For all reads in this region, generates the list of consensus sequences for realignment.
Reads to generate consensus sequences from.
Consensus sequences to use for realignment.
Performs any preprocessing specific to this consensus generation algorithm, e.
Reads to preprocess.
Reference genome bases covering this target.
The region covered by this target.
Generates targets to add to initial set of indel realignment targets, if additional targets are necessary.
Returns an option which wraps an RDD of indel realignment targets.
The CIGAR to process.
The number of alignment blocks that are alignment matches.