v139-final
(This version not released -- combined with v140-final)
Code changes:
- added download options for restriction enzyme track (Andy)
- extended some custom functions to allow multipe hgFindSpec tables to be used when multiple trackDb tables are used (Andy)
- fixed mRNA base coloring bug, made some other mods to base/codon coloring requested by David et al (Angie)
- mods to per-chrom downloads (doRepeatMasker.pl, makeDownloads.pl) (Angie)
- added new QA script - findLevel (Ann)
- implemented default group track ordering via default button on config page
(Robert)
- mods to support GAD track (Fan)
- fixed help bug, improved usage messages for phyloGif (Galt)
- added program for extracting PSL alignments from a file for each item in an lfs file (Rachel)
- various mods to snpLoad (Heather)
- added refs to isCustomTrack (Hiram)
- reworked webStartWrapperGatewayHeader (Hiram)
- mods to hgCustom, etc. (Kate)
- added routines to replace/remove item in hash table, convert to string (Kate)
- refactored custom track parsing to use customFactories (Jim)
- added param to pipelineOpen to redirect stderr (Mark)
- fixed bug in slDoubleCmp (Mark)
- added support for retrieving GTF protein_id files (Mark)
Data changes:
- reran doBlastz droSim1 vs droYak1 w/better params, also droSim1 vs droYak2 (Angie)
- started dm3 browser, using new automation scripts (Angie)
- resolved several -Wall warnings (Angie)
- removed DV track (Belinda)
- updated all_bacends PSL table for danRer3 (Rachel)
- added mm8 snp126 (Heather)
- updated hg17 dbRIP track with latest data (Hiram)
- added annotated frames to monDom4 multiz7way conservation track (Hiram)
- added rheMac2 N-SCAN track (Mark)