picard.fingerprint

Class GenotypeReader

java.lang.Object

picard.fingerprint.GenotypeReader

Deprecated.

Please use VCFFileReader instead of this class.

public class GenotypeReader
extends java.lang.Object

Class that abstracts away the source of genotypes and provides abilities to read them in from various sources into VariantContext objects

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	GenotypeReader.VariantIterator Deprecated. Small class to encapsulate an iterator over variants, optionally with a sequence dictionary.

Constructor Summary

Constructors

Constructor and Description
GenotypeReader() Deprecated.

Method Summary

Modifier and Type	Method and Description
GenotypeReader.VariantIterator	read(java.io.File file) Deprecated. Please use VCFFileReader in Picard-public instead of this class.
GenotypeReader.VariantIterator	read(java.io.File file, htsjdk.samtools.util.IntervalList intervals) Deprecated. Please use VCFFileReader in Picard-public instead of this class.

Methods inherited from class java.lang.Object

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

Constructor Detail

GenotypeReader

public GenotypeReader()

Deprecated.

Method Detail

read

public GenotypeReader.VariantIterator read(java.io.File file)

Deprecated. Please use VCFFileReader in Picard-public instead of this class.

Reads in a file that contains genotype data and returns an iterator over every entry in the file as VariantContext objects.

read

public GenotypeReader.VariantIterator read(java.io.File file,
                                           htsjdk.samtools.util.IntervalList intervals)

Deprecated. Please use VCFFileReader in Picard-public instead of this class.

Reads in the file and returns an iterator over the set of entries in the file that overlap with the interval supplied.