CRAMCompressionRecord (htsjdk 3.0.2 API)

java.lang.Object
- htsjdk.samtools.cram.structure.CRAMCompressionRecord

```
public class CRAMCompressionRecord
extends java.lang.Object
```
A CRAMRecord represents a SAMRecord that has been transformed to CRAM-style representation. This includes representing read bases as reference-relative read features, and representation of quality scores, tags, and BAM and CRAM flags.

Field Summary

Fields
Modifier and Type	Field and Description
`static int`	`CF_DETACHED`
`static int`	`CF_HAS_MATE_DOWNSTREAM`
`static int`	`CF_QS_PRESERVED_AS_ARRAY`
`static int`	`CF_UNKNOWN_BASES`
`static int`	`MF_MATE_NEG_STRAND`
`static int`	`MF_MATE_UNMAPPED`
`static byte`	`MISSING_QUALITY_SCORE`
`static int`	`NO_READGROUP_ID`

Constructor Summary

Constructors
Constructor and Description
`CRAMCompressionRecord(CRAMVersion cramVersion, CRAMEncodingStrategy encodingStrategy, SAMRecord samRecord, byte[] referenceBases, long sequentialIndex, java.util.Map<java.lang.String,java.lang.Integer> readGroupMap)` Create a CRAMRecord from a SAMRecord.
`CRAMCompressionRecord(long sequentialIndex, int bamFlags, int cramFlags, java.lang.String readName, int readLength, int referenceIndex, int alignmentStart, int templateSize, int mappingQuality, byte[] qualityScores, byte[] readBases, java.util.List<ReadTag> readTags, java.util.List<ReadFeature> readFeaturesList, int readGroupID, int mateFlags, int mateReferenceIndex, int mateAlignmentStart, int recordsToNextFragment)` Create a CRAMRecord from a set of values retrieved from a serialized Slice's data series streams.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`assignReadName()`
`boolean`	`equals(java.lang.Object o)`
`int`	`getAlignmentEnd()`
`int`	`getAlignmentStart()`
`int`	`getBAMFlags()`
`int`	`getCRAMFlags()`
`int`	`getMappingQuality()`
`int`	`getMateAlignmentStart()`
`int`	`getMateFlags()`
`int`	`getMateReferenceIndex()`
`CRAMCompressionRecord`	`getNextSegment()`
`CRAMCompressionRecord`	`getPreviousSegment()`
`byte[]`	`getQualityScores()`
`byte[]`	`getReadBases()`
`java.util.List<ReadFeature>`	`getReadFeatures()`
`int`	`getReadGroupID()`
`int`	`getReadLength()`
`java.lang.String`	`getReadName()`
`int`	`getRecordsToNextFragment()`
`int`	`getReferenceIndex()`
`long`	`getSequentialIndex()`
`MutableInt`	`getTagIdsIndex()`
`java.util.List<ReadTag>`	`getTags()`
`int`	`getTemplateSize()`
`int`	`hashCode()`
`boolean`	`isDetached()`
`static boolean`	`isDetached(int cramFlags)`
`boolean`	`isFirstSegment()`
`boolean`	`isForcePreserveQualityScores()`
`static boolean`	`isForcePreserveQualityScores(int cramFlags)`
`boolean`	`isHasMateDownStream()`
`static boolean`	`isHasMateDownStream(int cramFlags)`
`boolean`	`isLastSegment()`
`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.
`boolean`	`isPlaced()` Determine is read is "placed".
`boolean`	`isReadPaired()`
`boolean`	`isSecondaryAlignment()`
`boolean`	`isSegmentUnmapped()` Does this record have the mapped flag set? This is independent of placement/alignment status.
`static boolean`	`isSegmentUnmapped(int bamFlags)`
`boolean`	`isUnknownBases()`
`static boolean`	`isUnknownBases(int cramFlags)`
`void`	`resolveQualityScores()` Resolve the quality scores for this CRAM record based on preserved scores, read features and flags.
`void`	`restoreMateInfo()`
`void`	`restoreReadBases(CRAMReferenceRegion cramReferenceRegion, SubstitutionMatrix substitutionMatrix)` Restore the actual read bases for this record.
`void`	`setDetached(boolean detached)`
`void`	`setNextSegment(CRAMCompressionRecord nextSegment)`
`void`	`setPreviousSegment(CRAMCompressionRecord previousSegment)`
`void`	`setTagIdsIndex(MutableInt tagIdsIndex)`
`void`	`setToDetachedState()`
`SAMRecord`	`toSAMRecord(SAMFileHeader samFileHeader)` Create a SAMRecord from the CRAMRecord.

Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, toString, wait, wait, wait

Field Detail
- CF_QS_PRESERVED_AS_ARRAY
```
public static final int CF_QS_PRESERVED_AS_ARRAY
```
  See Also:
  
  Constant Field Values
- CF_DETACHED
```
public static final int CF_DETACHED
```
  See Also:
  
  Constant Field Values
- CF_HAS_MATE_DOWNSTREAM
```
public static final int CF_HAS_MATE_DOWNSTREAM
```
  See Also:
  
  Constant Field Values
- CF_UNKNOWN_BASES
```
public static final int CF_UNKNOWN_BASES
```
  See Also:
  
  Constant Field Values
- NO_READGROUP_ID
```
public static final int NO_READGROUP_ID
```
  See Also:
  
  Constant Field Values
- MISSING_QUALITY_SCORE
```
public static final byte MISSING_QUALITY_SCORE
```
  See Also:
  
  Constant Field Values
- MF_MATE_NEG_STRAND
```
public static final int MF_MATE_NEG_STRAND
```
  See Also:
  
  Constant Field Values
- MF_MATE_UNMAPPED
```
public static final int MF_MATE_UNMAPPED
```
  See Also:
  
  Constant Field Values

Constructor Detail

CRAMCompressionRecord

public CRAMCompressionRecord(CRAMVersion cramVersion,
                             CRAMEncodingStrategy encodingStrategy,
                             SAMRecord samRecord,
                             byte[] referenceBases,
                             long sequentialIndex,
                             java.util.Map<java.lang.String,java.lang.Integer> readGroupMap)

Create a CRAMRecord from a SAMRecord.

Parameters:: cramVersion -; encodingStrategy -; samRecord -; referenceBases -; sequentialIndex -; readGroupMap -

CRAMCompressionRecord

public CRAMCompressionRecord(long sequentialIndex,
                             int bamFlags,
                             int cramFlags,
                             java.lang.String readName,
                             int readLength,
                             int referenceIndex,
                             int alignmentStart,
                             int templateSize,
                             int mappingQuality,
                             byte[] qualityScores,
                             byte[] readBases,
                             java.util.List<ReadTag> readTags,
                             java.util.List<ReadFeature> readFeaturesList,
                             int readGroupID,
                             int mateFlags,
                             int mateReferenceIndex,
                             int mateAlignmentStart,
                             int recordsToNextFragment)

Create a CRAMRecord from a set of values retrieved from a serialized Slice's data series streams.

Parameters:: sequentialIndex -; bamFlags -; cramFlags -; readName -; readLength -; referenceIndex -; alignmentStart -; templateSize -; mappingQuality -; qualityScores -; readBases -; readTags -; readFeaturesList -; readGroupID -; mateFlags -; mateReferenceIndex -; mateAlignmentStart -; recordsToNextFragment -

Method Detail
- toSAMRecord
```
public SAMRecord toSAMRecord(SAMFileHeader samFileHeader)
```
  Create a SAMRecord from the CRAMRecord.
  
  Parameters:
  
  samFileHeader - SAMFileHeader
  
  Returns:
  
  a SAMRecord
- assignReadName
```
public void assignReadName()
```
- 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()
```
- setToDetachedState
```
public void setToDetachedState()
```
- 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 java.lang.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 java.util.List<ReadTag> getTags()
```
- getRecordsToNextFragment
```
public int getRecordsToNextFragment()
```
- getReadFeatures
```
public java.util.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()
```
- isHasMateDownStream
```
public boolean isHasMateDownStream()
```
- isHasMateDownStream
```
public static boolean isHasMateDownStream(int cramFlags)
```
- isDetached
```
public boolean isDetached()
```
- isDetached
```
public static boolean isDetached(int cramFlags)
```
- isForcePreserveQualityScores
```
public boolean isForcePreserveQualityScores()
```
- isForcePreserveQualityScores
```
public static boolean isForcePreserveQualityScores(int cramFlags)
```
- isUnknownBases
```
public boolean isUnknownBases()
```
- isUnknownBases
```
public static boolean isUnknownBases(int cramFlags)
```
- isReadPaired
```
public boolean isReadPaired()
```
- 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)
```
- isFirstSegment
```
public boolean isFirstSegment()
```
- isLastSegment
```
public boolean isLastSegment()
```
- setDetached
```
public void setDetached(boolean detached)
```
- equals
```
public boolean equals(java.lang.Object o)
```
  Overrides:
  
  equals in class java.lang.Object
- hashCode
```
public int hashCode()
```
  Overrides:
  
  hashCode in class java.lang.Object

Class CRAMCompressionRecord

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

CF_QS_PRESERVED_AS_ARRAY

CF_DETACHED

CF_HAS_MATE_DOWNSTREAM

CF_UNKNOWN_BASES

NO_READGROUP_ID

MISSING_QUALITY_SCORE

MF_MATE_NEG_STRAND

MF_MATE_UNMAPPED

Constructor Detail

CRAMCompressionRecord

CRAMCompressionRecord

Method Detail

toSAMRecord

assignReadName

isNormalized

resolveQualityScores

restoreReadBases

restoreMateInfo

setToDetachedState

isPlaced

getReadName

getAlignmentStart

getReadLength

getReadBases

getQualityScores

getMappingQuality

getReferenceIndex

getTemplateSize

getTags

getRecordsToNextFragment

getReadFeatures

getReadGroupID

getBAMFlags

getMateReferenceIndex

getMateAlignmentStart

setTagIdsIndex

getTagIdsIndex

getMateFlags

getCRAMFlags

getAlignmentEnd

getSequentialIndex

getNextSegment

setNextSegment

getPreviousSegment

setPreviousSegment

isSecondaryAlignment

isHasMateDownStream

isHasMateDownStream

isDetached

isDetached

isForcePreserveQualityScores

isForcePreserveQualityScores

isUnknownBases

isUnknownBases

isReadPaired

isSegmentUnmapped

isSegmentUnmapped

isFirstSegment

isLastSegment

setDetached

equals

hashCode