Adding in a bam QC filter, a read-only BAMFilter. Should work fine when composing with the BAMDupMarkFilter.
A read only filter for bam QC metrics. Currently it's only turned on with mark duplicates (so .bam output and sorted). Counts reads and duplicates. Gives same results as GATK. Still some debug output, will be fixed in future commits.

Next up are the implementation of the other Picard metrics. Might be best to keep all the QC metrics inside one filter (rather than having lots of filters - one per metric).
Read filter now produces standard Picard QC metrics; minus:
 - Number of Mismatching HQ Bases
 - Number of bases covered to >=20x depth
 - Fingerprinting

The table formatting utilizes a deprecated class: ostrstream. This causes a warning at compile time.

The table needs to be output to a file specified on the command line, currently it prints to stdout.
Merge branch 'MAPQ-matei' of https://github.com/amplab/snap into chartl_bam_qc_metrics

Conflicts:
	Makefile