Commits for angie

v294_preview to v294_preview2 (2013-12-16 to 2014-01-06) v294

• In MLQ #12367, the user got a blank screen when trying to view a CTusing a Mac-mangled BAM file. Of course we need to show an error message
  instead of SEGV/blank screen; but hgCustom also shouldn't have accepted
  the file as a custom track. It turns out that the samtools lib function
  samopen() may return a non-null file handler with a null header, when the
  header is invalid. So we need to check not only for null result from
  samopen, but also null header inside non-null result. Meanwhile, I noticed
  that hgCustom's error reporting was actually masking more detailed error
  messages from lib code, because of its use of errCatch around bamFileExists.
  errCatch only lets errAbort messages propagate, not warnings; bamFileExists
  has a warn() that is lost in transmission. I added bamFileAndIndexMustExist
  which uses errAbort so that errCatch in callers will get the more informative
  error instead of having to make up one of its own. trackHub checking code
  also needed this stronger form of checking. I also moved some duplicated
  (or triplicated) code in bamFile.c into functions.
  refs #12367
  
  • src/hg/lib/customFactory.c - lines changed 6, context: html, text, full: html, text
  • src/hg/lib/trackHub.c - lines changed 2, context: html, text, full: html, text
  • src/inc/bamFile.h - lines changed 4, context: html, text, full: html, text
  • src/lib/bamFile.c - lines changed 71, context: html, text, full: html, text
• Adding Jim's edwQaEvaluate/makefile to fix broken build.
  • src/hg/encode3/encodeDataWarehouse/edwQaEvaluate/makefile - lines changed 4, context: html, text, full: html, text
• Fixing compile-breaking error: undeclared variables.
  • src/hg/encode3/encodeDataWarehouse/edwScheduleAnalysis/edwScheduleAnalysis.c - lines changed 1, context: html, text, full: html, text
• Fixing compile warning (need TRUE not "TRUE").
  • src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/edwMakeValidFile.c - lines changed 1, context: html, text, full: html, text
• Oops, forgot to add stub for bamFileAndIndexMustExist to the #else (no USE_BAM) part of bamFile.cfixes #12401
  
  • src/lib/bamFile.c - lines changed 7, context: html, text, full: html, text
• Adding #ifdef USE_BAM around encodeDataWarehouse functions that call samtools lib functions.Otherwise compile breaks without USE_BAM and/or USE_SAMTABIX.
  
  • src/hg/encode3/encodeDataWarehouse/edwScheduleAnalysis/edwScheduleAnalysis.c - lines changed 10, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/edwLib.c - lines changed 4, context: html, text, full: html, text