File Changes for angie

v247_preview2 to v247_base (2011-02-08 to 2011-02-14) v247

• src/hg/encode/validateFiles/validateFiles.c
  • lines changed 2, context: html, text, full: html, text
    Feature #27 (table browser support for BAM): addition of BAM supportwithout enough #ifdef USE_BAM's led to compile errors without USE_BAM=1. Fix: add stub routines to bamFile.c so that the compile won't break, but informative error message will be printed if bamFile routines are called. I was hoping that this would obviate most of the #ifdef USE_BAM's currently in the tree, but actually most of those prevent CGIs from getting into trouble by offering BAM functionality when it isn't compiled in. So I left most current #ifdef USE_BAM's in place, but when future new code doesn't #ifdef, at least the compile won't break.
• src/hg/hgTables/bam.c
  • lines changed 4, context: html, text, full: html, text
    Feature #27 (table browser support for BAM): addition of BAM supportwithout enough #ifdef USE_BAM's led to compile errors without USE_BAM=1. Fix: add stub routines to bamFile.c so that the compile won't break, but informative error message will be printed if bamFile routines are called. I was hoping that this would obviate most of the #ifdef USE_BAM's currently in the tree, but actually most of those prevent CGIs from getting into trouble by offering BAM functionality when it isn't compiled in. So I left most current #ifdef USE_BAM's in place, but when future new code doesn't #ifdef, at least the compile won't break.
• src/hg/hgc/bamClick.c
  • lines changed 2, context: html, text, full: html, text
    Feature #27 (table browser support for BAM): addition of BAM supportwithout enough #ifdef USE_BAM's led to compile errors without USE_BAM=1. Fix: add stub routines to bamFile.c so that the compile won't break, but informative error message will be printed if bamFile routines are called. I was hoping that this would obviate most of the #ifdef USE_BAM's currently in the tree, but actually most of those prevent CGIs from getting into trouble by offering BAM functionality when it isn't compiled in. So I left most current #ifdef USE_BAM's in place, but when future new code doesn't #ifdef, at least the compile won't break.
• src/hg/inc/bamFile.h
  • lines changed 22, context: html, text, full: html, text
    Feature #27 (table browser support for BAM): addition of BAM supportwithout enough #ifdef USE_BAM's led to compile errors without USE_BAM=1. Fix: add stub routines to bamFile.c so that the compile won't break, but informative error message will be printed if bamFile routines are called. I was hoping that this would obviate most of the #ifdef USE_BAM's currently in the tree, but actually most of those prevent CGIs from getting into trouble by offering BAM functionality when it isn't compiled in. So I left most current #ifdef USE_BAM's in place, but when future new code doesn't #ifdef, at least the compile won't break.
• src/hg/lib/bamFile.c
  • lines changed 142, context: html, text, full: html, text
    Feature #27 (table browser support for BAM): addition of BAM supportwithout enough #ifdef USE_BAM's led to compile errors without USE_BAM=1. Fix: add stub routines to bamFile.c so that the compile won't break, but informative error message will be printed if bamFile routines are called. I was hoping that this would obviate most of the #ifdef USE_BAM's currently in the tree, but actually most of those prevent CGIs from getting into trouble by offering BAM functionality when it isn't compiled in. So I left most current #ifdef USE_BAM's in place, but when future new code doesn't #ifdef, at least the compile won't break.
  • lines changed 2, context: html, text, full: html, text
    MLQ #2810 (error compiling uscs genome browser): fixing a couplefunction declarations in USE_BAM=0 code, that would have been caught by compiling with the environment variable USE_BAM=0.
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    Track #671 (BDTNP for dm2): Added bdtnpDnase% to tablesIgnored for fly, thanks Greg.
• src/hg/makeDb/trackDb/drosophila/bdtnpDnase.html
  • lines changed 1, context: html, text, full: html, text
    Track #671 (BDTNP for dm2): Corrected the description of regions'default vis (squish not dense), thanks Greg.
• src/product/ex.hg.conf
  • lines changed 8, context: html, text, full: html, text
    Added some clarifying comments about central.domain and central.cookie inthe context of multiple mirror hosts. Removed bogus setting backupcentral.domain -- it is never used by the code. In retrospect, I think central.cookie and central.domain should have been named cookie.name and cookie.domain because they are distinct from the central database mysql profile. It's important that multiple central databases used by hosts in the same domain get separate cookie names, but having the central.* prefix on both db and cookie hasn't made that obvious in the past. :)