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]> git.donarmstrong.com Git - biopieces.git/history - code_perl/Maasha/Biopieces.pm

[biopieces.git] / code_perl / Maasha / Biopieces.pm

2013-04-29	martinahansen	fixed missing BP_TMP dir feature	blob \| commitdiff \| raw
2012-10-10	martinahansen	added some file locking to Biopieces.pm	blob \| commitdiff \| raw \| diff to current
2010-10-13	martinahansen	removed local logging causing trouble	blob \| commitdiff \| raw \| diff to current
2010-06-22	martinahansen	corrected type in log messages	blob \| commitdiff \| raw \| diff to current
2010-03-18	martinahansen	error handling and seq guess fix	blob \| commitdiff \| raw \| diff to current
2009-08-02	martinahansen	added get_embl_entry	blob \| commitdiff \| raw \| diff to current
2009-07-29	martinahansen	added embl_index	blob \| commitdiff \| raw \| diff to current
2009-07-29	martinahansen	added .biopiecesrc	blob \| commitdiff \| raw \| diff to current
2009-07-27	martinahansen	added list_mysql_databases	blob \| commitdiff \| raw \| diff to current
2009-07-07	martinahansen	minor changes	blob \| commitdiff \| raw \| diff to current
2009-06-23	martinahansen	fixes and stuff	blob \| commitdiff \| raw \| diff to current
2009-06-08	martinahansen	fixed minor bugs	blob \| commitdiff \| raw \| diff to current
2009-06-06	martinahansen	fixes but in removal of tmp_dir	blob \| commitdiff \| raw \| diff to current
2009-06-06	martinahansen	fixes done to tmp_dir	blob \| commitdiff \| raw \| diff to current
2009-06-06	martinahansen	fixing status	blob \| commitdiff \| raw \| diff to current
2009-05-23	martinahansen	migrated extract_seq	blob \| commitdiff \| raw \| diff to current
2009-05-23	martinahansen	rewrite begin	blob \| commitdiff \| raw \| diff to current
2009-05-12	martinahansen	split Biopieces.pm into BioRun.pm and Biopieces.pm	blob \| commitdiff \| raw \| diff to current
2009-05-12	martinahansen	changed wiki renderer	blob \| commitdiff \| raw \| diff to current
2008-12-17	martinahansen	fixed BED BUG	blob \| commitdiff \| raw \| diff to current
2008-12-11	martinahansen	added exon capabilities to calc_fixedstep	blob \| commitdiff \| raw \| diff to current
2008-12-11	martinahansen	calc_fixedstep reverted to perl	blob \| commitdiff \| raw \| diff to current
2008-12-11	martinahansen	fixed carriage return bug in read_ucsc_config	blob \| commitdiff \| raw \| diff to current
2008-12-09	martinahansen	added splice to get_genome_seq	blob \| commitdiff \| raw \| diff to current
2008-12-09	martinahansen	fixed bug in remove_ucsc_tracks	blob \| commitdiff \| raw \| diff to current
2008-12-08	martinahansen	minor fixes	blob \| commitdiff \| raw \| diff to current
2008-12-08	martinahansen	added --check to a number of Biopieces	blob \| commitdiff \| raw \| diff to current
2008-12-08	martinahansen	made check_bed optional	blob \| commitdiff \| raw \| diff to current
2008-12-05	martinahansen	added bed2tag_contigs as backend to assemble_tag_contigs	blob \| commitdiff \| raw \| diff to current
2008-12-05	martinahansen	added bed2fixedstep.c as backend to calc_fixedstep	blob \| commitdiff \| raw \| diff to current
2008-12-04	martinahansen	added python code	blob \| commitdiff \| raw \| diff to current
2008-11-24	martinahansen	fixed bugs in calc_fixedstep	blob \| commitdiff \| raw \| diff to current
2008-11-24	martinahansen	fixed bugs in assemble_tag_contigs	blob \| commitdiff \| raw \| diff to current
2008-11-24	martinahansen	major code upgrade 1	blob \| commitdiff \| raw \| diff to current
2008-11-21	martinahansen	fixed bug in compute	blob \| commitdiff \| raw \| diff to current
2008-11-18	martinahansen	clean up	blob \| commitdiff \| raw \| diff to current
2008-11-13	martinahansen	added -c switch to write_bed	blob \| commitdiff \| raw \| diff to current
2008-11-11	martinahansen	added ucscMakeTracks -b run to remove_ucsc_tracks	blob \| commitdiff \| raw \| diff to current
2008-11-11	martinahansen	finished remove_ucsc_tracks	blob \| commitdiff \| raw \| diff to current
2008-11-11	martinahansen	added remove_ucsc_tracks	blob \| commitdiff \| raw \| diff to current
2008-11-11	martinahansen	added -t to remove_mysql_tables	blob \| commitdiff \| raw \| diff to current
2008-11-11	martinahansen	swapped bedSort with bed_sort	blob \| commitdiff \| raw \| diff to current
2008-11-11	martinahansen	added mysql related Biopieces	blob \| commitdiff \| raw \| diff to current
2008-11-07	martinahansen	finished assemble_tag_contigs	blob \| commitdiff \| raw \| diff to current
2008-11-03	martinahansen	rewrote grab to get speed	blob \| commitdiff \| raw \| diff to current
2008-10-28	martinahansen	fixed compute	blob \| commitdiff \| raw \| diff to current
2008-10-28	martinahansen	fixed bug in compute and analyze_seq	blob \| commitdiff \| raw \| diff to current
2008-10-27	martinahansen	changed delimiter in REC_TYPE SOLID to ;	blob \| commitdiff \| raw \| diff to current
2008-10-02	martinahansen	added REC_TYPE to read_solid	blob \| commitdiff \| raw \| diff to current
2008-09-29	martinahansen	tada	blob \| commitdiff \| raw \| diff to current
2008-09-25	martinahansen	fixed ugly bug	blob \| commitdiff \| raw \| diff to current
2008-09-25	martinahansen	fixed rename bug	blob \| commitdiff \| raw \| diff to current
2008-09-23	martinahansen	fixed STDERR and verbose	blob \| commitdiff \| raw \| diff to current
2008-09-17	martinahansen	fixed tmp dir cleaner in Biopieces.pm	blob \| commitdiff \| raw \| diff to current
2008-09-16	martinahansen	added 5prime adaptor feature to remove_adaptor	blob \| commitdiff \| raw \| diff to current
2008-09-16	martinahansen	inline::c code for adaptor removal	blob \| commitdiff \| raw \| diff to current
2008-09-08	martinahansen	fixed 0 offset bug in remove_adaptor	blob \| commitdiff \| raw \| diff to current
2008-09-03	martinahansen	removed wiggle options from upload_to_ucsc	blob \| commitdiff \| raw \| diff to current
2008-09-03	martinahansen	fixed -S and -L for calc_fixedstep biopiece	blob \| commitdiff \| raw \| diff to current
2008-09-03	martinahansen	added calc_fixedstep biopiece	blob \| commitdiff \| raw \| diff to current
2008-09-01	martinahansen	read_solexa now handles both decimal and octal scores	blob \| commitdiff \| raw \| diff to current
2008-08-29	martinahansen	fixed bug in remove_adaptor	blob \| commitdiff \| raw \| diff to current
2008-08-29	martinahansen	fixed minor bugs in remove_adaptor	blob \| commitdiff \| raw \| diff to current
2008-08-29	martinahansen	added remove_adaptor biopiece	blob \| commitdiff \| raw \| diff to current
2008-08-29	martinahansen	fixed UCSC::get_psl_entry	blob \| commitdiff \| raw \| diff to current
2008-08-26	martinahansen	fixed bug in table name check	blob \| commitdiff \| raw \| diff to current
2008-08-26	martinahansen	added fixedStep format to upload_to_ucsc	blob \| commitdiff \| raw \| diff to current
2008-08-25	martinahansen	added --verbose run option for blast_seq	blob \| commitdiff \| raw \| diff to current
2008-08-22	martinahansen	fixed read_soft to deal with stupid Soft format feature	blob \| commitdiff \| raw \| diff to current
2008-08-22	martinahansen	added option to read_soft for selecting specific samples	blob \| commitdiff \| raw \| diff to current
2008-08-21	martinahansen	more updates of c and fixes to upload_to_ucsc	blob \| commitdiff \| raw \| diff to current
2008-08-14	martinahansen	updated read_solexa	blob \| commitdiff \| raw \| diff to current
2008-08-01	martinahansen	changed result key of count_records	blob \| commitdiff \| raw \| diff to current
2008-07-29	martinahansen	finished biopiece merge_records	blob \| commitdiff \| raw \| diff to current
2008-07-28	martinahansen	added new biopiece merge_records	blob \| commitdiff \| raw \| diff to current
2008-07-25	martinahansen	fixed zero entry tmp file bug in soap_seq	blob \| commitdiff \| raw \| diff to current
2008-07-25	martinahansen	fixed another annoying bug in clean_tmp()	blob \| commitdiff \| raw \| diff to current
2008-07-25	martinahansen	corrected bug in clean tmp to deal with permision problem	blob \| commitdiff \| raw \| diff to current
2008-07-24	martinahansen	added seed_size to soap_seq	blob \| commitdiff \| raw \| diff to current
2008-07-24	martinahansen	corrected ugly bug	blob \| commitdiff \| raw \| diff to current
2008-07-24	martinahansen	fixed cleanup of temporary files	blob \| commitdiff \| raw \| diff to current
2008-07-23	martinahansen	begin of status update	blob \| commitdiff \| raw \| diff to current
2008-07-22	martinahansen	added record2fasta to allow for aliasing of SEQ_NAME...	blob \| commitdiff \| raw \| diff to current
2008-07-21	martinahansen	fixed ugly bug in get_record	blob \| commitdiff \| raw \| diff to current
2008-07-21	martinahansen	corrected an ugly bug in get_record	blob \| commitdiff \| raw \| diff to current
2008-07-21	martinahansen	more soap_seq debugging	blob \| commitdiff \| raw \| diff to current
2008-07-21	martinahansen	debugging soap_seq	blob \| commitdiff \| raw \| diff to current
2008-07-21	martinahansen	added soap_seq	blob \| commitdiff \| raw \| diff to current
2008-07-21	martinahansen	changed wib dir from BP_DATA to ~/ucsc	blob \| commitdiff \| raw \| diff to current
2008-07-21	martinahansen	fixed local and global logging	blob \| commitdiff \| raw \| diff to current
2008-07-14	martinahansen	added phastcons to format_genome	blob \| commitdiff \| raw \| diff to current
2008-07-14	martinahansen	removed create_fixedstep_index	blob \| commitdiff \| raw \| diff to current
2008-07-14	martinahansen	added create_fixedstep_index	blob \| commitdiff \| raw \| diff to current
2008-07-14	martinahansen	added write_fixedstep	blob \| commitdiff \| raw \| diff to current
2008-07-14	martinahansen	added read_fixedstep	blob \| commitdiff \| raw \| diff to current
2008-07-10	martinahansen	fixed all defects from bug list	blob \| commitdiff \| raw \| diff to current
2008-07-10	martinahansen	added format_genome and list_genomes	blob \| commitdiff \| raw \| diff to current
2008-07-09	martinahansen	fixed print_usage	blob \| commitdiff \| raw \| diff to current
2008-07-09	martinahansen	fixed print_usage	blob \| commitdiff \| raw \| diff to current
2008-07-09	martinahansen	added --help	blob \| commitdiff \| raw \| diff to current
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