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)