phase out use of biobambam2

[keiranmraine]

Now samtools/htslib has been overhauled most of the tools we use in biobambam2 are available in an similarly efficient state but with a far shorter build time.

work through the mapping flows and drop use of biobambam2.

1-2 weeks work, also need to review other tools in stack specifically cgpPindel and BRASS.

This may be useful for multi pipe requirements:
samtools/samtools#774 (comment)