Package htsjdk.samtools

Class BAMRecord

java.lang.Object
htsjdk.samtools.SAMRecord
htsjdk.samtools.BAMRecord
All Implemented Interfaces:
HtsRecord, Locatable, Serializable, Cloneable
public class BAMRecord extends SAMRecord
Wrapper class for binary BAM records. Delays unpacking all data binary until requested.
See Also:

  • Field Details

    • CIGAR_SIZE_MULTIPLIER

      public static final short CIGAR_SIZE_MULTIPLIER
      Constant for converting between the number of operators in a Cigar and the length of the int[] array needed to represent it in the BAM format
      See Also:

    • MAX_CIGAR_OPERATORS

      public static final int MAX_CIGAR_OPERATORS
      Maximal number of cigar operators that can be represented normally in the cigar part of the bam record. Records that have larger cigars will have their Cigars encoded to int[] and placed in the CG tag in the attributes (BAM only) This should happen upon encoding. In place of the Cigar a sentinel value will be placed SN

      When a BAM record is decoded, the sentinel cigar informs of the existance of the CG tag, which is decoded and removed. The sentinel value is then replaced with the actual cigar (in memory).

      See Also:

    • MAX_CIGAR_ELEMENT_LENGTH

      public static final int MAX_CIGAR_ELEMENT_LENGTH
      See Also:

  • Constructor Details

    • BAMRecord

      protected BAMRecord(SAMFileHeader header, int referenceID, int coordinate, short readNameLength, short mappingQuality, int indexingBin, int cigarLen, int flags, int readLen, int mateReferenceID, int mateCoordinate, int insertSize, byte[] restOfData)
      Create a new BAM Record. If the reference sequence index or mate reference sequence index are any value other than NO_ALIGNMENT_REFERENCE_INDEX (-1), then the specified index values must exist in the sequence dictionary in the header argument.

  • Method Details

    • eagerDecode

      protected void eagerDecode()
      Force all the lazily-initialized attributes to be decoded.
      Overrides:
      eagerDecode in class SAMRecord

    • getVariableBinaryRepresentation

      public byte[] getVariableBinaryRepresentation()
      If this record has a valid binary representation of the variable-length portion of a binary record stored, return that byte array, otherwise return null. This will never be true for SAMRecords. It will be true for BAMRecords that have not been eagerDecoded(), and for which none of the data in the variable-length portion has been changed.
      Overrides:
      getVariableBinaryRepresentation in class SAMRecord

    • getAttributesBinarySize

      public int getAttributesBinarySize()
      Depending on the concrete implementation, the binary file size of attributes may be known without computing them all.
      Overrides:
      getAttributesBinarySize in class SAMRecord
      Returns:
      binary file size of attribute, if known, else -1.

    • setReadName

      public void setReadName(String value)
      Overrides:
      setReadName in class SAMRecord

    • setCigar

      public void setCigar(Cigar cigar)
      Description copied from class: SAMRecord
      For setting the Cigar string when changed. Note that this nulls the indexing bin, which would need to be recomputed on write (if needed). To avoid clobbering the indexing bin, use SAMRecord.initializeCigar(htsjdk.samtools.Cigar)
      Overrides:
      setCigar in class SAMRecord

    • setCigarString

      public void setCigarString(String value)
      Overrides:
      setCigarString in class SAMRecord

    • setReadBases

      public void setReadBases(byte[] value)
      Overrides:
      setReadBases in class SAMRecord

    • setBaseQualities

      public void setBaseQualities(byte[] value)
      Overrides:
      setBaseQualities in class SAMRecord

    • setAttribute

      protected void setAttribute(short tag, Object value, boolean isUnsignedArray)
      Overrides:
      setAttribute in class SAMRecord

    • clearAttributes

      public void clearAttributes()
      Removes all attributes.
      Overrides:
      clearAttributes in class SAMRecord

    • getReadLength

      public int getReadLength()
      Avoids decoding binary block to get read length.
      Overrides:
      getReadLength in class SAMRecord
      Returns:
      number of bases in the read.

    • getReadName

      public String getReadName()
      Overrides:
      getReadName in class SAMRecord

    • getReadNameLength

      public int getReadNameLength()
      Avoids decoding read name to get read name length. Do not include null terminator.
      Overrides:
      getReadNameLength in class SAMRecord
      Returns:
      length not including a null terminator.

    • getCigar

      public Cigar getCigar()
      Description copied from class: SAMRecord
      Do not modify the value returned by this method. If you want to change the Cigar, create a new Cigar and call setCigar() or call setCigarString()
      Overrides:
      getCigar in class SAMRecord
      Returns:
      Cigar object for the read, or null if there is none.

    • getCigarLength

      public int getCigarLength()
      Avoids decoding CIGAR in order to get length.
      Overrides:
      getCigarLength in class SAMRecord
      Returns:
      number of cigar elements (number + operator) in the cigar string.

    • getReadBases

      public byte[] getReadBases()
      Description copied from class: SAMRecord
      Do not modify the value returned by this method. If you want to change the bases, create a new byte[] and call setReadBases() or call setReadString().
      Overrides:
      getReadBases in class SAMRecord
      Returns:
      read sequence as ASCII bytes ACGTN=.

    • getBaseQualities

      public byte[] getBaseQualities()
      Description copied from class: SAMRecord
      Do not modify the value returned by this method. If you want to change the qualities, create a new byte[] and call setBaseQualities() or call setBaseQualityString().
      Overrides:
      getBaseQualities in class SAMRecord
      Returns:
      Base qualities, as binary phred scores (not ASCII).

    • getAttribute

      public Object getAttribute(short tag)
      Overrides:
      getAttribute in class SAMRecord
      Parameters:
      tag - Binary representation of a 2-char String tag as created by SAMTagUtil.
      See Also:

    • getBinaryAttributes

      protected SAMBinaryTagAndValue getBinaryAttributes()
      Overrides:
      getBinaryAttributes in class SAMRecord
      Returns:
      Pointer to the first of the tags. Returns null if there are no tags.