CRAM: Interaction between APDelta and Multi-Reference Slices

[jmthibault79]

Summary of a discussion with a note for future investigation:

Container Compression Headers have their APDelta flag set when the file is Coordinate Sorted, which affects the behavior of the alignmentStart / alignmentDelta fields in the Container's CramCompressionRecords. Suppose we had a Multi-Reference Slice in a Container with APDelta = true.

• How would we calculate alignmentDelta between two consecutive records with differing references?
• Does the concept of a delta even make sense here?
• Do we have sufficient guards against this happening, if it's a problem?

This came up when I broke a test on a private branch by assuming that a Multi-Ref context automatically implies APDelta = false. Removing that assumption fixed the test.

CramContainerStreamWriter looks like a good start for this investigation, particularly DEFAULT_SLICES_PER_CONTAINER and DEFAULT_RECORDS_PER_SLICE

[jmthibault79]

Note: the spec requires Multi-Ref to NOT be delta-encoded (section 10.2), so we should enforce this. Also note that we no longer store alignmentDelta after #1304