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2009-10-21	martinahansen	fixed dna/DNA bug in Align.pm	commit \| commitdiff \| tree
2009-10-19	martinahansen	added XHTML	commit \| commitdiff \| tree
2009-10-18	martinahansen	added write_gff	commit \| commitdiff \| tree
2009-10-17	martinahansen	renaming create_blast_db to create_blast_index	commit \| commitdiff \| tree
2009-10-17	martinahansen	changed options in create_blast_db	commit \| commitdiff \| tree
2009-09-30	martinahansen	fixed bug in get_genome_seq	commit \| commitdiff \| tree
2009-09-29	martinahansen	fixed STRAND in SAM format	commit \| commitdiff \| tree
2009-09-28	martinahansen	added SAM.pm	commit \| commitdiff \| tree
2009-09-28	martinahansen	added bwa_seq	commit \| commitdiff \| tree
2009-09-21	martinahansen	added assemble_contigs	commit \| commitdiff \| tree
2009-09-21	martinahansen	added format to compute	commit \| commitdiff \| tree
2009-09-21	martinahansen	cleaned up calc_fixedstep	commit \| commitdiff \| tree
2009-09-18	martinahansen	added features to calc_fixedstep	commit \| commitdiff \| tree
2009-09-18	martinahansen	added strand to assemble_tag_contigs	commit \| commitdiff \| tree
2009-09-18	martinahansen	added ugly hack to assemble_tag_contigs	commit \| commitdiff \| tree
2009-09-18	martinahansen	added align_two_seq.c	commit \| commitdiff \| tree
2009-09-18	martinahansen	fixed issue 18	commit \| commitdiff \| tree
2009-09-17	martinahansen	added get_seq	commit \| commitdiff \| tree
2009-09-16	martinahansen	fixed match_seq bug	commit \| commitdiff \| tree
2009-09-09	martinahansen	fixed bug in psl2bed conversion	commit \| commitdiff \| tree
2009-09-09	martinahansen	fixed wrap blunder in Fasta.pm	commit \| commitdiff \| tree
2009-09-09	martinahansen	added BED entry output to check_bed	commit \| commitdiff \| tree
2009-09-08	martinahansen	added BWA index support	commit \| commitdiff \| tree
2009-09-08	martinahansen	unfucked bowtie_index	commit \| commitdiff \| tree
2009-09-08	martinahansen	fuckup	commit \| commitdiff \| tree
2009-09-07	martinahansen	sanitized create_bowtie_index code	commit \| commitdiff \| tree
2009-09-07	martinahansen	sanitized create_bowtie_seq	commit \| commitdiff \| tree
2009-09-07	martinahansen	fixed solexa/phred code	commit \| commitdiff \| tree
2009-09-04	martinahansen	changed options of read_solexa and read_fastq - undocumented	commit \| commitdiff \| tree
2009-09-04	martinahansen	added mate_pair_dist	commit \| commitdiff \| tree
2009-09-04	martinahansen	disabled quality score conversion in FASTQ and Solexa	commit \| commitdiff \| tree
2009-09-02	martinahansen	fixed issues in fastq handling	commit \| commitdiff \| tree
2009-08-28	martinahansen	more work on AlignTwoSeq	commit \| commitdiff \| tree
2009-08-27	martinahansen	working on AlignTwoSeq	commit \| commitdiff \| tree
2009-08-25	martinahansen	fixed cpu switch in bowtie_seq	commit \| commitdiff \| tree
2009-08-20	martinahansen	finished rescan_seq	commit \| commitdiff \| tree
2009-08-20	martinahansen	added more range to plot_lendist	commit \| commitdiff \| tree
2009-08-18	martinahansen	updated rescan_seq	commit \| commitdiff \| tree
2009-08-14	martinahansen	added rescan_seq Restriction Enzyme scanner	commit \| commitdiff \| tree
2009-08-14	martinahansen	polished RestrictEnz.pm	commit \| commitdiff \| tree
2009-08-14	martinahansen	added RestrictEnz.pm	commit \| commitdiff \| tree
2009-08-12	martinahansen	added analyze_gc	commit \| commitdiff \| tree
2009-08-10	martinahansen	added nifty # detail to read_tab	commit \| commitdiff \| tree
2009-08-10	martinahansen	added --logscale_y switch to relevant plot_* biopieces	commit \| commitdiff \| tree
2009-08-10	martinahansen	disabled utest for C code	commit \| commitdiff \| tree
2009-08-10	martinahansen	added --no_gaps switch in blast_seq	commit \| commitdiff \| tree
2009-08-04	martinahansen	added a skip_scores switch to read_solexa and read_fastq	commit \| commitdiff \| tree
2009-08-02	martinahansen	fix embl parser	commit \| commitdiff \| tree
2009-08-02	martinahansen	finishing read_embl	commit \| commitdiff \| tree
2009-08-02	martinahansen	added get_embl_entry	commit \| commitdiff \| tree
2009-07-29	martinahansen	added embl_index	commit \| commitdiff \| tree
2009-07-29	martinahansen	added .biopiecesrc	commit \| commitdiff \| tree
2009-07-28	martinahansen	finished write_mysql	commit \| commitdiff \| tree
2009-07-28	martinahansen	changed read_solexa	commit \| commitdiff \| tree
2009-07-28	martinahansen	added quality threshold to read_fastq	commit \| commitdiff \| tree
2009-07-27	martinahansen	added write_mysql	commit \| commitdiff \| tree
2009-07-27	martinahansen	fixed list_mysql_databases	commit \| commitdiff \| tree
2009-07-27	martinahansen	added list_mysql_databases	commit \| commitdiff \| tree
2009-07-25	martinahansen	fixed feature in analyze_vals, issue 3	commit \| commitdiff \| tree
2009-07-24	martinahansen	fixed Gwiki colors	commit \| commitdiff \| tree
2009-07-23	martinahansen	fixed bowtie_seq	commit \| commitdiff \| tree
2009-07-23	martinahansen	fixed bowtie_seq	commit \| commitdiff \| tree
2009-07-23	martinahansen	added Bowtie.pm	commit \| commitdiff \| tree
2009-07-23	martinahansen	added create_bowtie_index	commit \| commitdiff \| tree
2009-07-23	martinahansen	added verbose stuff to bowtie_seq	commit \| commitdiff \| tree
2009-07-23	martinahansen	added verbose stuff to format_genome	commit \| commitdiff \| tree
2009-07-23	martinahansen	addid term colors to list_genomes	commit \| commitdiff \| tree
2009-07-23	martinahansen	added options to bowtie_seq	commit \| commitdiff \| tree
2009-07-22	martinahansen	added some args to bowtie_seq	commit \| commitdiff \| tree
2009-07-21	martinahansen	added test_common.c	commit \| commitdiff \| tree
2009-07-21	martinahansen	fixed bowtie_seq	commit \| commitdiff \| tree
2009-07-21	martinahansen	added read_fastq biopiece	commit \| commitdiff \| tree
2009-07-20	martinahansen	added bowtie_seq biopiece	commit \| commitdiff \| tree
2009-07-20	martinahansen	added bowtie to format_genome	commit \| commitdiff \| tree
2009-07-19	martinahansen	adding to ruby source	commit \| commitdiff \| tree
2009-07-12	martinahansen	more ruby stuff	commit \| commitdiff \| tree
2009-07-11	martinahansen	fixed bug in read_embl	commit \| commitdiff \| tree
2009-07-10	martinahansen	speedup of analyze_seq 3 fold	commit \| commitdiff \| tree
2009-07-10	martinahansen	added str_analyze to Common.pm	commit \| commitdiff \| tree
2009-07-10	martinahansen	fixed bug in create_vmatch_index	commit \| commitdiff \| tree
2009-07-10	martinahansen	fixed bug in remove_indels	commit \| commitdiff \| tree
2009-07-10	martinahansen	mucking with c and makefiles	commit \| commitdiff \| tree
2009-07-08	martinahansen	use warnings added to perl modules	commit \| commitdiff \| tree
2009-07-08	martinahansen	added use strict to all biopieces	commit \| commitdiff \| tree
2009-07-08	martinahansen	changed shebang	commit \| commitdiff \| tree
2009-07-07	martinahansen	minor changes	commit \| commitdiff \| tree
2009-07-04	martinahansen	updated seq.rb	commit \| commitdiff \| tree
2009-07-03	martinahansen	last cleanups	commit \| commitdiff \| tree
2009-07-03	martinahansen	clearning ruby dir	commit \| commitdiff \| tree
2009-07-01	martinahansen	changed seq_type from string to symbols in ruby	commit \| commitdiff \| tree
2009-07-01	martinahansen	changed seq_type from string to symbols in ruby	commit \| commitdiff \| tree
2009-06-30	martinahansen	updated ruby code	commit \| commitdiff \| tree
2009-06-30	martinahansen	cleanded up test_seq.rb	commit \| commitdiff \| tree
2009-06-30	martinahansen	added unit testing for ruby	commit \| commitdiff \| tree
2009-06-30	martinahansen	added unit testing for ruby	commit \| commitdiff \| tree
2009-06-30	martinahansen	added unit testing for ruby	commit \| commitdiff \| tree
2009-06-29	martinahansen	added seq.rb	commit \| commitdiff \| tree
2009-06-23	martinahansen	fixes and stuff	commit \| commitdiff \| tree
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
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