File Changes for angie

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

• src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/edwMakeValidFile.c
  • lines changed 1, context: html, text, full: html, text
    Fixing compile warning (need TRUE not "TRUE").
• src/hg/encode3/encodeDataWarehouse/edwQaEvaluate/makefile
  • lines changed 4, context: html, text, full: html, text
    Adding Jim's edwQaEvaluate/makefile to fix broken build.
• src/hg/encode3/encodeDataWarehouse/edwScheduleAnalysis/edwScheduleAnalysis.c
  • lines changed 1, context: html, text, full: html, text
    Fixing compile-breaking error: undeclared variables.
  • lines changed 10, 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/lib/edwLib.c
  • lines changed 4, 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/lib/customFactory.c
  • lines changed 6, context: html, text, full: html, text
    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/trackHub.c
  • lines changed 2, context: html, text, full: html, text
    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/inc/bamFile.h
  • lines changed 4, context: html, text, full: html, text
    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/lib/bamFile.c
  • lines changed 71, context: html, text, full: html, text
    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
    
  • lines changed 7, context: html, text, full: html, text
    Oops, forgot to add stub for bamFileAndIndexMustExist to the #else (no USE_BAM) part of bamFile.cfixes #12401