clinseq: add additional filtering options to snv-indel-report and related clean up

This pull request covers a few issues relating to the snv-indel-report step in clin-seq
- Fix a bug that resulted in some 'normal' samples not being identified correctly due to a case sensitive regex that should not have been
- Remove redundancy in code the grabs ref-align builds and related sample meta data for the snv-indel-report
- Add some additional sample metadata to the snv-indel-report subject legends file to help identify similar problems in the future
- Add some additional filtering options to remove likely false positives from the snv-indel-report results.  One of these is now engaged by default resulting in changes to test results
- Update the test results for the snv-indel-report test and the clin-seq build test to accompany this PR