Eric Banks 1e396af4d0 Two reduce reads updates/fixes: ... 1. Removing old legacy code that was capping the positional depth for reduced reads to 127. Unfortunately this cap affectively performs biased down-sampling and throws off e.g. FS numbers. Added end to end unit test that depth counts in RR can be higher than max byte. Some md5s change in the RR tests because depths are now (correctly) no longer capped at 127. 2. Down-sampling in ReduceReads was not safe as it could remove het compressed consensus reads. Refactored it so that it can only remove non-consensus reads.		2013-08-01 14:34:59 -04:00
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gatk/walkers	Two reduce reads updates/fixes:	2013-08-01 14:34:59 -04:00
utils	Removed native method call	2013-07-30 13:59:58 -04:00