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2010-06-28	martinahansen	added usearch_seq biopiece	commit \| commitdiff \| tree
2010-06-26	martinahansen	corrected typo	commit \| commitdiff \| tree
2010-06-22	martinahansen	messing with exit in ruby - still	commit \| commitdiff \| tree
2010-06-22	martinahansen	corrected type in log messages	commit \| commitdiff \| tree
2010-06-21	martinahansen	polishing exit in ruby code	commit \| commitdiff \| tree
2010-06-17	martinahansen	added list switch to *_vals biopieces	commit \| commitdiff \| tree
2010-06-17	martinahansen	added list switch to mean_vals	commit \| commitdiff \| tree
2010-06-17	martinahansen	added fixedstep biopieces	commit \| commitdiff \| tree
2010-06-16	martinahansen	schrubbing UCSC.pm code	commit \| commitdiff \| tree
2010-06-16	martinahansen	fixed s/Common/Filesys/ renaming in UCSC.pm	commit \| commitdiff \| tree
2010-06-16	martinahansen	ruby code fixing exit	commit \| commitdiff \| tree
2010-06-16	martinahansen	ruby code fixing exit	commit \| commitdiff \| tree
2010-06-15	martinahansen	ruby code schrubbing	commit \| commitdiff \| tree
2010-06-14	martinahansen	fixed unit tests for biopieces.rb	commit \| commitdiff \| tree
2010-05-28	martinahansen	trouble with list of list and class Cast	commit \| commitdiff \| tree
2010-05-28	martinahansen	splitting class Biopieces	commit \| commitdiff \| tree
2010-05-28	martinahansen	splitting class Biopieces	commit \| commitdiff \| tree
2010-05-28	martinahansen	updating ruby code	commit \| commitdiff \| tree
2010-05-28	martinahansen	cleaned up ruby dir	commit \| commitdiff \| tree
2010-05-27	martinahansen	ruby unit tests refactored	commit \| commitdiff \| tree
2010-05-27	martinahansen	updated biopieces code	commit \| commitdiff \| tree
2010-05-25	martinahansen	added plot_scores fix	commit \| commitdiff \| tree
2010-05-25	martinahansen	added plot_scores	commit \| commitdiff \| tree
2010-05-20	martinahansen	fixed missing SEQ_LEN in read_454	commit \| commitdiff \| tree
2010-05-20	martinahansen	added solexa_str_mean to read_454	commit \| commitdiff \| tree
2010-05-20	martinahansen	added bp_scripts directory and stats scripts	commit \| commitdiff \| tree
2010-05-19	martinahansen	added read_454 and write_454 (and ruby stuff)	commit \| commitdiff \| tree
2010-05-18	martinahansen	extract seq now also extract SCORES if present	commit \| commitdiff \| tree
2010-05-18	martinahansen	fixed harmless bug in remove_adaptor	commit \| commitdiff \| tree
2010-05-14	martinahansen	cleaning up ruby code dir	commit \| commitdiff \| tree
2010-05-11	martinahansen	fixed bug in write_fixedstep	commit \| commitdiff \| tree
2010-04-27	martinahansen	fixed speed issue with track_ruler in BGB	commit \| commitdiff \| tree
2010-04-26	martinahansen	optimized track_ruler in BGB	commit \| commitdiff \| tree
2010-04-20	martinahansen	added trimming of scores to remove_adaptor	commit \| commitdiff \| tree
2010-04-06	martinahansen	fixing undef $clade bug in BGB	commit \| commitdiff \| tree
2010-03-31	martinahansen	dna page session export bug in BGB	commit \| commitdiff \| tree
2010-03-30	martinahansen	fixed 0 defined bug in BGB	commit \| commitdiff \| tree
2010-03-22	martinahansen	ugly fix of BGB ladder problem	commit \| commitdiff \| tree
2010-03-22	martinahansen	fixing ladder bug in BGB	commit \| commitdiff \| tree
2010-03-19	martinahansen	added PDF/SVG export to BGB	commit \| commitdiff \| tree
2010-03-19	martinahansen	added grid to BGB	commit \| commitdiff \| tree
2010-03-18	martinahansen	added collapsable tracks to BGB	commit \| commitdiff \| tree
2010-03-18	martinahansen	BGB cleanup	commit \| commitdiff \| tree
2010-03-18	martinahansen	error handling and seq guess fix	commit \| commitdiff \| tree
2010-03-17	martinahansen	removed indexing from BGB_upload	commit \| commitdiff \| tree
2010-03-15	martinahansen	added N block switch to blat_seq	commit \| commitdiff \| tree
2010-03-14	martinahansen	fixed minor BGB bug	commit \| commitdiff \| tree
2010-03-14	martinahansen	fixed BGB issues terrible	commit \| commitdiff \| tree
2010-03-14	martinahansen	added persistent sessions to BGB	commit \| commitdiff \| tree
2010-03-13	martinahansen	fixed login issue in BGB	commit \| commitdiff \| tree
2010-03-13	martinahansen	changed BGB session format to JSON	commit \| commitdiff \| tree
2010-03-13	martinahansen	added static link to BGB	commit \| commitdiff \| tree
2010-03-08	martinahansen	tweaks to blat_seq to avoid introns in fastMap - still...	commit \| commitdiff \| tree
2010-03-05	martinahansen	layout of wiggle improved	commit \| commitdiff \| tree
2010-03-05	martinahansen	wiggle tracks display - almost there	commit \| commitdiff \| tree
2010-03-05	martinahansen	fixing wiggle tracks in BGB	commit \| commitdiff \| tree
2010-03-04	martinahansen	reworked list_inflate/deflate	commit \| commitdiff \| tree
2010-03-04	martinahansen	chasing wiggle bug	commit \| commitdiff \| tree
2010-03-03	martinahansen	fixed bug in list_deflate	commit \| commitdiff \| tree
2010-03-03	martinahansen	fixed empty Q_ID val in BGB	commit \| commitdiff \| tree
2010-03-03	martinahansen	added find_gaps	commit \| commitdiff \| tree
2010-03-02	martinahansen	fixed bug in Seq.pm	commit \| commitdiff \| tree
2010-03-02	martinahansen	cleaned up BGB track code	commit \| commitdiff \| tree
2010-03-02	martinahansen	merged BGB::Common.pm to BGB::Track.pm	commit \| commitdiff \| tree
2010-03-02	martinahansen	BGB cleanup of index.cgi	commit \| commitdiff \| tree
2010-03-02	martinahansen	BGB cleanup of hrefs	commit \| commitdiff \| tree
2010-03-01	martinahansen	added center navigation to BGB	commit \| commitdiff \| tree
2010-03-01	martinahansen	added wiggle to BGB	commit \| commitdiff \| tree
2010-03-01	martinahansen	added wiggle to BGB	commit \| commitdiff \| tree
2010-02-11	martinahansen	fixed issue in KISS.pm but more found	commit \| commitdiff \| tree
2010-02-11	martinahansen	added option for database search to blat_seq	commit \| commitdiff \| tree
2010-02-10	martinahansen	fixed feature width issue	commit \| commitdiff \| tree
2010-02-10	martinahansen	added arrows to BGB	commit \| commitdiff \| tree
2010-02-09	martinahansen	added color routine to Draw.pm	commit \| commitdiff \| tree
2010-02-09	martinahansen	moving back to binned index and using JSON for storing	commit \| commitdiff \| tree
2010-02-09	martinahansen	changed kiss score to bit_score instead of eval	commit \| commitdiff \| tree
2010-02-06	martinahansen	added search function to NClist.pm	commit \| commitdiff \| tree
2010-02-06	martinahansen	fixed BGB search function	commit \| commitdiff \| tree
2010-02-06	martinahansen	debugging search function in NClists.pm	commit \| commitdiff \| tree
2010-02-06	martinahansen	added search function to NClist.pm	commit \| commitdiff \| tree
2010-02-06	martinahansen	removed dir check from create_bowtie_index	commit \| commitdiff \| tree
2010-02-06	martinahansen	shifted to NC list in BGB	commit \| commitdiff \| tree
2010-02-06	martinahansen	added uniq_seq	commit \| commitdiff \| tree
2010-02-06	martinahansen	fix of read_kiss code comments	commit \| commitdiff \| tree
2010-02-05	martinahansen	fixed bugs in BGB	commit \| commitdiff \| tree
2010-02-03	martinahansen	added NClist.pm	commit \| commitdiff \| tree
2010-01-31	martinahansen	fixed sequence type guessing in create_blast_index	commit \| commitdiff \| tree
2010-01-29	martinahansen	changed sorting in BGB	commit \| commitdiff \| tree
2010-01-28	martinahansen	repair on plot_karyogram	commit \| commitdiff \| tree
2010-01-28	martinahansen	repair on plot_karyogram	commit \| commitdiff \| tree
2010-01-26	martinahansen	fixed a number of issues - grave bug in complement_seq!	commit \| commitdiff \| tree
2010-01-25	martinahansen	add q_id specificity to assemblo_contigs	commit \| commitdiff \| tree
2010-01-25	martinahansen	added strand specificity fo assemble_contigs	commit \| commitdiff \| tree
2010-01-24	martinahansen	cleanup BGB stuff	commit \| commitdiff \| tree
2010-01-22	martinahansen	fixed URI::Escape on q_id in BGB	commit \| commitdiff \| tree
2010-01-21	martinahansen	added plot_lines	commit \| commitdiff \| tree
2010-01-19	martinahansen	changed uclust engine from CD-hit to uclust	commit \| commitdiff \| tree
2010-01-19	martinahansen	fixed strand bug in SAM.pm	commit \| commitdiff \| tree
2010-01-13	martinahansen	changed engine in cluster_seq to uclust	commit \| commitdiff \| tree
2010-01-12	martinahansen	added cluster_seq	commit \| commitdiff \| tree
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