v148-preview - 4 Dec. 2006

Code changes:

• Fixes to next-exon button. (Andy)
• Mods to doWindowMasker.pl script. (Andy)
• Resolved many -Wall warnings. (Angie)
• Removed local forcing of HG_WARN to HG_WARN_ERR so it can be controlled for entire source tree in common.mk. (Angie)
• Added htmlTextOut for flyBase2005Zref.synonyms because it sometimes contains non-HTML markup tags. (Angie)
• Ongoing GSID work. (Fan)
• Added meta tags to suppress caching so that cartReset cgi will always be executed when browser processes URL with cartReset. (Galt)
• Fixed hgBlat top menubar by processing an org change before the cart initialization call that draws the top menu. (Galt)
• Added code to hgBlat to detect DB change and respond by clearing the position variable (fixed problem with position variable being out of synch, which affected several cgis). (Galt)
• Final tweaks to the SNP sequences from last week's code review. (Heather)
• Incorporated ortho alleles UI feedback from Jim/David into hgc.c and snp125Ui.c. (Heather)
• Mod to customFactory: chromStart must be < than chromEnd. (Hiram)
• Assorted mods to doWindowMasker.pl. (Hiram)
• Added support for hg17 encodeEvoFold track. (Jakob)
• Ongoing work on hgGenome. (Jim)
• Moved hgTables/javascript.c to hg/lib/jsHelper.c, did some "librarifying". (Jim)
• Added auto-recogntion of Affymetrix 500k IDs to chromGraphFactory (added markerRecognizer to accomplish this). (Jim)
• Added htmlNbSpaces to htmshell. (Jim)
• Added separate configuration edit box to hgCustom Update page. (Kate)
• Added variant of BED5 float tables for ENCODE and other p-value tracks. (Kate)
• Fixed RT #1427 in hgCustom navigation (visiting track UI causes Update page to appear instead of Manage page). (Kate)
• Added code to hdb.c to connect to hgcentarchive server and return NULL rather than abort if can't connect. Added function to check whether liftOver chain files exist in /gbdb, check this when geting the list of liftOver To database. (Rachel)
• Added check to hgLiftOver.c and hgConvert.c for connection to hgcentarchive. If no connection, report that archived DBs are unavailable. (Rachel)

Data changes:

• Added dm3 chain/net to new fly assemblies. (Angie)
• Added BGI SNPs and Coverage for galGal3. (Angie)
• Reloaded gv* tables for Locus Variants track. (Belinda)
• Removed specific mention of BTKbase from Locus Variants track description and replaced with general IDbases. (Belinda)
• Updated mm8 miRNA track using new data from 3rd party. (Fan)
• Added search for uniGene_3. (Fan)
• Mods for gsidTable: removed unneeded second hidden form, added count of number of records passing filter displayed at the bottom. (Galt)
• Work on oryLat1. (Hiram)
• Updated ENCODE EvoFold track. (Jakob)
• Edited methods on affyZonWildType description page. (Rachel)