Package org.broadinstitute.hellbender.utils.read
package org.broadinstitute.hellbender.utils.read
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ClassDescriptionEasy to use creator of artificial BAM files for testing Allows us to make a stream of reads or an index BAM file with read having the following properties - coming from n samples - of fixed read length and aligned to the genome with M operator - having N reads per alignment start - skipping N bases between each alignment start - starting at a given alignment startthis fake iterator allows us to look at how specific piles of reads are handledImplementation of the
GATKReadinterface for theAlignmentRecordclass.This class allows code that manipulates cigars to do so naively by handling complications such as merging consecutive identical operators within the builder.Adds flow information to the usual GATKRead.utility class for flow based readAll available evidence coming from a single biological fragment.Unified read interface for use throughout the GATK.Converts a GATKRead to a BDG AlignmentRecordInterface for classes that are able to write GATKReads to some output destination.A comparator for headerless SAMRecords that exactly matches the ordering of theSAMRecordCoordinateComparatorIt is useful to define a key such that the key will occur at most once among the primary alignments in a given file (assuming the file is valid).Constants for use with the GATKRead interfaceComparator for sorting Reads by coordinate.compareGATKReadby queryname duplicates the exact ordering ofSAMRecordQueryNameComparatorPossible output formats when writing reads.A miscellaneous collection of utilities for working with reads, headers, etc.A GATKRead writer that writes to a SAM/BAM file.Implementation of theGATKReadinterface for theSAMRecordclass.