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.
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: https://github.com/samtools/samtools/issues/774#issuecomment-365550905