git.donarmstrong.com Git - biopieces.git/history

]> git.donarmstrong.com Git - biopieces.git/history - bp_bin

2009-11-25	martinahansen	more KISS	tree \| commitdiff
2009-11-24	martinahansen	kiss_sort()	tree \| commitdiff
2009-11-24	martinahansen	fixed KISS	tree \| commitdiff
2009-11-24	martinahansen	rewrote upload_to_KISS	tree \| commitdiff
2009-11-16	martinahansen	hacked read_soft to deal with soft_files wo platform...	tree \| commitdiff
2009-11-16	martinahansen	misc changes	tree \| commitdiff
2009-11-09	martinahansen	added analyze_snp	tree \| commitdiff
2009-11-04	martinahansen	fixed details in bowtie_seq	tree \| commitdiff
2009-10-30	martinahansen	added read_sam	tree \| commitdiff
2009-10-29	martinahansen	fixed bug in patscan_seq	tree \| commitdiff
2009-10-29	martinahansen	modified split_seq	tree \| commitdiff
2009-10-27	martinahansen	more work on KISS	tree \| commitdiff
2009-10-27	martinahansen	revised KISS format	tree \| commitdiff
2009-10-23	martinahansen	removed jbrowse support	tree \| commitdiff
2009-10-21	martinahansen	changed KISS format	tree \| commitdiff
2009-10-21	martinahansen	added upload_to_KISS	tree \| commitdiff
2009-10-21	martinahansen	added kiss biopieces	tree \| commitdiff
2009-10-21	martinahansen	fixed dna/DNA bug in Align.pm	tree \| commitdiff
2009-10-18	martinahansen	added write_gff	tree \| commitdiff
2009-10-17	martinahansen	renaming create_blast_db to create_blast_index	tree \| commitdiff
2009-10-17	martinahansen	changed options in create_blast_db	tree \| commitdiff
2009-09-30	martinahansen	fixed bug in get_genome_seq	tree \| commitdiff
2009-09-28	martinahansen	added bwa_seq	tree \| commitdiff
2009-09-21	martinahansen	added assemble_contigs	tree \| commitdiff
2009-09-21	martinahansen	added format to compute	tree \| commitdiff
2009-09-21	martinahansen	cleaned up calc_fixedstep	tree \| commitdiff
2009-09-18	martinahansen	added features to calc_fixedstep	tree \| commitdiff
2009-09-18	martinahansen	added strand to assemble_tag_contigs	tree \| commitdiff
2009-09-18	martinahansen	added ugly hack to assemble_tag_contigs	tree \| commitdiff
2009-09-17	martinahansen	added get_seq	tree \| commitdiff
2009-09-16	martinahansen	fixed match_seq bug	tree \| commitdiff
2009-09-09	martinahansen	added BED entry output to check_bed	tree \| commitdiff
2009-09-08	martinahansen	added BWA index support	tree \| commitdiff
2009-09-08	martinahansen	unfucked bowtie_index	tree \| commitdiff
2009-09-08	martinahansen	fuckup	tree \| commitdiff
2009-09-07	martinahansen	sanitized create_bowtie_index code	tree \| commitdiff
2009-09-07	martinahansen	sanitized create_bowtie_seq	tree \| commitdiff
2009-09-07	martinahansen	fixed solexa/phred code	tree \| commitdiff
2009-09-04	martinahansen	changed options of read_solexa and read_fastq - undocum...	tree \| commitdiff
2009-09-04	martinahansen	added mate_pair_dist	tree \| commitdiff
2009-09-04	martinahansen	disabled quality score conversion in FASTQ and Solexa	tree \| commitdiff
2009-09-02	martinahansen	fixed issues in fastq handling	tree \| commitdiff
2009-08-28	martinahansen	more work on AlignTwoSeq	tree \| commitdiff
2009-08-27	martinahansen	working on AlignTwoSeq	tree \| commitdiff
2009-08-25	martinahansen	fixed cpu switch in bowtie_seq	tree \| commitdiff
2009-08-20	martinahansen	finished rescan_seq	tree \| commitdiff
2009-08-18	martinahansen	updated rescan_seq	tree \| commitdiff
2009-08-14	martinahansen	added rescan_seq Restriction Enzyme scanner	tree \| commitdiff
2009-08-12	martinahansen	added analyze_gc	tree \| commitdiff
2009-08-10	martinahansen	added nifty # detail to read_tab	tree \| commitdiff
2009-08-10	martinahansen	added --logscale_y switch to relevant plot_* biopieces	tree \| commitdiff
2009-08-10	martinahansen	added --no_gaps switch in blast_seq	tree \| commitdiff
2009-08-04	martinahansen	added a skip_scores switch to read_solexa and read_fastq	tree \| commitdiff
2009-08-02	martinahansen	added get_embl_entry	tree \| commitdiff
2009-07-29	martinahansen	added embl_index	tree \| commitdiff
2009-07-29	martinahansen	added .biopiecesrc	tree \| commitdiff
2009-07-28	martinahansen	finished write_mysql	tree \| commitdiff
2009-07-28	martinahansen	changed read_solexa	tree \| commitdiff
2009-07-28	martinahansen	added quality threshold to read_fastq	tree \| commitdiff
2009-07-27	martinahansen	added write_mysql	tree \| commitdiff
2009-07-27	martinahansen	fixed list_mysql_databases	tree \| commitdiff
2009-07-27	martinahansen	added list_mysql_databases	tree \| commitdiff
2009-07-25	martinahansen	fixed feature in analyze_vals, issue 3	tree \| commitdiff
2009-07-23	martinahansen	fixed bowtie_seq	tree \| commitdiff
2009-07-23	martinahansen	fixed bowtie_seq	tree \| commitdiff
2009-07-23	martinahansen	added create_bowtie_index	tree \| commitdiff
2009-07-23	martinahansen	added verbose stuff to bowtie_seq	tree \| commitdiff
2009-07-23	martinahansen	added verbose stuff to format_genome	tree \| commitdiff
2009-07-23	martinahansen	addid term colors to list_genomes	tree \| commitdiff
2009-07-23	martinahansen	added options to bowtie_seq	tree \| commitdiff
2009-07-22	martinahansen	added some args to bowtie_seq	tree \| commitdiff
2009-07-21	martinahansen	fixed bowtie_seq	tree \| commitdiff
2009-07-21	martinahansen	added read_fastq biopiece	tree \| commitdiff
2009-07-20	martinahansen	added bowtie_seq biopiece	tree \| commitdiff
2009-07-20	martinahansen	added bowtie to format_genome	tree \| commitdiff
2009-07-11	martinahansen	fixed bug in read_embl	tree \| commitdiff
2009-07-10	martinahansen	speedup of analyze_seq 3 fold	tree \| commitdiff
2009-07-10	martinahansen	fixed bug in create_vmatch_index	tree \| commitdiff
2009-07-10	martinahansen	fixed bug in remove_indels	tree \| commitdiff
2009-07-08	martinahansen	added use strict to all biopieces	tree \| commitdiff
2009-07-08	martinahansen	changed shebang	tree \| commitdiff
2009-07-07	martinahansen	minor changes	tree \| commitdiff
2009-06-23	martinahansen	fixes and stuff	tree \| commitdiff
2009-06-17	martinahansen	fixed a number of bugs in PSL	tree \| commitdiff
2009-06-16	martinahansen	added VMATCH support to get_genome_seq	tree \| commitdiff
2009-06-15	martinahansen	added indel_seq	tree \| commitdiff
2009-06-15	martinahansen	added mutate_seq	tree \| commitdiff
2009-06-15	martinahansen	added non-overlapping feature to split_seq	tree \| commitdiff
2009-06-11	martinahansen	added Data::Dumper support to bioscript	tree \| commitdiff
2009-06-09	martinahansen	fixed bug in plot_histogram	tree \| commitdiff
2009-06-09	martinahansen	fixed bug in read_tab	tree \| commitdiff
2009-06-08	martinahansen	rewrote bioscript	tree \| commitdiff
2009-06-08	martinahansen	rewrote bioscript	tree \| commitdiff
2009-06-08	martinahansen	fixed minor bugs	tree \| commitdiff
2009-06-06	martinahansen	fixed bug in format_genome	tree \| commitdiff
2009-06-06	martinahansen	fixes done to tmp_dir	tree \| commitdiff
2009-06-06	martinahansen	implementing status solution	tree \| commitdiff
2009-06-06	martinahansen	removed variables bulk type	tree \| commitdiff
2009-06-06	martinahansen	fixing status	tree \| commitdiff
2009-06-05	martinahansen	added align_pair_seq	tree \| commitdiff
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