CaptureStatsBAM5_extended.java and WGS_Stats_v1.java contain a lot of duplicated code

[bpow]

There is a lot of similarity between CaptureStatsBAM5_extended.java and WGS_Stats_v1.java-- similar enough that it is hard to tell where they are different and it may be difficult to maintain them as separate files (making sure that fixes make it to both). Code would ideally be refactored to make them in the same file with an option selecting different code paths as appropriate.

[cbuhay]

Thank you for your feedback. We already have refactored code combining the utility of the two programs. We simply chose not to upload it here because we are still internally testing.