WIP: Makes bas output more logically comparable to pre 4.1.x release outputs

[keiranmraine]

For discussion only, do not merge: @am3, @kathryn-beal @drjsanger

• pre 4.1.0 bam stats didn't include qc_failed for any statistic, new does (with bugs).
• Subtracting qc_failed* reads from total_reads* proves that internal data in question is fine, used pipeline lane level bas files to confirm this.
• All of the stats that require mapped reads shouldn't include qcfail, which is why these values look wildly out.

This hotfix will resolve the above issues making BAS outputs directly comparable for all fields except total_reads* and fields introduced in 4.1.0+.

[ghost]

Changes look reasonable to me.

[keiranmraine]

Verified results against broken and pre 4.1.0 version. Appropriate fields correlate (mixed between the 2).