Use Picard tools's CompareSAMs for verifying SAM equality in end-to-end tests
At the moment we're using cmp to verify the equality of SAM files in the end-to-end testing pipeline. Are byte-by-byte comparisons too stringent in this case? If so, consider using CompareSAMs from Picard tools for more lenient comparisons.
At the moment, CompareSAMs is broken, as it reports the same file as being different from itself. See their issues #284 and #260. Both issues were closed ages ago, but it's still an issue in their (latest at this time) 2.27.4 release.