Package org.broadinstitute.hellbender.transformers
package org.broadinstitute.hellbender.transformers
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ClassDescriptionTrims (hard clips) adapter sequences from read ends.Clips reads on both ends using base quality scoresRead transformer intended to replicate DRAGEN behavior for handling mapping qualities.Masks read bases and base qualities using the symmetric DUST algorithmA read transformer to convert IUPAC bases (i.e.A read transformer to modify the mapping quality of reads with MQ=255 to reads with MQ=60Checks for and errors out (or fixes if requested) when it detects reads with base qualities that are not encoded with phred-scaled quality scores.A read transformer that refactors NDN cigar elements to one N element.Trims (hard clips) soft-clipped bases due to the following artifact: When a sequence and its reverse complement occur near opposite ends of a fragment DNA damage (especially in the case of FFPE samples and ancient DNA) can disrupt base-pairing causing a single-strand loop of the sequence and its reverse complement, after which end repair copies the true 5' end of the fragment onto the 3' end of the fragment.Classes which perform transformations from GATKRead -> GATKRead should implement this interface by overriding
SerializableFunction<GATKRead,GATKRead>#apply(GATKRead)Masks read bases with a supra-threshold number of A/T's or G/C's within a given window size.Removes /1 or /2 and any whitespace from the end of the read name if presentClasses which perform transformations fromVariantContext->VariantContextshould implement this interface by overriding< VariantContext ,VariantContext>#apply(VariantContext)Created by jonn on 6/26/18.