v158-final - 1 May 2007    (Pairings)

Code changes:

• Updates to switchDbTss track code. (Andy)
• Added utility for coloredExon track-making (utils/colorExonToBed/coloredExon.c). (Andy)
• Fixed hgFind.c to look for unsplit gold table first. (Angie)
• Changed instance of cartUsualInt to cgiUsualInt in a !useCart secrion of phyloGif code. (Angie)
• Added -useHashedName to mafSplit.c for splitting by target when we need a repeatable many-to-one mapping of sequence names to split file names. (Angie)
• Mods to makePushQSql.pl automation script. (Angie)
• Modified refreshNamedSessionCustomTracks.c -- Instead of directly connecting to the central db named on the command line, use hConnectCentral so that the hg.conf file's main connection info is still for the genome db's, which may be required for hGetMinIndexLength when reading in custom tracks. Changed hgTracks.c to make sure Locus Variants searched items are displayed even if the category is hidden. (Belinda)
• Work on history/tubeTree -- the source used to draw the PRAME tree. (Brian)
• Changed psLineTo to a global in ine/psGfx.h. (Brian)
• Added support for exaptedRepeats track. (Craig)
• Updated GeneSorter for KGIII-specific processing. (Fan)
• Fixed GeneSorter go.c -- with KGIII, the protein field in knownCanonical is no longer a UniProt ID. (Fan)
• Ongoing work on GSID. (Galt)
• Added alternate entry point in lib/cart.c to support additional optional header info, e.g. can use for META tags. (Galt)
• Added pixel-fattened routines to pscmGfx.c for line & polygon including stroked outline, added use of new pixel-fattened polygons in hCytoBand.c for good-looking centromere. (Galt)
• Added support for ENCODE Gencode RACEfrags track to hgTracks.c. (Rachel)
• Added definition for lfNoIntronLines to hgTracks.h -- used to flag that no lines should be drawn between exon blocks. (Rachel)
• Modified colors for CNP subtracks. (Heather)
• Added fix to wiggleCart.c for problem of recognizing autoScale=on from custom tracks. (Hiram)
• Modified memalloc.c to show errno on failed malloc calls. (Hiram)
• Added UCSC ID to title in hgGene.c. (Jim)
• Work on mm8 KGIII. (Jim)
• Made singleExonMacOverlap a command line paramenter in txBedToGraph. (Jim)
• Tweaked output format of makeOrthoAtgTable.c for Webb's paper. (Jim)
• Added link to user survey from hgGateway, hgTracks. (Kate)
• Added support for multiple conservation wiggles in wigMaf tracks to several modules. (Kate)

Data changes:

• Reloaded ORegAnno tracks on hg18, dm2. (Belinda)
• Added human proteins track for bosTau3, ornAna1. (Brian)
• Added hg18 exaptedRepeats track. (Craig)
• Generated comparative alignments w/equCab1 for several organismsl. (Fan)
• Added new Illumina arrays to hg18 SNP Array track. (Heather)
• Split up processing for delConrad and delMcCarroll to properly handle delConrad thickStart/thickEnd. (Heather)
• Ongoing work on new worm assemblies. (Hiram)
• Prepped cavPor2, eriEur1, oryCun1, sorAra1 for multiple alignment. (Kate)
• More work on 28way alignment. (Kate)