v187-preview - 15 July 2008    (Pairings)

Code changes:

• Added stderr logging message to lib/jksql.c to show mysql_error when connection attempt fails, even when we don't abort. (Angie)
• Mod to lib/carts.c: when making a new copy of saved-session custom tracks, make new copies of any auxiliary files referenced in the main custom track file. (Angie)
• Added copyFileToTrash to lib/trashDir.c. (Angie)
• Updated mouseStuff/mafToAxt/mafToAxt.c to handle more than one sequence in a block from the same species. (Brian)
• Added hg/ratStuff/mafBedSubset/mafBedSubset.c -- utility that is faster and smarter than mafsInRegion but has additional burdens. (Brian)
• Added custom option to hgLoadMaf.c to forefo using extFile or history tables. (Brian)
• More mods for custom MAFs. (Brian)
• Ongoing work on GSID. (Fan)
• Increased max protein count and added checks for overflowing MAXN in a few protein modules. (Fan)
• Added simple has resize optimization to lib/hash.c. (Galt)
• Cleaned up a few items for easier maintenance in hgTrackUi and hgTracks. (Kate)
• Bug fix to hgc/magClick.c to provide link to conservation stats when cart is clean. (Kate)
• Ongoing parasol update, added first draft of updated docs for parasol v12. (Galt)
• Replaced some strdup with cloneString in lib/hdb.c and hgFind.c to ensure that everything goes through memory management. (Jim)
• Replaced error with warning in protein/pbCalDist.c until we figure out what to do with the amino acid "u". (Jim)
• Updated proteins/spToProtein.c code. (Jim)
• Ongoing work on ENCODE validator. (Larry)
• Added utils/aumation/HgDb.pm -- class interface to the mysql databases. (Larry)
• Ongoing work on TranMap tracks. (Mark)
• Removed code from lib/pscmGfx.c that caused vertical one-pixel bars to be omitted in reverse mode ps/pdf files. (Mark)
• Ongoing work on instinct. (Steve, Zack)
• Removed obsolete function calls, other code clean-up in several modules. (Tim)

Data changes:

• Initial work on tarSyr1, pteVam1, turTru1, vicPac1. (Brian)
• More work on ce6. (Hiram)
• Finishing bits to UCSC Genes update, updated proteins db. (Jim)
• Work on nemVec1. (Kord)
• More work on equCab2. (Larry)
• Finished cavPor3 multiz8way. (Tim)