Added logging options for map-to-frags and to cluster-reads functions on a per read and per alignment basis. Also fixed the clustering such that all reads are written out to either the keep or discard bams (previously, some reads were not being written to either, and were therefore being lost which could screw up downstream comparisons during workflow analysis).
Added logging options for map-to-frags and to cluster-reads functions on a per read and per alignment basis. Also fixed the clustering such that all reads are written out to either the keep or discard bams (previously, some reads were not being written to either, and were therefore being lost which could screw up downstream comparisons during workflow analysis).