Commits for hiram

v242_preview to v242_base (2010-10-05 to 2010-10-12) v242

• cache calls to hTrackDbForTrack and hFindTableInfo to fix slow queries on contig-based assemblies
  • src/hg/hgTables/bedList.c - lines changed 33, context: html, text, full: html, text
• identify source of alloc error
  • src/lib/memalloc.c - lines changed 1, context: html, text, full: html, text
• priPac1 has become priPac2
  • src/hg/makeDb/trackDb/worm/ce9/trackDb.ra - lines changed 2, context: html, text, full: html, text
• reworked priPac1 to be priPac2 in the 10-way and working on phastCons
  • src/hg/makeDb/doc/ce9.txt - lines changed 274, context: html, text, full: html, text
• trying a cache of loadTrackDb result
  • src/hg/hgTables/bedList.c - lines changed 33, context: html, text, full: html, text
  • src/hg/lib/hdb.c - lines changed 13, context: html, text, full: html, text
• eliminate the chrom argument from function hTrackDb() in hdb.c
  • src/hg/encode/hgEncodeDataVersions/hgEncodeDataVersions.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgApi/hgApi.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgGenome/import.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTables/hgTables.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgc/hgc.c - lines changed 2, context: html, text, full: html, text
  • src/hg/inc/hdb.h - lines changed 7, context: html, text, full: html, text
  • src/hg/lib/hdb.c - lines changed 9, context: html, text, full: html, text
  • src/hg/lib/hui.c - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/makeTrackIndex/makeTrackIndex.c - lines changed 1, context: html, text, full: html, text
• these free operations are currently dangerous with cached tdb
  • src/hg/lib/trackDb.c - lines changed 6, context: html, text, full: html, text
• there are no calls to hTrackDb(NULL) except in obsolete hgText.c
  • src/hg/lib/hdb.c - lines changed 1, context: html, text, full: html, text
• done with phastCons starting on phyloP for 10-way
  • src/hg/makeDb/doc/ce9.txt - lines changed 175, context: html, text, full: html, text
• adjust priorities on the 10-way tracks and now displaying phastCons both graphs and first phyloP
  • src/hg/makeDb/trackDb/worm/ce9/trackDb.ra - lines changed 9, context: html, text, full: html, text
• done with 10-way alignment
  • src/hg/makeDb/trackDb/worm/ce9/trackDb.ra - lines changed 3, context: html, text, full: html, text
• back out the hTrackDb caching, doesn't work
  • src/hg/lib/hdb.c - lines changed 8, context: html, text, full: html, text
  • src/hg/lib/trackDb.c - lines changed 4, context: html, text, full: html, text
• done with blastCe9SG ce9 sangerGene tblastn
  • src/hg/makeDb/doc/bruMal1.txt - lines changed 177, context: html, text, full: html, text
  • src/hg/makeDb/doc/caeRem3.txt - lines changed 175, context: html, text, full: html, text
  • src/hg/makeDb/doc/cb3.txt - lines changed 178, context: html, text, full: html, text
  • src/hg/makeDb/doc/melHap1.txt - lines changed 173, context: html, text, full: html, text
  • src/hg/makeDb/doc/melInc1.txt - lines changed 173, context: html, text, full: html, text
• done with all 9 tblastn.ce9SG
  • src/hg/makeDb/doc/bruMal1.txt - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/doc/caeJap3.txt - lines changed 180, context: html, text, full: html, text
  • src/hg/makeDb/doc/caePb2.txt - lines changed 181, context: html, text, full: html, text
  • src/hg/makeDb/doc/caeRem3.txt - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/doc/cb3.txt - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/doc/haeCon1.txt - lines changed 179, context: html, text, full: html, text
  • src/hg/makeDb/doc/melHap1.txt - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/doc/melInc1.txt - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/doc/priPac2.txt - lines changed 179, context: html, text, full: html, text
• adding blastCe9SG
  • src/hg/makeDb/trackDb/worm/trackDb.ra - lines changed 19, context: html, text, full: html, text
• adding blastCe9SG business, this should be done from trackDb variables ...
  • src/hg/hgc/hgc.c - lines changed 7, context: html, text, full: html, text