Class Sam2CramRecordFactory


  • public class Sam2CramRecordFactory
    extends Object
    • Field Detail

      • captureAllTags

        public boolean captureAllTags
      • preserveReadNames

        public boolean preserveReadNames
      • captureTags

        public final Set<String> captureTags
      • ignoreTags

        public final Set<String> ignoreTags
    • Constructor Detail

      • Sam2CramRecordFactory

        public Sam2CramRecordFactory​(byte[] refBases,
                                     SAMFileHeader samFileHeader,
                                     Version version)
    • Method Detail

      • createCramRecord

        public CramCompressionRecord createCramRecord​(SAMRecord record)
        Create a CramCompressionRecord.
        Parameters:
        record - If the input record does not have an associated SAMFileHeader, it will be updated with the header used for the factory in order to allow reference indices to be resolved.
        Returns:
        CramCompressionRecord
      • getRefBases

        public byte[] getRefBases()
      • setRefBases

        public void setRefBases​(byte[] refBases)
      • getBaseCount

        public long getBaseCount()
      • getFeatureCount

        public long getFeatureCount()