Mark DePristo e19c24f3ee Bugfix for HaplotypeCaller error: Only one of refStart or refStop must be < 0, not both ... -- This occurred because we were reverting reads with soft clips that would produce reads with negative (or 0) alignment starts. From such reads we could end up with adaptor starts that were negative and that would ultimately produce the "Only one of refStart or refStop must be < 0, not both" error in the FragmentUtils merging code (which would revert and adaptor clip reads). -- We now hard clip away bases soft clipped reverted bases that fall before the 1-based contig start in revertSoftClippedBases. -- Replace buggy cigarFromString with proper SAM-JDK call TextCigarCodec.getSingleton().decode(cigarString) -- Added unit tests for reverting soft clipped bases that create a read before the contig -- [delivers #50892431]		2013-06-04 10:33:46 -04:00
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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	Bugfix for HaplotypeCaller error: Only one of refStart or refStop must be < 0, not both	2013-06-04 10:33:46 -04:00
test	Bugfix for HaplotypeCaller error: Only one of refStart or refStop must be < 0, not both	2013-06-04 10:33:46 -04:00