Package htsjdk.samtools.cram.build
Class Sam2CramRecordFactory
- java.lang.Object
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- htsjdk.samtools.cram.build.Sam2CramRecordFactory
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public class Sam2CramRecordFactory extends Object
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Field Summary
Fields Modifier and Type Field Description boolean
captureAllTags
Set<String>
captureTags
Set<String>
ignoreTags
boolean
preserveReadNames
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Constructor Summary
Constructors Constructor Description Sam2CramRecordFactory(byte[] refBases, SAMFileHeader samFileHeader, Version version)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description CramCompressionRecord
createCramRecord(SAMRecord record)
Create a CramCompressionRecord.long
getBaseCount()
long
getFeatureCount()
Map<String,Integer>
getReadGroupMap()
byte[]
getRefBases()
void
setRefBases(byte[] refBases)
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Constructor Detail
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Sam2CramRecordFactory
public Sam2CramRecordFactory(byte[] refBases, SAMFileHeader samFileHeader, Version version)
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Method Detail
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createCramRecord
public CramCompressionRecord createCramRecord(SAMRecord record)
Create a CramCompressionRecord.- Parameters:
record
- If the input record does not have an associated SAMFileHeader, it will be updated with the header used for the factory in order to allow reference indices to be resolved.- Returns:
- CramCompressionRecord
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getRefBases
public byte[] getRefBases()
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setRefBases
public void setRefBases(byte[] refBases)
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getBaseCount
public long getBaseCount()
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getFeatureCount
public long getFeatureCount()
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