David Roazen bc65f6326f Detect incomplete reads from BAM schedule file in BAMSchedule before they become buffer underflows ... This fix is similar, but distinct from the earlier fix to GATKBAMIndex. If we fail to read in a complete 3-integer bin header from the BAM schedule file that the engine has written, throw a ReviewedStingException (since this is our problem, not the user's) rather than allowing a cryptic buffer underflow error to occur. Note that this change does not fix the underlying problem in the engine, if there is one (there may be an as-yet-undetected bug in the code that writes the bam schedule). It will just make it easier for us to identify what's going wrong in the future.		2012-03-09 12:33:48 -05:00
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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	Detect incomplete reads from BAM schedule file in BAMSchedule before they become buffer underflows	2012-03-09 12:33:48 -05:00
test	Avoid buffer underflow in GATKBAMIndex by detecting premature EOF in BAM indices	2012-03-08 15:30:44 -05:00