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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
2008-12-05	martinahansen	added bed2tag_contigs.c	commit \| commitdiff \| tree
2008-12-05	martinahansen	added bed2fixedstep.c as backend to calc_fixedstep	commit \| commitdiff \| tree
2008-12-05	martinahansen	fixed bed2fixedstep.c	commit \| commitdiff \| tree
2008-12-04	martinahansen	added python code	commit \| commitdiff \| tree
2008-12-04	martinahansen	added bed2fixedstep.c	commit \| commitdiff \| tree
2008-11-30	martinahansen	added barray.c and cleaned hash.c	commit \| commitdiff \| tree
2008-11-28	martinahansen	removed GIW2008 poster to docs and added to featured...	commit \| commitdiff \| tree
2008-11-28	martinahansen	added GIW2008 poster to docs	commit \| commitdiff \| tree
2008-11-27	martinahansen	added c power to calc_fixedstep	commit \| commitdiff \| tree
2008-11-24	martinahansen	fixed bugs in calc_fixedstep	commit \| commitdiff \| tree
2008-11-24	martinahansen	fixed bugs in assemble_tag_contigs	commit \| commitdiff \| tree
2008-11-24	martinahansen	major code upgrade 1	commit \| commitdiff \| tree
2008-11-21	martinahansen	fixed bug in compute	commit \| commitdiff \| tree
2008-11-18	martinahansen	doc update	commit \| commitdiff \| tree
2008-11-18	martinahansen	clean up	commit \| commitdiff \| tree
2008-11-13	martinahansen	added -c switch to write_bed	commit \| commitdiff \| tree
2008-11-11	martinahansen	added ucscMakeTracks -b run to remove_ucsc_tracks	commit \| commitdiff \| tree
2008-11-11	martinahansen	finished remove_ucsc_tracks	commit \| commitdiff \| tree
2008-11-11	martinahansen	fix date and time in ucsc config	commit \| commitdiff \| tree
2008-11-11	martinahansen	added remove_ucsc_tracks	commit \| commitdiff \| tree
2008-11-11	martinahansen	added -t to remove_mysql_tables	commit \| commitdiff \| tree
2008-11-11	martinahansen	swapped bedSort with bed_sort	commit \| commitdiff \| tree
2008-11-11	martinahansen	added mysql related Biopieces	commit \| commitdiff \| tree
2008-11-07	martinahansen	finished assemble_tag_contigs	commit \| commitdiff \| tree
2008-11-03	martinahansen	rewrote grab to get speed	commit \| commitdiff \| tree
2008-10-28	martinahansen	fixed compute	commit \| commitdiff \| tree
2008-10-28	martinahansen	fixed bug in compute and analyze_seq	commit \| commitdiff \| tree
2008-10-27	martinahansen	changed delimiter in REC_TYPE SOLID to ;	commit \| commitdiff \| tree
2008-10-02	martinahansen	added REC_TYPE to read_solid	commit \| commitdiff \| tree
2008-09-29	martinahansen	empty change to Seq.pm	commit \| commitdiff \| tree
2008-09-29	martinahansen	tada	commit \| commitdiff \| tree
2008-09-25	martinahansen	fixed ugly bug	commit \| commitdiff \| tree
2008-09-25	martinahansen	fixed rename bug	commit \| commitdiff \| tree
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
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