New test and proposed fix for EXCLUDE_UNALIGNED = true and default
S=Y,MT
Remove test output from repository; add asserts
Streamline logic, independent output paths for test data
Merge branch 'independent_tests' into exclude_unaligned
Merge branch 'independent_tests' into exclude_unaligned
Version 1.13: EXCLUDE_UNALIGNED=true for SplitBamByChromosome
Merge remote branch 'kt6-remote/exclude_unaligned' into devel
Flip version back to 1.12 as we have not released that yet