org.broadinstitute.hellbender.tools.spark.sv

Class StructuralVariationDiscoveryPipelineSpark.InMemoryAlignmentParser

java.lang.Object

org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment.AlignedContigGenerator

org.broadinstitute.hellbender.tools.spark.sv.StructuralVariationDiscoveryPipelineSpark.InMemoryAlignmentParser

All Implemented Interfaces:

java.io.Serializable

Enclosing class:

StructuralVariationDiscoveryPipelineSpark

public static final class StructuralVariationDiscoveryPipelineSpark.InMemoryAlignmentParser
extends AlignedContigGenerator
implements scala.Serializable

See Also:

Serialized Form

Method Summary

Modifier and Type	Method and Description
static java.util.List<AlignedContig>	filterAndConvertToAlignedContigDirect(java.lang.Iterable<AlignedAssemblyOrExcuse> alignedAssemblyOrExcuseIterable, java.util.List<java.lang.String> refNames, htsjdk.samtools.SAMFileHeader header) Filter out "failed" assemblies, unmapped and secondary (i.e.
static org.apache.spark.api.java.JavaRDD<AlignedContig>	filterAndConvertToAlignedContigViaSAM(java.util.List<AlignedAssemblyOrExcuse> alignedAssemblyOrExcuseList, htsjdk.samtools.SAMFileHeader header, org.apache.spark.api.java.JavaSparkContext ctx) Filters out "failed" assemblies, unmapped and secondary (i.e.
org.apache.spark.api.java.JavaRDD<AlignedContig>	getAlignedContigs()
static java.lang.Iterable<AlignedContig>	getAlignedContigsInOneAssembly(AlignedAssemblyOrExcuse alignedAssembly, java.util.List<java.lang.String> refNames, htsjdk.samtools.SAMFileHeader header) Work on "successful" assembly and turn its contigs' alignments to custom AlignmentInterval format.

Methods inherited from class java.lang.Object

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

Method Detail

filterAndConvertToAlignedContigViaSAM

public static org.apache.spark.api.java.JavaRDD<AlignedContig> filterAndConvertToAlignedContigViaSAM(java.util.List<AlignedAssemblyOrExcuse> alignedAssemblyOrExcuseList,
                                                                                                     htsjdk.samtools.SAMFileHeader header,
                                                                                                     org.apache.spark.api.java.JavaSparkContext ctx)

Filters out "failed" assemblies, unmapped and secondary (i.e. "XA") alignments, and turn the alignments of contigs into custom AlignmentInterval format. Should be generating the same output as filterAndConvertToAlignedContigDirect(Iterable, List, SAMFileHeader); and currently this assertion is tested in AlignedContigGeneratorUnitTest#testConvertAlignedAssemblyOrExcuseToAlignedContigsDirectAndConcordanceWithSAMRoute()

filterAndConvertToAlignedContigDirect

public static java.util.List<AlignedContig> filterAndConvertToAlignedContigDirect(java.lang.Iterable<AlignedAssemblyOrExcuse> alignedAssemblyOrExcuseIterable,
                                                                                  java.util.List<java.lang.String> refNames,
                                                                                  htsjdk.samtools.SAMFileHeader header)

Filter out "failed" assemblies, unmapped and secondary (i.e. "XA") alignments, and turn the alignments of contigs into custom AlignmentInterval format. Should be generating the same output as filterAndConvertToAlignedContigViaSAM(List, SAMFileHeader, JavaSparkContext); and currently this assertion is tested in AlignedContigGeneratorUnitTest#testConvertAlignedAssemblyOrExcuseToAlignedContigsDirectAndConcordanceWithSAMRoute()

getAlignedContigsInOneAssembly

public static java.lang.Iterable<AlignedContig> getAlignedContigsInOneAssembly(AlignedAssemblyOrExcuse alignedAssembly,
                                                                               java.util.List<java.lang.String> refNames,
                                                                               htsjdk.samtools.SAMFileHeader header)

Work on "successful" assembly and turn its contigs' alignments to custom AlignmentInterval format.

getAlignedContigs

public org.apache.spark.api.java.JavaRDD<AlignedContig> getAlignedContigs()

Specified by:

getAlignedContigs in class AlignedContigGenerator