v154-preview - 5 Mar. 2007    (Pairings)

Code changes:

• Added linkable position on CGAP Sage track details page. (Andy)
• In hgTracks/linkedFeaturesDrawAt, don't draw each codon if zoomed out past the codon-per-pixel level. lf->codons might still be non-NULL so that we can OverdrawDiff later, so gate it with zoom level. (Angie)
• Changed galaxy connection to galaxy2 in several modules. Allow all output formats to be sent to galaxy. (Belinda)
• Fixed zoom-in problem resulting in 2000-bp view. (Brian) live. (Angie)
• Tweaked customFactoryTestExistence -- now touches custom tracks that are
• Updated spDbAddVarSplice.c to put out accession IDs as variants' displayID instead of parents' displayID. (Fan)
• Added password change capability to gsidMember. (Galt)
• Fixed date problems in paraHub. (Galt)
• Ongoing work on HapMap track. (Heather)
• Updated customFactory.c -- use of the hgLoadBed for the loader to streamline argument passing, now handling negative scores in bed files submitted for custom tracks. (Hiram)
• Implemented -allowNegativeScores option in hgLoadBed.c. (Hiram)
• Added percent-masked printouts with -showPercent argument -- faSize.c (Hiram)
• Ongoing work on Known Genes III. (Jim)
• Work on GeneSorter for hg18a. (Jim)
• Added some makefiles to higher-level visiGene dirs, corrected warnings. (Jim)
• Made fromProbePsl case (knownToVisiGene.c) more precise and ~1000x faster. (Jim)
• Mark TB-generated custom tracks to indicate they have not been through the factory parser, although they are written to the trash file. This notifies customTrackSave that they need to be rewritten, assuring they will land in the database. (Kate)
• Exclude special TB setting from original track line used by update screen. (Kate)
• Added support to GenBank processing for hg18 CCDS. (Mark)
• Added support for retroGene track. (Robert)
• hgTracks mod -- show arrows in retroGene track even when small gaps present in annotation. (Robert)

Data changes:

• Added GeneTrap for mm6-8. (Angie)
• Completed horse (equCab1) initial release. (Fan)
• Completed lizard (anoCar1) initial release. (Hiram)
• Added hg18a for preliminary KGIII testing. (Jim)
• Preliminary run of hg18 25-way alignment. (Kate)
• 2X mammals (cavPor2, eriEur1) for hg18 28-way alignment. (Kate)
• Updated CCDS for hg17, hg18, mm8. (Mark)
• Added retroGene tables. (Robert)