Update DEEPVARIANT/* modules to support phasing.

[awgymer]

Update the split processes for DEEPVARIANT to support using phased read inputs passed between processes.

Also fix the capture pattern for small model call records output in MAKE_EXAMPLES for prefixes containing a .

See google/deepvariant#1078 for more details on the root cause of these issues and need to fix.

PR checklist

Closes #XXX

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[SPPearce]

The tests and linting are sad.

[awgymer]

Yeah, setting the phasing to false fixes the tests but I am waiting for some feedback on whether a hard failure like this is expected with the WGS mode (some of their docs suggest it only intended for ONT/Pacbio)