RNA-seq: filter primary alignments with samtools
RNA-seq: filter primary alignments with samtools

Avoids use of sambamba view with multiple cores, which causes segfaults
on some systems. Thanks to @skanwal

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