Package htsjdk.variant.vcf

Class VCFUtils

java.lang.Object

htsjdk.variant.vcf.VCFUtils

public class VCFUtils
extends Object

Constructor Summary

Constructors

Constructor	Description
VCFUtils()

Method Summary

Modifier and Type	Method	Description
static File	createTemporaryIndexedVcfFile(String prefix, String suffix)	This method creates a temporary VCF file and its appropriately named index file, and will delete them on exit.
static File	createTemporaryIndexedVcfFromInput(File vcfFile, String tempFilePrefix)	This method makes a copy of the input VCF and creates an index file for it in the same location.
static List<VCFContigHeaderLine>	makeContigHeaderLines(SAMSequenceDictionary refDict, File referenceFile)	Create VCFHeaderLines for each refDict entry, and optionally the assembly if referenceFile != null
static double	parseVcfDouble(String str)	Parses a String as a Double, being tolerant for case-insensitive NaN and Inf/Infinity.
static Set<VCFHeaderLine>	smartMergeHeaders(Collection<VCFHeader> headers, boolean emitWarnings)
static VCFHeader	withUpdatedContigs(VCFHeader oldHeader, File referenceFile, SAMSequenceDictionary refDict)	Add / replace the contig header lines in the VCFHeader with the in the reference file and master reference dictionary
static Set<VCFHeaderLine>	withUpdatedContigsAsLines(Set<VCFHeaderLine> oldLines, File referenceFile, SAMSequenceDictionary refDict)
static Set<VCFHeaderLine>	withUpdatedContigsAsLines(Set<VCFHeaderLine> oldLines, 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 Details

VCFUtils

public VCFUtils()

Method Details

smartMergeHeaders

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

Throws:

IllegalStateException

withUpdatedContigs

public static VCFHeader withUpdatedContigs(VCFHeader oldHeader,
 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 Set<VCFHeaderLine> withUpdatedContigsAsLines(Set<VCFHeaderLine> oldLines,
 File referenceFile,
 SAMSequenceDictionary refDict)

withUpdatedContigsAsLines

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

makeContigHeaderLines

public static List<VCFContigHeaderLine> makeContigHeaderLines(SAMSequenceDictionary refDict,
 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

createTemporaryIndexedVcfFile

public static File createTemporaryIndexedVcfFile(String prefix,
 String suffix)
                                          throws IOException

This method creates a temporary VCF file and its appropriately named index file, and will delete them on exit.

Parameters:

prefix - - The prefix string to be used in generating the file's name; must be at least three characters long

suffix - - The suffix string to be used in generating the file's name; may be null, in which case the suffix ".tmp" will be used

Returns:

A File object referencing the newly created temporary VCF file

Throws:

IOException - - if a file could not be created.

createTemporaryIndexedVcfFromInput

public static File createTemporaryIndexedVcfFromInput(File vcfFile,
 String tempFilePrefix)
                                               throws IOException

This method makes a copy of the input VCF and creates an index file for it in the same location. This is done so that we don't need to store the index file in the same repo The copy of the input is done so that it and its index are in the same directory which is typically required.

Parameters:

vcfFile - the vcf file to index

Returns:

File a vcf file (index file is created in same path).

Throws:

IOException

parseVcfDouble

public static double parseVcfDouble(String str)

Parses a String as a Double, being tolerant for case-insensitive NaN and Inf/Infinity.