osteosarc 0.13.2

Faster read extraction (#80).

• Leave out mates with no position. extract_reads(..., fetch_pairs=True, unplaced_mates=False), or osteosarc reads --placed-mates:
  • It gives what fetch_pairs=True gives, less the mates that didn't align and have no position of their own, as STAR stores them. Finding those means reading every such read in the BAM.
  • Six extractions from an RNA-seq BAM took 40 s instead of 68 s: the same reads, less 28 unplaced mates.
  • Bundles can opt in with make_bundle(..., unplaced_mates=False) or test-data make --placed-mates. By default they keep every mate, as before.
• osteosarc reads SAMPLE reads a sample's BAMs four at a time, and the first error stops those not yet begun.
• Time limit. An extraction's limit covers all its samtools runs.

Additive: nothing is removed or renamed.