htsjdk.samtools.cram.structure

Class CRAMRecordReadFeatures

java.lang.Object

htsjdk.samtools.cram.structure.CRAMRecordReadFeatures

public class CRAMRecordReadFeatures
extends java.lang.Object

Class for handling the read features for a CRAMCompressionRecord.

Constructor Summary

Constructors

Constructor and Description
CRAMRecordReadFeatures() Create a CRAMRecordReadFeatures with no actual read features (i.e.
CRAMRecordReadFeatures(java.util.List<ReadFeature> readFeatures) Create a CRAMRecordReadFeatures from a list of read features consumed from a stream.
CRAMRecordReadFeatures(SAMRecord samRecord, byte[] bamReadBases, byte[] refBases) Create the read features for a given SAMRecord.

Method Summary

Modifier and Type	Method and Description
boolean	equals(java.lang.Object o)
int	getAlignmentEnd(int alignmentStart, int readLength)
Cigar	getCigarForReadFeatures(int readLength) Get a Cigar fo this set of read features.
java.util.List<ReadFeature>	getReadFeaturesList()
int	hashCode()
static byte[]	restoreReadBases(java.util.List<ReadFeature> readFeatures, boolean isUnknownBases, int readAlignmentStart, int readLength, CRAMReferenceRegion cramReferenceRegion, SubstitutionMatrix substitutionMatrix) Get the read bases for a CRAMRecord given a set of read feaures and a reference region.

Methods inherited from class java.lang.Object

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

Constructor Detail

CRAMRecordReadFeatures

public CRAMRecordReadFeatures()

Create a CRAMRecordReadFeatures with no actual read features (i.e. an unmapped record).

CRAMRecordReadFeatures

public CRAMRecordReadFeatures(java.util.List<ReadFeature> readFeatures)

Create a CRAMRecordReadFeatures from a list of read features consumed from a stream.

Parameters:

readFeatures -

CRAMRecordReadFeatures

public CRAMRecordReadFeatures(SAMRecord samRecord,
                              byte[] bamReadBases,
                              byte[] refBases)

Create the read features for a given SAMRecord.

Parameters:

samRecord - the SAMRecord for which to create read features

bamReadBases - a modifiable copy of the readbases from the original SAM/BAM record, with the individual bases mapped to BAM bases (upper case)

refBases - the reference bases for the entire reference contig to which this record is mapped

Method Detail

getReadFeaturesList

public final java.util.List<ReadFeature> getReadFeaturesList()

getAlignmentEnd

public int getAlignmentEnd(int alignmentStart,
                           int readLength)

getCigarForReadFeatures

public Cigar getCigarForReadFeatures(int readLength)

Get a Cigar fo this set of read features.

Parameters:

readLength -

Returns:

restoreReadBases

public static byte[] restoreReadBases(java.util.List<ReadFeature> readFeatures,
                                      boolean isUnknownBases,
                                      int readAlignmentStart,
                                      int readLength,
                                      CRAMReferenceRegion cramReferenceRegion,
                                      SubstitutionMatrix substitutionMatrix)

Get the read bases for a CRAMRecord given a set of read feaures and a reference region.

Parameters:

readFeatures - list of ReadFeatures for this record. may be null

isUnknownBases - true if CF_UNKNOWN_BASES CRAM flag is set for this read

readAlignmentStart - 1-based CRAM record alignment start

readLength - read length for this read

cramReferenceRegion - CRAMReferenceRegion spanning the reference bases required for this read, if reference-compressed. It is the caller's responsibility to have already fetched the correct bases (that is, the CRAMReferenceRegion's current bases must overlap this read's reference span. It is permissible for the region's span to be less than the entire read span in the case where the read span exceeds beyond the end of the underlying reference sequence.

substitutionMatrix - substitution matrix to use for base resolution

Returns:

byte[] of read bases for this read

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object