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

Class ReadMetadata

java.lang.Object

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

public class ReadMetadata
extends java.lang.Object

A bag of data about reads: contig name to id mapping, fragment length statistics by read group, mean length. The fragment length statistics pertain to a library, but they're accessed by read group. (I.e., in the readGroupToFragmentStatistics map, all read groups that are derived from a given library point to the same set of statistics.)

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	ReadMetadata.LibraryRawStatistics
static class	ReadMetadata.PartitionBounds A class to track the genomic location of the start of the first and last mapped reads in a partition.
static class	ReadMetadata.PartitionStatistics
static class	ReadMetadata.Serializer

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	CDF_PREFIX

Constructor Summary

Constructors

Constructor and Description
ReadMetadata(java.util.Set<java.lang.Integer> crossContigIgnoreSet, htsjdk.samtools.SAMFileHeader header, int maxTrackedFragmentLength, org.apache.spark.api.java.JavaRDD<GATKRead> unfilteredReads, SVReadFilter filter, org.apache.logging.log4j.Logger logger)

Method Summary

Modifier and Type	Method and Description
static java.lang.String[]	buildContigIDToNameArray(java.util.Map<java.lang.String,java.lang.Integer> nameToIDMap)
static java.util.Map<java.lang.String,java.lang.Integer>	buildContigNameToIDMap(htsjdk.samtools.SAMSequenceDictionary dictionary)
static java.util.Map<java.lang.String,java.lang.String>	buildGroupToLibMap(htsjdk.samtools.SAMFileHeader header)
float	getAccurateKmerCoverage(int kSize)
java.util.Map<java.lang.String,LibraryStatistics>	getAllLibraryStatistics()
int	getAvgReadLen()
int	getContigID(java.lang.String contigName)
java.lang.String	getContigName(int contigID)
java.util.Map<java.lang.String,java.lang.Integer>	getContigNameMap()
float	getCoverage()
java.lang.String	getLibraryName(java.lang.String readGroupName)
LibraryStatistics	getLibraryStatistics(java.lang.String libraryName)
int	getMaxMedianFragmentSize()
long	getMaxReadsInPartition()
float	getMeanBaseQuality()
int	getMedianPartitionSpan()
int	getNPartitions()
long	getNReads()
long	getNRefBases()
ReadMetadata.PartitionBounds	getPartitionBounds(int partitionIdx)
float	getZishScore(java.lang.String readGroup, int fragmentSize)
boolean	ignoreCrossContigID(int contigID)
static void	writeMetadata(ReadMetadata readMetadata, java.lang.String filename)

Methods inherited from class java.lang.Object

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

Field Detail

CDF_PREFIX

public static final java.lang.String CDF_PREFIX

See Also:

Constant Field Values

Constructor Detail

ReadMetadata

public ReadMetadata(java.util.Set<java.lang.Integer> crossContigIgnoreSet,
                    htsjdk.samtools.SAMFileHeader header,
                    int maxTrackedFragmentLength,
                    org.apache.spark.api.java.JavaRDD<GATKRead> unfilteredReads,
                    SVReadFilter filter,
                    org.apache.logging.log4j.Logger logger)

Method Detail

ignoreCrossContigID

public boolean ignoreCrossContigID(int contigID)

getContigNameMap

public java.util.Map<java.lang.String,java.lang.Integer> getContigNameMap()

getContigID

public int getContigID(java.lang.String contigName)

getContigName

public java.lang.String getContigName(int contigID)

getLibraryName

public java.lang.String getLibraryName(java.lang.String readGroupName)

getZishScore

public float getZishScore(java.lang.String readGroup,
                          int fragmentSize)

getNReads

public long getNReads()

getAvgReadLen

public int getAvgReadLen()

getNRefBases

public long getNRefBases()

getNPartitions

public int getNPartitions()

getPartitionBounds

public ReadMetadata.PartitionBounds getPartitionBounds(int partitionIdx)

getMaxReadsInPartition

public long getMaxReadsInPartition()

getCoverage

public float getCoverage()

getMeanBaseQuality

public float getMeanBaseQuality()

getAccurateKmerCoverage

public float getAccurateKmerCoverage(int kSize)

getMedianPartitionSpan

public int getMedianPartitionSpan()

getAllLibraryStatistics

public java.util.Map<java.lang.String,LibraryStatistics> getAllLibraryStatistics()

getLibraryStatistics

public LibraryStatistics getLibraryStatistics(java.lang.String libraryName)

getMaxMedianFragmentSize

public int getMaxMedianFragmentSize()

buildContigNameToIDMap

public static java.util.Map<java.lang.String,java.lang.Integer> buildContigNameToIDMap(htsjdk.samtools.SAMSequenceDictionary dictionary)

buildContigIDToNameArray

public static java.lang.String[] buildContigIDToNameArray(java.util.Map<java.lang.String,java.lang.Integer> nameToIDMap)

buildGroupToLibMap

public static java.util.Map<java.lang.String,java.lang.String> buildGroupToLibMap(htsjdk.samtools.SAMFileHeader header)

writeMetadata

public static void writeMetadata(ReadMetadata readMetadata,
                                 java.lang.String filename)