v138-final - 07-24-2006

Code changes:

• Several mods to microarray/expression code: e.g., way to limit # of rows loaded, require min # of measurements for mean/median when combing arrays, etc. (Andy)
• Mod to checkHgFindSpec.c - on single match, list name, browserName, description (Angie)
• Added utils/simplePartition.pl - computes a partition of a .2bit, creating as many dir levels as needed to guarantee <-1000 dir size (Angie)
• Upgraded pslCDnaGenomeMatch.c to snp126 format (Robert)
• Fixed bug causing browser to crash on some 3-base MAF alignments (Brian)
• Added GAD to hgGene (Fan)
• Added more attibute types to gvUi.c (Belinda)
• Cleaned up sample row output problems on hgTables schema display under certain conditions (Hiram)
• Added filtering for known/not known disease state, allele frequency in dbRIP (Hiram)
• Refinements to dbRIP track code (Hiram)
• Added allele homozygosity and heterozygosity calculated frequencies to polyGenotype.* (Hiram)
• Added check for chimp chroms that no longer exist under new numbering scheme (Kate)
• Removed many obsolete files (Mark)
• Reorganized some code in blastToPsl (Mark)
• Added org label to transMap alignment tracks (Mark)
• Redid MGC details page, refactored MGC/CCDS modules to support this (Mark)
• Added option to genePred to handle implied stop codon outside of CDS (Mark0
• Added more table-building functions to web.* (Mark)
• Refactored several modules in hg/overlapSelect in prep for reading directly from DB tables, added -overlapBases option (Mark)
• Added -impliedStopAfterCds option to utils/gtfToGenePred/gtfToGenePred.c (Mark)

Data changes:

• Added affyHumanExon arrays (Andy)
• Work on galGal3 (Angie)
• Added CENSOR Repeats track (Robert)
• Mods to GAD track (Fan)
• Reloaded mm8/monDom4 chains/nets (Hiram)
• Added panTro2 conservation track, Genscan, quality scores (Kate)
• Reloaded canFam2 nscanPep to fix naming bug (Mark)
• Removed bogus MGC genes config in genbank.conf for monDom4 (Mark)
• Added gi column to gbCdnaInfo (Mark)