org.seqdoop.hadoop_bam.util

Class SAMHeaderReader

java.lang.Object

org.seqdoop.hadoop_bam.util.SAMHeaderReader

public final class SAMHeaderReader
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
static String	VALIDATION_STRINGENCY_PROPERTY A String property corresponding to a ValidationStringency value.

Constructor Summary

Constructors

Constructor and Description
SAMHeaderReader()

Method Summary

Modifier and Type	Method and Description
static htsjdk.samtools.cram.ref.ReferenceSource	getReferenceSource(org.apache.hadoop.conf.Configuration conf)
static htsjdk.samtools.ValidationStringency	getValidationStringency(org.apache.hadoop.conf.Configuration conf)
static htsjdk.samtools.SAMFileHeader	readSAMHeaderFrom(InputStream in, org.apache.hadoop.conf.Configuration conf) Does not close the stream.
static htsjdk.samtools.SAMFileHeader	readSAMHeaderFrom(org.apache.hadoop.fs.Path path, org.apache.hadoop.conf.Configuration conf)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

VALIDATION_STRINGENCY_PROPERTY

public static final String VALIDATION_STRINGENCY_PROPERTY

A String property corresponding to a ValidationStringency value. If set, the given stringency is used when any part of the Hadoop-BAM library reads SAM or BAM.

See Also:

Constant Field Values

Constructor Detail

SAMHeaderReader

public SAMHeaderReader()

Method Detail

readSAMHeaderFrom

public static htsjdk.samtools.SAMFileHeader readSAMHeaderFrom(org.apache.hadoop.fs.Path path,
                                                              org.apache.hadoop.conf.Configuration conf)
                                                       throws IOException

Throws:

IOException

readSAMHeaderFrom

public static htsjdk.samtools.SAMFileHeader readSAMHeaderFrom(InputStream in,
                                                              org.apache.hadoop.conf.Configuration conf)

Does not close the stream.

getValidationStringency

public static htsjdk.samtools.ValidationStringency getValidationStringency(org.apache.hadoop.conf.Configuration conf)

getReferenceSource

public static htsjdk.samtools.cram.ref.ReferenceSource getReferenceSource(org.apache.hadoop.conf.Configuration conf)