Commits for aamp

v254_preview to v254_preview2 (2011-07-05 to 2011-07-12) v254

• Separated BAM code into that which must compile into jkhgap.a (and be linked with mysql), and that which can go into jkweb.a (most of it). Older BAM open, fetch, and exists functions call the new ones with the UDC fuse root parameter set to the hg.conf setting. It is not yet clear to me if the UdcFuseRoot parameter can be set to NULL and used in a general way.
  • src/hg/inc/bamFile.h - lines changed 94, context: html, text, full: html, text
  • src/hg/lib/bamFile.c - lines changed 644, context: html, text, full: html, text
  • src/inc/bamUdc.h - lines changed 132, context: html, text, full: html, text
  • src/lib/bamUdc.c - lines changed 686, context: html, text, full: html, text
  • src/lib/makefile - lines changed 1, context: html, text, full: html, text
• changed the errAbort back to a warning. Also fixing (hopefully fixing) problem loading the index of local BAM files. with remote BAM files a chdir to a trash dir is made where the index is automatically downloaded however if the index is local, then the chdir is actually moving away from the index file and it cannot load correctly. so I check if the file is a URL or not first.
  • src/lib/bamUdc.c - lines changed 8, context: html, text, full: html, text
• compile-error fixed: unused var
  • src/lib/bamUdc.c - lines changed 4, context: html, text, full: html, text