v159-preview - 8 May 2007    (Pairings)

Code changes:

• Fixed hgTracks.c, linkedFeaturesLabelNextPrevItem -- update cart position so that links using only hgsid (like PDF/PS) will correctly get new position. (Angie)
• Mod to automation/makeGenomeDb.pl -- when an assembly includes AGP but we fetch chrM from GenBank, make fake gap/gold entry to avoid featureBits anomalies. Also, include all_est in template trackDb.ra for scaffold-based, in case it's needed. (Angie)
• Fix to wigMafTrack.c to correct problem printing garbage past end of string. (Brian)
• Ongoing work on GSID. (Fan, Galt)
• Fixed GS go.c problem w/KGIII, corrected logic for KGIII-specific processing for protein lookup. (Fan)
• Added logic to pbGlobal.c to handle empty query string. (Fan)
• Added more Illumina choices to upload types in hgGenome/upload.c. (Galt)
• Fixed hgTracks bug caused by missing close quote on A-tag HREF. (Galt)
• Mods to hgc -- removed htcCdnaAliInWindow for hgBlat type="user" alignments, added support for hgBlat results to htcCdnaAliInWindow(). (Galt)
• Added Illumina 550 and 650 beadchip support to lib/chromGraphFactory. (Galt)
• Updated lib/psGfx.c to support display in ghostview 4.x. (Galt)
• Changed set-clip routine call in pscmGfx.c. (Galt)
• Minor hapmapTrack.c tweak. (Heather)
• Fixed customFactory.c error msgs when chrom names are case-sensitive, which may cause trouble. (Hiram)
• Modified hgLoadWiggle.c -- indicate chrom name case-sensitivity when can't find size. (Hiram)
• Mods to several files to fix SPARC compilation problems. (Hiram)
• Mods to protein/pbCalDist, pbCalResStd. (Jim)
• Fixed problem w/hgTables/correlate.c on Conservation tracks introduced by multiple wiggle feature. (Kate)
• Improved TB correlate support for wigMaf-type tracks. (Kate)
• Modified hgTrackUi.c -- removed defaults button from MAF tracks that don't have default species off set. (Kate)
• Removed 1-pixel adjustment to wiggle track height in hgTrack.c -- it results in misplaced map boxes. (Kate)
• Fxied problems in wigMafTrack.c with base-level display of wiggleless wigMaf tracks introduced with the multiple wiggle feature. (Kate)
• Added support for priority.ra files that override trackDb in the same fashion as visibility.ra files. (Kate)

Data changes:

• Work on ornAna1. (Angie)
• Minor tweaks to horse. (Fan)
• Added ENCODE ChIP/chip track from Stanford. (Heather)
• Finished up work on 5 worms. (Hiram)
• Added nibbImageProbes to mm8. (Jim)
• Added DNA replication origins data from U. VA. (Kate)
• Added new tracks for UC Davis ChIP/chip data. (Ting)