htsjdk.variant.vcf

Class VCFUtils

java.lang.Object

htsjdk.variant.vcf.VCFUtils

public class VCFUtils
extends java.lang.Object

Constructor Summary

Constructors

Constructor and Description
VCFUtils()

Method Summary

Methods

Modifier and Type	Method and Description
static java.util.List<VCFContigHeaderLine>	makeContigHeaderLines(SAMSequenceDictionary refDict, java.io.File referenceFile) Create VCFHeaderLines for each refDict entry, and optionally the assembly if referenceFile != null
static java.util.Set<VCFHeaderLine>	smartMergeHeaders(java.util.Collection<VCFHeader> headers, boolean emitWarnings)
static VCFHeader	withUpdatedContigs(VCFHeader oldHeader, java.io.File referenceFile, SAMSequenceDictionary refDict) Add / replace the contig header lines in the VCFHeader with the in the reference file and master reference dictionary
static java.util.Set<VCFHeaderLine>	withUpdatedContigsAsLines(java.util.Set<VCFHeaderLine> oldLines, java.io.File referenceFile, SAMSequenceDictionary refDict)
static java.util.Set<VCFHeaderLine>	withUpdatedContigsAsLines(java.util.Set<VCFHeaderLine> oldLines, java.io.File referenceFile, SAMSequenceDictionary refDict, boolean referenceNameOnly)

Methods inherited from class java.lang.Object

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

Constructor Detail

VCFUtils

public VCFUtils()

Method Detail

smartMergeHeaders

public static java.util.Set<VCFHeaderLine> smartMergeHeaders(java.util.Collection<VCFHeader> headers,
                                             boolean emitWarnings)
                                                      throws java.lang.IllegalStateException

Throws:

java.lang.IllegalStateException

withUpdatedContigs

public static VCFHeader withUpdatedContigs(VCFHeader oldHeader,
                           java.io.File referenceFile,
                           SAMSequenceDictionary refDict)

Add / replace the contig header lines in the VCFHeader with the in the reference file and master reference dictionary

Parameters:

oldHeader - the header to update

referenceFile - the file path to the reference sequence used to generate this vcf

refDict - the SAM formatted reference sequence dictionary

withUpdatedContigsAsLines

public static java.util.Set<VCFHeaderLine> withUpdatedContigsAsLines(java.util.Set<VCFHeaderLine> oldLines,
                                                     java.io.File referenceFile,
                                                     SAMSequenceDictionary refDict)

withUpdatedContigsAsLines

public static java.util.Set<VCFHeaderLine> withUpdatedContigsAsLines(java.util.Set<VCFHeaderLine> oldLines,
                                                     java.io.File referenceFile,
                                                     SAMSequenceDictionary refDict,
                                                     boolean referenceNameOnly)

makeContigHeaderLines

public static java.util.List<VCFContigHeaderLine> makeContigHeaderLines(SAMSequenceDictionary refDict,
                                                        java.io.File referenceFile)

Create VCFHeaderLines for each refDict entry, and optionally the assembly if referenceFile != null

Parameters:

refDict - reference dictionary

referenceFile - for assembly name. May be null

Returns:

list of vcf contig header lines