commitdiff \| tree
2008-09-16	martinahansen	inline::c code for adaptor removal	commit \| commitdiff \| tree
2008-09-16	martinahansen	minor updates	commit \| commitdiff \| tree
2008-09-11	martinahansen	bed_sort created	commit \| commitdiff \| tree
2008-09-11	martinahansen	added bed stuff to c code	commit \| commitdiff \| tree
2008-09-10	martinahansen	added copyright to c stuff	commit \| commitdiff \| tree
2008-09-10	martinahansen	bipartite_scan polish2	commit \| commitdiff \| tree
2008-09-10	martinahansen	linked list sort added	commit \| commitdiff \| tree
2008-09-10	martinahansen	bipartite_scan polish	commit \| commitdiff \| tree
2008-09-08	martinahansen	fixed 0 offset bug in remove_adaptor	commit \| commitdiff \| tree
2008-09-08	martinahansen	added sort to bipartite_scan.c	commit \| commitdiff \| tree
2008-09-05	martinahansen	bipartite_scan now working	commit \| commitdiff \| tree
2008-09-05	martinahansen	added c temp file dir	commit \| commitdiff \| tree
2008-09-05	martinahansen	added unit test to mem.c	commit \| commitdiff \| tree
2008-09-04	martinahansen	bipartite_scan.c alpha	commit \| commitdiff \| tree
2008-09-03	martinahansen	removed wiggle options from upload_to_ucsc	commit \| commitdiff \| tree
2008-09-03	martinahansen	fixed -S and -L for calc_fixedstep biopiece	commit \| commitdiff \| tree
2008-09-03	martinahansen	added calc_fixedstep biopiece	commit \| commitdiff \| tree
2008-09-01	martinahansen	read_solexa now handles both decimal and octal scores	commit \| commitdiff \| tree
2008-08-29	martinahansen	fixed bug in remove_adaptor	commit \| commitdiff \| tree
2008-08-29	martinahansen	fixed minor bugs in remove_adaptor	commit \| commitdiff \| tree
2008-08-29	martinahansen	added remove_adaptor biopiece	commit \| commitdiff \| tree
2008-08-29	martinahansen	added remove_adaptor biopiece	commit \| commitdiff \| tree
2008-08-29	martinahansen	fixed UCSC::get_psl_entry	commit \| commitdiff \| tree
2008-08-28	martinahansen	fix of \r feature in Fasta::get_entry	commit \| commitdiff \| tree
2008-08-28	martinahansen	read_fasta fix for stupid \r	commit \| commitdiff \| tree
2008-08-26	martinahansen	fixed bug in table name check	commit \| commitdiff \| tree
2008-08-26	martinahansen	made speedup for repeat-O-matic	commit \| commitdiff \| tree
2008-08-26	martinahansen	added fixedStep format to upload_to_ucsc	commit \| commitdiff \| tree
2008-08-25	martinahansen	clean-write of repeat-O-matic	commit \| commitdiff \| tree
2008-08-25	martinahansen	added --verbose run option for blast_seq	commit \| commitdiff \| tree
2008-08-25	martinahansen	added revcomp_dna to repeat-O-matic	commit \| commitdiff \| tree
2008-08-22	martinahansen	fixed read_soft to deal with stupid Soft format feature	commit \| commitdiff \| tree
2008-08-22	martinahansen	added option to read_soft for selecting specific samples	commit \| commitdiff \| tree
2008-08-21	martinahansen	finished c fasta parser	commit \| commitdiff \| tree
2008-08-21	martinahansen	finished c fasta parser	commit \| commitdiff \| tree
2008-08-21	martinahansen	fixed format_genome	commit \| commitdiff \| tree
2008-08-21	martinahansen	fixed bug in vmatch_index	commit \| commitdiff \| tree
2008-08-21	martinahansen	fixed %d->%f for log10 in upload_to_ucsc	commit \| commitdiff \| tree
2008-08-21	martinahansen	more updates of c and fixes to upload_to_ucsc	commit \| commitdiff \| tree
2008-08-18	martinahansen	another c code upgrade	commit \| commitdiff \| tree
2008-08-14	martinahansen	updated read_solexa	commit \| commitdiff \| tree
2008-08-14	martinahansen	unit test of mem.c done	commit \| commitdiff \| tree
2008-08-13	martinahansen	update of c libs	commit \| commitdiff \| tree
2008-08-05	martinahansen	fixing up c code	commit \| commitdiff \| tree
2008-08-01	martinahansen	changed result key of count_records	commit \| commitdiff \| tree
2008-07-29	martinahansen	reverted code for format_genome in order to make vmatch_seq...	commit \| commitdiff \| tree
2008-07-29	martinahansen	correcting bug in Match.pm	commit \| commitdiff \| tree
2008-07-29	martinahansen	finished biopiece merge_records	commit \| commitdiff \| tree
2008-07-28	martinahansen	added new biopiece merge_records	commit \| commitdiff \| tree
2008-07-25	martinahansen	fixed zero entry tmp file bug in soap_seq	commit \| commitdiff \| tree
2008-07-25	martinahansen	fixed another annoying bug in clean_tmp()	commit \| commitdiff \| tree
2008-07-25	martinahansen	corrected bug in clean tmp to deal with permision problem	commit \| commitdiff \| tree
2008-07-25	martinahansen	changed error output to fit on screen	commit \| commitdiff \| tree
2008-07-24	martinahansen	added seed_size to soap_seq	commit \| commitdiff \| tree
2008-07-24	martinahansen	corrected ugly bug	commit \| commitdiff \| tree
2008-07-24	martinahansen	fixed cleanup of temporary files	commit \| commitdiff \| tree
2008-07-23	martinahansen	begin of status update	commit \| commitdiff \| tree
2008-07-22	martinahansen	added record2fasta to allow for aliasing of SEQ_NAME...	commit \| commitdiff \| tree
2008-07-21	martinahansen	updated upload_to_ucsc wiki and added a secure free...	commit \| commitdiff \| tree
2008-07-21	martinahansen	fixed ugly bug in get_record	commit \| commitdiff \| tree
2008-07-21	martinahansen	corrected an ugly bug in get_record	commit \| commitdiff \| tree
2008-07-21	martinahansen	more soap_seq debugging	commit \| commitdiff \| tree
2008-07-21	martinahansen	debugging soap_seq	commit \| commitdiff \| tree
2008-07-21	martinahansen	added soap_seq	commit \| commitdiff \| tree
2008-07-21	martinahansen	changed wib dir from BP_DATA to ~/ucsc	commit \| commitdiff \| tree
2008-07-21	martinahansen	updated list_genomes wiki and bashrc	commit \| commitdiff \| tree
2008-07-21	martinahansen	fixed local and global logging	commit \| commitdiff \| tree
2008-07-20	martinahansen	added a variable argument list example to c scr	commit \| commitdiff \| tree
2008-07-20	martinahansen	cleaning c source dir	commit \| commitdiff \| tree
2008-07-17	martinahansen	fixing bashrc	commit \| commitdiff \| tree
2008-07-17	martinahansen	fixing bashrc	commit \| commitdiff \| tree
2008-07-17	martinahansen	removed bp_usage dir from source trunk (should be root...	commit \| commitdiff \| tree
2008-07-17	martinahansen	unmessing wiki dir	commit \| commitdiff \| tree
2008-07-17	martinahansen	cleaning bp_usage	commit \| commitdiff \| tree
2008-07-17	martinahansen	cleaning bp_usage	commit \| commitdiff \| tree
2008-07-17	martinahansen	cleaning bp_usage	commit \| commitdiff \| tree
2008-07-17	martinahansen	format_genome fix	commit \| commitdiff \| tree
2008-07-17	martinahansen	removed log directory	commit \| commitdiff \| tree
2008-07-14	martinahansen	added phastcons to format_genome	commit \| commitdiff \| tree
2008-07-14	martinahansen	removed create_fixedstep_index	commit \| commitdiff \| tree
2008-07-14	martinahansen	added create_fixedstep_index	commit \| commitdiff \| tree
2008-07-14	martinahansen	added write_fixedstep	commit \| commitdiff \| tree
2008-07-14	martinahansen	added read_fixedstep	commit \| commitdiff \| tree
2008-07-10	martinahansen	fixed all defects from bug list	commit \| commitdiff \| tree
2008-07-10	martinahansen	added format_genome and list_genomes	commit \| commitdiff \| tree
2008-07-09	martinahansen	fixed print_usage	commit \| commitdiff \| tree
2008-07-09	martinahansen	fixed print_usage	commit \| commitdiff \| tree
2008-07-09	martinahansen	added --help	commit \| commitdiff \| tree
2008-07-09	martinahansen	removed & from all Perl Modules	commit \| commitdiff \| tree
2008-07-08	martinahansen	added disable internal link ! to Gwiki	commit \| commitdiff \| tree
2008-07-02	martinahansen	even more wikis	commit \| commitdiff \| tree
2008-07-01	martinahansen	more wikis	commit \| commitdiff \| tree
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