org.broadinstitute.hellbender.utils.bwa

Class BwaMemAlignmentUtils

java.lang.Object

org.broadinstitute.hellbender.utils.bwa.BwaMemAlignmentUtils

public class BwaMemAlignmentUtils
extends java.lang.Object

Utils to move data from a BwaMemAlignment into a GATKRead, or into a SAM tag.

Constructor Summary

Constructors

Constructor and Description
BwaMemAlignmentUtils()

Method Summary

Modifier and Type	Method and Description
static htsjdk.samtools.SAMRecord	applyAlignment(java.lang.String readName, byte[] basesArg, byte[] qualsArg, java.lang.String readGroup, org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment alignment, java.util.List<java.lang.String> refNames, htsjdk.samtools.SAMFileHeader header, boolean softClipAlts, boolean alwaysGenerateASandXS) Builds a SAMRecord from unaligned read data and an alignment.
static java.lang.String	asTag(org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment alignment, java.util.List<java.lang.String> refNames) Describes an alignment as a string for use in an SA tag, for example.
static java.util.Map<org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment,java.lang.String>	createSATags(java.util.List<org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment> alignments, java.util.List<java.lang.String> refNames) Produces an SA tag for each primary line and supplemental alignment as a map from alignment to tag value.
static java.util.stream.Stream<htsjdk.samtools.SAMRecord>	toSAMStreamForRead(java.lang.String readName, byte[] contigSequence, java.util.List<org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment> alignments, htsjdk.samtools.SAMFileHeader header, java.util.List<java.lang.String> refNames, htsjdk.samtools.SAMReadGroupRecord contigAlignmentsReadGroup)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

BwaMemAlignmentUtils

public BwaMemAlignmentUtils()

Method Detail

applyAlignment

public static htsjdk.samtools.SAMRecord applyAlignment(java.lang.String readName,
                                                       byte[] basesArg,
                                                       byte[] qualsArg,
                                                       java.lang.String readGroup,
                                                       org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment alignment,
                                                       java.util.List<java.lang.String> refNames,
                                                       htsjdk.samtools.SAMFileHeader header,
                                                       boolean softClipAlts,
                                                       boolean alwaysGenerateASandXS)

Builds a SAMRecord from unaligned read data and an alignment. qualsArg can be null. readGroup can be null. Also, BWA does this odd thing, supplying AS and XS tags for unaligned reads. To produce SAM records that are byte-identical to the ones created by the bwa mem command line, call this method with alwaysGenerateASandXS=true.

createSATags

public static java.util.Map<org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment,java.lang.String> createSATags(java.util.List<org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment> alignments,
                                                                                                                   java.util.List<java.lang.String> refNames)

Produces an SA tag for each primary line and supplemental alignment as a map from alignment to tag value.

asTag

public static java.lang.String asTag(org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment alignment,
                                     java.util.List<java.lang.String> refNames)

Describes an alignment as a string for use in an SA tag, for example.

toSAMStreamForRead

public static java.util.stream.Stream<htsjdk.samtools.SAMRecord> toSAMStreamForRead(java.lang.String readName,
                                                                                    byte[] contigSequence,
                                                                                    java.util.List<org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment> alignments,
                                                                                    htsjdk.samtools.SAMFileHeader header,
                                                                                    java.util.List<java.lang.String> refNames,
                                                                                    htsjdk.samtools.SAMReadGroupRecord contigAlignmentsReadGroup)