Constructor Detail

• CRAMRecordReadFeatures

  public CRAMRecordReadFeatures()

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

• CRAMRecordReadFeatures

  public CRAMRecordReadFeatures​(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 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​(List<ReadFeature> readFeatures,
                                        boolean isUnknownBases,
                                        int readAlignmentStart,
                                        int readLength,
                                        byte[] referenceBases,
                                        int zeroBasedReferenceOffset,
                                        SubstitutionMatrix substitutionMatrix)

  Get the set of readBases given these read features.

  Parameters:

  isUnknownBases -

  readAlignmentStart - 1-based alignment start for this record

  readLength -

  referenceBases -

  zeroBasedReferenceOffset -

  substitutionMatrix -

  Returns:

• equals

  public boolean equals​(Object o)

  Overrides:

  equals in class Object

• hashCode

  public int hashCode()

  Overrides:

  hashCode in class Object