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Analyses done in https://github.com/broadinstitute/gatk/issues/1056 show that resulting bams are identical (tested on bams up to 30GB of size so far).\r\n\r\nAdded a test for it - note that it uses a 27MB file that is not in LFS, which may be a problem. (we could switch to using the standard BAM and using -L to limit territory. Using full file takes 3-4 minutes which is too slow for testing)\r\n\r\nAlso added some utility methods to a few testing classes so that we can test this properly. Added full tests for added functionality. \r\n\r\n@lbergelson  please review 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