Package org.broadinstitute.hellbender.tools.spark.sv.evidence

Class AlignedAssemblyOrExcuse

java.lang.Object

org.broadinstitute.hellbender.tools.spark.sv.evidence.AlignedAssemblyOrExcuse

public final class AlignedAssemblyOrExcuse
extends Object

An assembly with its contigs aligned to reference, or a reason that there isn't an assembly.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static final class	AlignedAssemblyOrExcuse.Serializer

Constructor Summary

Constructors

Constructor	Description
AlignedAssemblyOrExcuse(int assemblyId, String errorMessage)
AlignedAssemblyOrExcuse(int assemblyId, org.broadinstitute.hellbender.utils.fermi.FermiLiteAssembly assembly, int secondsInAssembly, List<List<org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment>> contigAlignments)

Method Summary

Modifier and Type	Method	Description
static String	formatAssemblyID(int assemblyId)
static String	formatContigName(int assemblyId, int contigIdx)
org.broadinstitute.hellbender.utils.fermi.FermiLiteAssembly	getAssembly()
int	getAssemblyId()
List<List<org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment>>	getContigAlignments()	List is equal in length to the number of contigs in the assembly.
String	getErrorMessage()	Either this is null, or the assembly and list of alignments is null.
int	getSecondsInAssembly()
boolean	isNotFailure()
Stream<htsjdk.samtools.SAMRecord>	toSAMStreamForAlignmentsOfThisAssembly(htsjdk.samtools.SAMFileHeader header, List<String> refNames, htsjdk.samtools.SAMReadGroupRecord contigAlignmentsReadGroup)
static void	writeIntervalFile(String intervalFile, htsjdk.samtools.SAMFileHeader header, List<SVInterval> intervals, List<AlignedAssemblyOrExcuse> intervalDispositions)	write a file describing each interval

Methods inherited from class java.lang.Object

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

Constructor Details

AlignedAssemblyOrExcuse

public AlignedAssemblyOrExcuse(int assemblyId,
 String errorMessage)

AlignedAssemblyOrExcuse

public AlignedAssemblyOrExcuse(int assemblyId,
 org.broadinstitute.hellbender.utils.fermi.FermiLiteAssembly assembly,
 int secondsInAssembly,
 List<List<org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment>> contigAlignments)

Method Details

getSecondsInAssembly

public int getSecondsInAssembly()

getAssemblyId

public int getAssemblyId()

getErrorMessage

public String getErrorMessage()

Either this is null, or the assembly and list of alignments is null.

isNotFailure

public boolean isNotFailure()

getAssembly

public org.broadinstitute.hellbender.utils.fermi.FermiLiteAssembly getAssembly()

getContigAlignments

public List<List<org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment>> getContigAlignments()

List is equal in length to the number of contigs in the assembly.

toSAMStreamForAlignmentsOfThisAssembly

public Stream<htsjdk.samtools.SAMRecord> toSAMStreamForAlignmentsOfThisAssembly(htsjdk.samtools.SAMFileHeader header,
 List<String> refNames,
 htsjdk.samtools.SAMReadGroupRecord contigAlignmentsReadGroup)

formatContigName

public static String formatContigName(int assemblyId,
 int contigIdx)

formatAssemblyID

public static String formatAssemblyID(int assemblyId)

writeIntervalFile

public static void writeIntervalFile(String intervalFile,
 htsjdk.samtools.SAMFileHeader header,
 List<SVInterval> intervals,
 List<AlignedAssemblyOrExcuse> intervalDispositions)

write a file describing each interval