Package htsjdk.samtools

Class BAMRecordCodec

java.lang.Object
htsjdk.samtools.BAMRecordCodec
All Implemented Interfaces:
SortingCollection.Codec<SAMRecord>, Cloneable
public class BAMRecordCodec extends Object implements SortingCollection.Codec<SAMRecord>
Class for translating between in-memory and disk representation of BAMRecord.

  • Constructor Details

  • Method Details

    • clone

      public BAMRecordCodec clone()
      Description copied from interface: SortingCollection.Codec
      Must return a cloned copy of the codec that can be used independently of the original instance. This is required so that multiple codecs can exist simultaneously that each is reading a separate file.
      Specified by:
      clone in interface SortingCollection.Codec<SAMRecord>
      Overrides:
      clone in class Object

    • setOutputStream

      public void setOutputStream(OutputStream os)
      Sets the output stream that records will be written to.
      Specified by:
      setOutputStream in interface SortingCollection.Codec<SAMRecord>

    • setOutputStream

      public void setOutputStream(OutputStream os, String filename)
      Sets the output stream that records will be written to.

    • setInputStream

      public void setInputStream(InputStream is)
      Sets the input stream that records will be read from.
      Specified by:
      setInputStream in interface SortingCollection.Codec<SAMRecord>

    • setInputStream

      public void setInputStream(InputStream is, String filename)
      Sets the input stream that records will be read from.

    • encode

      public void encode(SAMRecord alignment)
      Write object to OutputStream. Reference and mate reference indices must be resolvable, which either means that these have been set into the SAMRecord directly, or the SAMRecord must have a header assigned into it so that reference names can be resolved into indices.
      Specified by:
      encode in interface SortingCollection.Codec<SAMRecord>
      Parameters:
      alignment - Record to be written.

    • makeSentinelCigar

      public static Cigar makeSentinelCigar(Cigar cigar)
      Create a "Sentinel" cigar that will be placed in BAM file when the actual cigar has more than 0xffff operator, which are not supported by the bam format. The actual cigar will be encoded and placed in the CG attribute.
      Parameters:
      cigar - actual cigar to create sentinel cigar for
      Returns:
      sentinel cigar xSyN with readLength (x) and referenceLength (y) matching the input cigar.

    • decode

      public SAMRecord decode()
      Read the next record from the input stream and convert into a java object.
      Specified by:
      decode in interface SortingCollection.Codec<SAMRecord>
      Returns:
      null if no more records. Should throw exception if EOF is encountered in the middle of a record.