v153-final - 26 Feb. 2007    (Pairings)

Code changes:

• Modified UI options for CGAP SAGE track, added 3 mb display limit. (Andy)
• Added new indel display options for double-sided inserts, query inserts, and valid polyA tail query inserts. (Angie)
• Mods to inc/dnautil.h: added tailPolyASize and headPolyTSize to measure size without masking. Fixed off-by-one error in trimSize calculation for headPolyT. Changed new polyA/T sizing routines to be looser than the masking routines. (Angie)
• Bug fix to chopString in cartLoadSettings. (Angie)
• Edits to hgTables files to fix Galaxy connection for Galaxy2; also added MAF output. (Belinda)
• Removed 2 methods from hgTables.c that were replaced by parameterized doMetaData method. (Bob)
• Added support for Roman numerals up to XXI for stickleback (except for chrX). (Bob)
• Added support in hgTracks.c for zooming out to ranges less than 30 bp. (Brian)
• GSID mod to improve security for member passwords. (Galt)
• Work on hapmapAllelesOrtho. (Heather)
• Mod to hgTracks.c to display contig/scaffold count and total genome size on chromInfoPage display. (Hiram)
• Added gateway pages, pix for several organisms. (Hiram)
• Ongoing work on Known Genes III. (Jim)
• Renamed doRHmap function to doZfishRHmap because it is specific to zfish. (Rachel)
• Added code to hgc.c to process rhMapZfishInfo table, which now includes a ZFIN ID. Added function to create ZFIN custom URL to link to ZFIN site via ZFIN IDs. (Rachel)

Data changes:

• Added CGAP SAGE track. (Andy)
• Updates to several trackDb.ra files: Removed obsolete settings for cdsDrawDefault, cdsDrawOptions and pslSequenceBases. Upgraded baseColorDefault to diffCodons for native mRNAs. Added some recent settings from the top-level to lower-level definitions that were missing them. Added new indel* settings (invisible unless hg.conf has browser.indelOptions set), so that native mRNAs have double-sided insert, query insert and polyA display on by default; other GenBank tracks will have double-sided insert and query insert on by default.
• Added ornAna1 chain/net to hg18. (Angie)
• Initial work on equCab1 (horse) browser. (Fan)
• Added VISTA Enhancers track. (Galt)
• knownToVisiGene table updates. (Galt)
• Work on bosTau3. (Heather)
• Added hg17 snpRecombRateHapmapPhase2. (Heather)
• Work on anoCar1 (lizard) browser and alignments to other organism. (Hiram)
• Reran hg18/medaka alignments to correctly cover human randoms. (Hiram)
• Work on hg18 20-something multiple alignment. (Kate)
• Mods to GO ordering for worms, zebrafish. (Kate)
• Remade the danRer4 RH map track to fix some problems. (Rachel)
• Remade danRer3 RH map track using Blat filtering parameters determined for RH map markers on danRer4. (Rachel)