Package htsjdk.samtools.cram.structure

Class CRAMRecordReadFeatures

java.lang.Object
htsjdk.samtools.cram.structure.CRAMRecordReadFeatures
public class CRAMRecordReadFeatures extends Object
Class for handling the read features for a CRAMCompressionRecord.

  • Constructor Details

    • 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 Details

    • 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, 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(Object o)
      Overrides:
      equals in class Object

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object