Improve filtering of reads.
Improve filtering of reads.

Filtering is now carried out prior to down-sampling, to avoid the
selection of reads that would subsequently be filtered. Filtering
now removes unmapped reads, secondary alignments, reads that failed
QC, PCR duplicates, and chimeric alignments (proposed addition to
SAM/BAM specification).

ginolhac/mapDamage,ginolhac/mapDamage,ginolhac/mapDamage