Package org.broadinstitute.hellbender.utils.locusiterator

package org.broadinstitute.hellbender.utils.locusiterator
  • Classes
    Class
    Description
    AlignmentContextIteratorBuilder
    Create an iterator for traversing alignment contexts in a specified manner.
    AlignmentStateMachine
    Steps a single read along its alignment to the genome The logical model for generating extended events is as follows: the "record state" implements the traversal along the reference; thus stepForwardOnGenome() returns on every and only on actual reference bases.
    IntervalAlignmentContextIterator
    For special cases where we want to emit AlignmentContexts regardless of whether we have an overlap with a given interval.
    LIBSDownsamplingInfo
    Simple wrapper about the information LIBS needs about downsampling
    LocusIteratorByState
    Iterator that traverses a SAM File, accumulating information on a per-locus basis Produces AlignmentContext objects, that contain ReadPileups of PileupElements.