File Changes for angie
switch to commits view, user indexv294_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
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