Class CRAMCompressionRecord

Method Details

• toSAMRecord

  public SAMRecord toSAMRecord(SAMFileHeader samFileHeader)

  Create a SAMRecord from the CRAMRecord.

  Parameters:

  samFileHeader - SAMFileHeader

  Returns:

  a SAMRecord

• assignReadName

  public void assignReadName()

  Assign a synthetic read name based on the sequential index if no name was decoded. Propagates the name to linked next/previous segments.

  Note: supplementary and secondary reads are always DETACHED (never mate-linked), so they have no nextSegment/previousSegment and name propagation won’t help them. This is only safe because htsjdk always sets preserveReadNames=true when encoding (see CompressionHeaderFactory.createCompressionHeader(List, boolean)). If lossy read name mode were ever implemented, supplementary/secondary reads in different slices from their primaries would receive synthetic names that don’t match. htslib avoids this by forcing name preservation whenever SA tags are present and when not all template reads are in the same slice.

• isNormalized

  public boolean isNormalized()

  When a CRAM record is read from a CRAM stream, it is "raw" in that the record's read bases, quality scores, and mate graph are not stored directly as part of the record. These values must be resolved through the separate process of normalization, which is performed at Slice granularity (all records in a Slice are normalized at the same time). (see Slice.normalizeCRAMRecords(List, CRAMReferenceRegion)).

  Returns:

  true if this record is normalized

• resolveQualityScores

  public void resolveQualityScores()

  Resolve the quality scores for this CRAM record based on preserved scores, read features and flags.

• restoreReadBases

  public void restoreReadBases(CRAMReferenceRegion cramReferenceRegion, SubstitutionMatrix substitutionMatrix)

  Restore the actual read bases for this record.

  Parameters:

  cramReferenceRegion - CRAMReferenceRegion spanning the reference bases for this record, if reference bases are required (may be null for records with RR=false in the compression header)

  substitutionMatrix - substitution matrix to use for this record

• restoreMateInfo

  public void restoreMateInfo()

  Restore mate information by walking the linked list of segments starting from this record, setting mate fields on each segment pair, and computing template length.

• setToDetachedState

  public void setToDetachedState()

  Mark this record as detached — mate info stored explicitly via MF, NS, NP, TS data series.

• isPlaced

  public boolean isPlaced()

  Determine is read is "placed". For consistency with the rest of htsjdk, this only consults the alignmentStart (placed reads should also have a valid reference index, and unplaced reads should be unmapped; those two abberant conditions are logged as warnings).

  Returns:

  true if the record is placed

  See Also:

  • isSegmentUnmapped()

• getReadName

  public String getReadName()

• getAlignmentStart

  public int getAlignmentStart()

• getReadLength

  public int getReadLength()

• getReadBases

  public byte[] getReadBases()

• getQualityScores

  public byte[] getQualityScores()

• getMappingQuality

  public int getMappingQuality()

• getReferenceIndex

  public int getReferenceIndex()

• getTemplateSize

  public int getTemplateSize()

• getTags

  public List<ReadTag> getTags()

• getRecordsToNextFragment

  public int getRecordsToNextFragment()

• getReadFeatures

  public List<ReadFeature> getReadFeatures()

• getReadGroupID

  public int getReadGroupID()

  Returns:

  read group id, or NO_READGROUP_ID if no read group assigned

• getBAMFlags

  public int getBAMFlags()

• getMateReferenceIndex

  public int getMateReferenceIndex()

• getMateAlignmentStart

  public int getMateAlignmentStart()

• setTagIdsIndex

  public void setTagIdsIndex(MutableInt tagIdsIndex)

• getTagIdsIndex

  public MutableInt getTagIdsIndex()

• getMateFlags

  public int getMateFlags()

• getCRAMFlags

  public int getCRAMFlags()

• getAlignmentEnd

  public int getAlignmentEnd()

  Returns:

  the initialized alignmentEnd

• getSequentialIndex

  public long getSequentialIndex()

• getNextSegment

  public CRAMCompressionRecord getNextSegment()

• setNextSegment

  public void setNextSegment(CRAMCompressionRecord nextSegment)

• getPreviousSegment

  public CRAMCompressionRecord getPreviousSegment()

• setPreviousSegment

  public void setPreviousSegment(CRAMCompressionRecord previousSegment)

• isSecondaryAlignment

  public boolean isSecondaryAlignment()

  Return true if this record has the secondary alignment BAM flag set.

• isHasMateDownStream

  public boolean isHasMateDownStream()

  Return true if this record's CRAM flags indicate a downstream mate in the same slice.

• isHasMateDownStream

  public static boolean isHasMateDownStream(int cramFlags)

  Test the has-mate-downstream bit in the given CRAM flags value.

• isDetached

  public boolean isDetached()

  Return true if this record stores mate information explicitly (detached state).

• isDetached

  public static boolean isDetached(int cramFlags)

  Test the detached bit in the given CRAM flags value.

• isForcePreserveQualityScores

  public boolean isForcePreserveQualityScores()

  Return true if quality scores are preserved as a full array for this record.

• isForcePreserveQualityScores

  public static boolean isForcePreserveQualityScores(int cramFlags)

  Test the quality-scores-preserved-as-array bit in the given CRAM flags value.

• isUnknownBases

  public boolean isUnknownBases()

  Return true if the original sequence was unknown (SEQ="*").

• isUnknownBases

  public static boolean isUnknownBases(int cramFlags)

  Test the unknown-bases bit in the given CRAM flags value.

• isReadPaired

  public boolean isReadPaired()

  Return true if this record has the read-paired BAM flag set.

• isSegmentUnmapped

  public boolean isSegmentUnmapped()

  Does this record have the mapped flag set? This is independent of placement/alignment status. Unmapped records may be stored in the same Slices and Containers as mapped records if they are placed.

  Returns:

  true if the record is unmapped

  See Also:

  • isPlaced()

• isSegmentUnmapped

  public static boolean isSegmentUnmapped(int bamFlags)

  Test the segment-unmapped bit in the given BAM flags value.

• isFirstSegment

  public boolean isFirstSegment()

  Return true if this record is the first segment in the template.

• isLastSegment

  public boolean isLastSegment()

  Return true if this record is the last segment in the template.

• setDetached

  public void setDetached(boolean detached)

  Set or clear the detached CRAM flag (mate info stored explicitly).

• equals

  public boolean equals(Object o)

  Overrides:

  equals in class Object

• hashCode

  public int hashCode()

  Overrides:

  hashCode in class Object