Parameters for Mapping Filtering

introduce some new and rename a couple of existing parameters that are linked to filtering of read mappings before they are passed to the annotation mapper:

create EnumSet "SAMfilters" with the values

Validation Stringency: switches stringency for validating several SAM flags
PrimaryOnly (replaces "useFlags"): only allow primary alignments
MatesOnly: only allow read pairs that are linked by the SAM file (no exhaustive combination)