Package htsjdk.samtools.sra

Class SRALazyRecord

java.lang.Object
htsjdk.samtools.SAMRecord
htsjdk.samtools.sra.SRALazyRecord
All Implemented Interfaces:
HtsRecord, Locatable, Serializable, Cloneable
public class SRALazyRecord extends SAMRecord
Extends SAMRecord so that any of the fields will be loaded only when needed. Since SRA is a column oriented database, it is very inefficient to load all the fields at once. However, loading only set of actually needed fields will be even faster than in row oriented databases. Because of that we are providing lazy loading of fields, flags and attributes. Created by andrii.nikitiuk on 8/25/15.
See Also:

  • Constructor Details

  • Method Details

    • detachFromIterator

      public void detachFromIterator()
      Is being called when original NGS iterator is being moved to the next object. Later, if any of uninitialized fields is requested, either Read object or Alignment has to be retrieved from ReadCollection

    • getAlignmentStart

      public int getAlignmentStart()
      Overrides:
      getAlignmentStart in class SAMRecord
      Returns:
      1-based inclusive leftmost position of the sequence remaining after clipping, or 0 if there is no position, e.g. for unmapped read.

    • setAlignmentStart

      public void setAlignmentStart(int value)
      Overrides:
      setAlignmentStart in class SAMRecord
      Parameters:
      value - 1-based inclusive leftmost position of the sequence remaining after clipping or 0 if there is no position, e.g. for unmapped read.

    • getMappingQuality

      public int getMappingQuality()
      Overrides:
      getMappingQuality in class SAMRecord
      Returns:
      phred scaled mapping quality. 255 implies valid mapping but quality is hard to compute.

    • setMappingQuality

      public void setMappingQuality(int value)
      Overrides:
      setMappingQuality in class SAMRecord

    • getReferenceName

      public String getReferenceName()
      Overrides:
      getReferenceName in class SAMRecord
      Returns:
      Reference name, or NO_ALIGNMENT_REFERENCE_NAME (*) if the record has no reference name

    • setReferenceName

      public void setReferenceName(String value)
      Description copied from class: SAMRecord
      Sets the reference name for this record. If the record has a valid SAMFileHeader and the reference name is present in the associated sequence dictionary, the record's reference index will also be updated with the corresponding sequence index. If referenceName is NO_ALIGNMENT_REFERENCE_NAME, sets the reference index to NO_ALIGNMENT_REFERENCE_INDEX.
      Overrides:
      setReferenceName in class SAMRecord
      Parameters:
      value - - must not be null

    • getReferenceIndex

      public Integer getReferenceIndex()
      Description copied from class: SAMRecord
      Returns the reference index for this record. If the reference name for this record has previously been resolved against the sequence dictionary, the corresponding index is returned directly. Otherwise, the record must have a non-null SAMFileHeader that can be used to resolve the index for the record's current reference name, unless the reference name is NO_ALIGNMENT_REFERENCE_NAME. If the record has a header, and the name does not appear in the header's sequence dictionary, the value NO_ALIGNMENT_REFERENCE_INDEX (-1) will be returned. If the record does not have a header, an IllegalStateException is thrown.
      Overrides:
      getReferenceIndex in class SAMRecord
      Returns:
      Index in the sequence dictionary of the reference sequence. If the read has no reference sequence, or if the reference name is not found in the sequence index, NO_ALIGNMENT_REFERENCE_INDEX (-1) is returned.

    • setReferenceIndex

      public void setReferenceIndex(int value)
      Description copied from class: SAMRecord
      Updates the reference index. The record must have a valid SAMFileHeader unless the referenceIndex parameter equals NO_ALIGNMENT_REFERENCE_INDEX, and the reference index must appear in the header's sequence dictionary. If the reference index is valid, the reference name will also be resolved and updated to the name for the sequence dictionary entry corresponding to the index.
      Overrides:
      setReferenceIndex in class SAMRecord
      Parameters:
      value - Must either equal NO_ALIGNMENT_REFERENCE_INDEX (-1) indicating no reference, or the record must have a SAMFileHeader and the index must exist in the associated sequence dictionary.

    • getCigarString

      public String getCigarString()
      Overrides:
      getCigarString in class SAMRecord

    • setCigarString

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

    • 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.

    • setCigar

      public void setCigar(Cigar value)
      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

    • 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=.

    • setReadBases

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

    • 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).

    • setBaseQualities

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

    • getMateAlignmentStart

      public int getMateAlignmentStart()
      Overrides:
      getMateAlignmentStart in class SAMRecord
      Returns:
      1-based inclusive leftmost position of the clipped mate sequence, or 0 if there is no position.

    • setMateAlignmentStart

      public void setMateAlignmentStart(int value)
      Overrides:
      setMateAlignmentStart in class SAMRecord

    • getMateReferenceName

      public String getMateReferenceName()
      Overrides:
      getMateReferenceName in class SAMRecord
      Returns:
      Mate reference name, or NO_ALIGNMENT_REFERENCE_NAME (*) if the record has no mate reference name

    • setMateReferenceName

      public void setMateReferenceName(String value)
      Description copied from class: SAMRecord
      Sets the mate reference name for this record. If the record has a valid SAMFileHeader and the mate reference name is present in the associated sequence dictionary, the record's mate reference index will also be updated with the corresponding sequence index. If mateReferenceName is NO_ALIGNMENT_REFERENCE_NAME, sets the mate reference index to NO_ALIGNMENT_REFERENCE_INDEX.
      Overrides:
      setMateReferenceName in class SAMRecord
      Parameters:
      value - - must not be null

    • getMateReferenceIndex

      public Integer getMateReferenceIndex()
      Description copied from class: SAMRecord
      Returns the mate reference index for this record. If the mate reference name for this record has previously been resolved against the sequence dictionary, the corresponding index is returned directly. Otherwise, the record must have a non-null SAMFileHeader that can be used to resolve the index for the record's current mate reference name, unless the mate reference name is NO_ALIGNMENT_REFERENCE_NAME. If the record has a header, and the name does not appear in the header's sequence dictionary, the value NO_ALIGNMENT_REFERENCE_INDEX (-1) will be returned. If the record does not have a header, an IllegalStateException is thrown.
      Overrides:
      getMateReferenceIndex in class SAMRecord
      Returns:
      Index in the sequence dictionary of the mate reference sequence. If the read has no mate reference sequence, or if the mate reference name is not found in the sequence index, NO_ALIGNMENT_REFERENCE_INDEX (-1) is returned.

    • setMateReferenceIndex

      public void setMateReferenceIndex(int value)
      Description copied from class: SAMRecord
      Updates the mate reference index. The record must have a valid SAMFileHeader, and the mate reference index must appear in the header's sequence dictionary, unless the mateReferenceIndex parameter equals NO_ALIGNMENT_REFERENCE_INDEX. If the mate reference index is valid, the mate reference name will also be resolved and updated to the name for the sequence dictionary entry corresponding to the index.
      Overrides:
      setMateReferenceIndex in class SAMRecord
      Parameters:
      value - Must either equal NO_ALIGNMENT_REFERENCE_INDEX (-1) indicating no reference, or the record must have a SAMFileHeader and the index must exist in the associated sequence dictionary.

    • getInferredInsertSize

      public int getInferredInsertSize()
      Overrides:
      getInferredInsertSize in class SAMRecord
      Returns:
      insert size (difference btw 5' end of read invalid input: '&' 5' end of mate), if possible, else 0. Negative if mate maps to lower position than read.

    • setInferredInsertSize

      public void setInferredInsertSize(int value)
      Overrides:
      setInferredInsertSize in class SAMRecord

    • getFlags

      public int getFlags()
      Description copied from class: SAMRecord
      It is preferable to use the get*Flag() methods that handle the flag word symbolically.
      Overrides:
      getFlags in class SAMRecord

    • setFlags

      public void setFlags(int value)
      Overrides:
      setFlags in class SAMRecord

    • getReadNegativeStrandFlag

      public boolean getReadNegativeStrandFlag()
      Description copied from class: SAMRecord
      strand of the query (false for forward; true for reverse strand).
      Overrides:
      getReadNegativeStrandFlag in class SAMRecord

    • setReadNegativeStrandFlag

      public void setReadNegativeStrandFlag(boolean flag)
      Description copied from class: SAMRecord
      strand of the query (false for forward; true for reverse strand).
      Overrides:
      setReadNegativeStrandFlag in class SAMRecord

    • getReadPairedFlag

      public boolean getReadPairedFlag()
      Description copied from class: SAMRecord
      the read is paired in sequencing, no matter whether it is mapped in a pair.
      Overrides:
      getReadPairedFlag in class SAMRecord

    • setReadPairedFlag

      public void setReadPairedFlag(boolean flag)
      Description copied from class: SAMRecord
      the read is paired in sequencing, no matter whether it is mapped in a pair.
      Overrides:
      setReadPairedFlag in class SAMRecord

    • getProperPairFlag

      public boolean getProperPairFlag()
      Description copied from class: SAMRecord
      the read is mapped in a proper pair (depends on the protocol, normally inferred during alignment).
      Overrides:
      getProperPairFlag in class SAMRecord

    • setProperPairFlag

      public void setProperPairFlag(boolean flag)
      Description copied from class: SAMRecord
      the read is mapped in a proper pair (depends on the protocol, normally inferred during alignment).
      Overrides:
      setProperPairFlag in class SAMRecord

    • isSecondaryAlignment

      public boolean isSecondaryAlignment()
      Overrides:
      isSecondaryAlignment in class SAMRecord
      Returns:
      whether the alignment is secondary (an alternative alignment of the read).

    • setSecondaryAlignment

      public void setSecondaryAlignment(boolean flag)
      Description copied from class: SAMRecord
      set whether this alignment is secondary (an alternative alignment of the read).
      Overrides:
      setSecondaryAlignment in class SAMRecord

    • getMateNegativeStrandFlag

      public boolean getMateNegativeStrandFlag()
      Description copied from class: SAMRecord
      strand of the mate (false for forward; true for reverse strand).
      Overrides:
      getMateNegativeStrandFlag in class SAMRecord

    • setMateNegativeStrandFlag

      public void setMateNegativeStrandFlag(boolean flag)
      Description copied from class: SAMRecord
      strand of the mate (false for forward; true for reverse strand).
      Overrides:
      setMateNegativeStrandFlag in class SAMRecord

    • getMateUnmappedFlag

      public boolean getMateUnmappedFlag()
      Description copied from class: SAMRecord
      the mate is unmapped.
      Overrides:
      getMateUnmappedFlag in class SAMRecord

    • setMateUnmappedFlag

      public void setMateUnmappedFlag(boolean flag)
      Description copied from class: SAMRecord
      the mate is unmapped.
      Overrides:
      setMateUnmappedFlag in class SAMRecord

    • getFirstOfPairFlag

      public boolean getFirstOfPairFlag()
      Description copied from class: SAMRecord
      the read is the first read in a pair.
      Overrides:
      getFirstOfPairFlag in class SAMRecord

    • setFirstOfPairFlag

      public void setFirstOfPairFlag(boolean flag)
      Description copied from class: SAMRecord
      the read is the first read in a pair.
      Overrides:
      setFirstOfPairFlag in class SAMRecord

    • getSecondOfPairFlag

      public boolean getSecondOfPairFlag()
      Description copied from class: SAMRecord
      the read is the second read in a pair.
      Overrides:
      getSecondOfPairFlag in class SAMRecord

    • setSecondOfPairFlag

      public void setSecondOfPairFlag(boolean flag)
      Description copied from class: SAMRecord
      the read is the second read in a pair.
      Overrides:
      setSecondOfPairFlag in class SAMRecord

    • 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:

    • setAttribute

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

    • setAttribute

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

    • clearAttributes

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

    • setAttributes

      protected void setAttributes(SAMBinaryTagAndValue attributes)
      Description copied from class: SAMRecord
      Replace any existing attributes with the given linked item. NOTE: this method is intended to only be called from subclasses.
      Overrides:
      setAttributes in class SAMRecord

    • getBinaryAttributes

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

    • isUnsignedArrayAttribute

      public boolean isUnsignedArrayAttribute(String tag)
      Overrides:
      isUnsignedArrayAttribute in class SAMRecord
      Returns:
      True if this tag is an unsigned array, else false.

    • equals

      public boolean equals(Object o)
      For records equality, we should only compare read id, reference and position on the reference. Since read id is a constructor parameter, we only need to make sure that reference info is loaded.
      Overrides:
      equals in class SAMRecord
      Parameters:
      o - other
      Returns:
      comparison result

    • hashCode

      public int hashCode()
      The same approach as with 'equals' method. We only load reference and position.
      Overrides:
      hashCode in class SAMRecord

    • clone

      public Object clone() throws CloneNotSupportedException
      Performs a deep copy of the SAMRecord and detaches a copy from NGS iterator
      Overrides:
      clone in class SAMRecord
      Returns:
      new object
      Throws:
      CloneNotSupportedException

    • format

      public String format()
      Overrides:
      format in class SAMRecord
      Returns:
      String representation of this.

    • isValid

      public List<SAMValidationError> isValid(boolean firstOnly)
      Description copied from class: SAMRecord
      Perform various validations of SAMRecord. Note that this method deliberately returns null rather than Collections.emptyList() if there are no validation errors, because callers tend to assume that if a non-null list is returned, it is modifiable. A record with null a header may be validated by the isValid method, but the reference and mate reference indices, read group, sequence dictionary, and alignment start will not be fully validated unless a header is present.
      Overrides:
      isValid in class SAMRecord
      Parameters:
      firstOnly - return only the first error if true, false otherwise
      Returns:
      null if valid. If invalid, returns a list of error messages.