Speedup TODOS

[nboley]

1. make sure that reads are being piped (instead of written to temporary files) whenever possible
2. whenever reads are being piped from samtools use the -u command so that the intermediate blocks aren't compressed

• use the compression level option when piping from sambamba
  3) when/writing bams to/.from samtools use the -@ option to use additional compression threads
  4) it's only really important to use sambamba for indexing and sorting
  • QUESTION: is it faster to sort and then pipe from samtools than use sambamba with an intermediate file?
    5) Consider using samtools rmdup or sambamba markdup to avoid the picard tools bottleneck