org.bdgenomics.adam.algorithms.consensus
For all reads in this region, generates the list of consensus sequences for realignment.
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.
Performs any preprocessing specific to this consensus generation algorithm, e.g., indel normalization.
Reads to preprocess.
Reference genome bases covering this target.
The region covered by this target.
Preprocessed reads.
Generates targets to add to initial set of indel realignment targets, if additional targets are necessary.
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.
Trait for generating consensus sequences for INDEL realignment.
INDEL realignment scores read alignments against the reference genome and a set of "consensus" sequences. These consensus sequences represent alternate alleles/haplotypes, and can be generated via a variety of methods (e.g., seen in previous projects --> 1kg INDELs, seen in read alignments, etc). This trait provides an interface that a consensus generation method should implement to provide it's consensus sequences to the realigner.