BQSR: add spark workarounds to BaseRecalibratorSpark
BQSR: add spark workarounds to BaseRecalibratorSpark

Fixes #2252

lbeltrame/bcbio-nextgen,chapmanb/bcbio-nextgen,vladsaveliev/bcbio-nextgen,a113n/bcbio-nextgen,a113n/bcbio-nextgen,lbeltrame/bcbio-nextgen,a113n/bcbio-nextgen,vladsaveliev/bcbio-nextgen,chapmanb/bcbio-nextgen,lbeltrame/bcbio-nextgen,chapmanb/bcbio-nextgen,vladsaveliev/bcbio-nextgen