htsjdk.variant.vcf

Class AbstractVCFCodec

java.lang.Object

htsjdk.tribble.AbstractFeatureCodec<T,LineIterator>

htsjdk.tribble.AsciiFeatureCodec<VariantContext>

htsjdk.variant.vcf.AbstractVCFCodec

All Implemented Interfaces:

FeatureCodec<VariantContext,LineIterator>, NameAwareCodec

Direct Known Subclasses:

VCF3Codec, VCFCodec

public abstract class AbstractVCFCodec
extends AsciiFeatureCodec<VariantContext>
implements NameAwareCodec

Field Summary

Fields

Modifier and Type	Field and Description
protected java.util.Map<java.lang.String,java.util.List<Allele>>	alleleMap
protected boolean	doOnTheFlyModifications If true, then we'll magically fix up VCF headers on the fly when we read them in
protected java.util.HashMap<java.lang.String,java.util.List<java.lang.String>>	filterHash
protected java.lang.String[]	genotypeParts
protected VCFHeader	header
protected int	lineNo
protected java.lang.String[]	locParts
static int	MAX_ALLELE_SIZE_BEFORE_WARNING
protected java.lang.String	name
protected static int	NUM_STANDARD_FIELDS
protected java.lang.String[]	parts
protected java.lang.String	remappedSampleName If non-null, we will replace the sample name read from the VCF header with this sample name.
protected java.util.Map<java.lang.String,java.lang.String>	stringCache
static boolean	validate
protected VCFHeaderVersion	version
protected boolean	warnedAboutNoEqualsForNonFlag

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	AbstractVCFCodec()

Method Summary

Modifier and Type	Method and Description
static boolean	canDecodeFile(java.lang.String potentialInput, java.lang.String MAGIC_HEADER_LINE)
LazyGenotypesContext.LazyData	createGenotypeMap(java.lang.String str, java.util.List<Allele> alleles, java.lang.String chr, int pos) create a genotype map
VariantContext	decode(java.lang.String line) decode the line into a feature (VariantContext)
Feature	decodeLoc(java.lang.String line) the fast decode function
void	disableOnTheFlyModifications() Forces all VCFCodecs to not perform any on the fly modifications to the VCF header of VCF records.
protected void	generateException(java.lang.String message)
protected static void	generateException(java.lang.String message, int lineNo)
protected java.lang.String	getCachedString(java.lang.String str) Return a cached copy of the supplied string.
java.lang.String	getName() get the name of this codec
protected static Allele	oneAllele(java.lang.String index, java.util.List<Allele> alleles) create a an allele from an index and an array of alleles
protected static java.util.List<Allele>	parseAlleles(java.lang.String ref, java.lang.String alts, int lineNo) parse out the alleles
protected abstract java.util.List<java.lang.String>	parseFilters(java.lang.String filterString) parse the filter string, first checking to see if we already have parsed it in a previous attempt
protected static java.util.List<Allele>	parseGenotypeAlleles(java.lang.String GT, java.util.List<Allele> alleles, java.util.Map<java.lang.String,java.util.List<Allele>> cache) parse genotype alleles from the genotype string
protected VCFHeader	parseHeaderFromLines(java.util.List<java.lang.String> headerStrings, VCFHeaderVersion version) create a VCF header from a set of header record lines
protected static java.lang.Double	parseQual(java.lang.String qualString) parse out the qual value
void	setName(java.lang.String name) set the name of this codec
void	setRemappedSampleName(java.lang.String remappedSampleName) Replaces the sample name read from the VCF header with the remappedSampleName.
VCFHeader	setVCFHeader(VCFHeader header, VCFHeaderVersion version) Explicitly set the VCFHeader on this codec.

Methods inherited from class htsjdk.tribble.AsciiFeatureCodec

close, decode, isDone, makeIndexableSourceFromStream, makeSourceFromStream, readActualHeader, readHeader

Methods inherited from class htsjdk.tribble.AbstractFeatureCodec

decodeLoc, getFeatureType

Methods inherited from class java.lang.Object

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

Methods inherited from interface htsjdk.tribble.FeatureCodec

canDecode

Field Detail

MAX_ALLELE_SIZE_BEFORE_WARNING

public static final int MAX_ALLELE_SIZE_BEFORE_WARNING

NUM_STANDARD_FIELDS

protected static final int NUM_STANDARD_FIELDS

See Also:

Constant Field Values

header

protected VCFHeader header

version

protected VCFHeaderVersion version

alleleMap

protected java.util.Map<java.lang.String,java.util.List<Allele>> alleleMap

validate

public static boolean validate

parts

protected java.lang.String[] parts

genotypeParts

protected java.lang.String[] genotypeParts

locParts

protected final java.lang.String[] locParts

filterHash

protected java.util.HashMap<java.lang.String,java.util.List<java.lang.String>> filterHash

name

protected java.lang.String name

lineNo

protected int lineNo

stringCache

protected java.util.Map<java.lang.String,java.lang.String> stringCache

warnedAboutNoEqualsForNonFlag

protected boolean warnedAboutNoEqualsForNonFlag

doOnTheFlyModifications

protected boolean doOnTheFlyModifications

If true, then we'll magically fix up VCF headers on the fly when we read them in

remappedSampleName

protected java.lang.String remappedSampleName

If non-null, we will replace the sample name read from the VCF header with this sample name. This feature works only for single-sample VCFs.

Constructor Detail

AbstractVCFCodec

protected AbstractVCFCodec()

Method Detail

parseFilters

protected abstract java.util.List<java.lang.String> parseFilters(java.lang.String filterString)

parse the filter string, first checking to see if we already have parsed it in a previous attempt

Parameters:

filterString - the string to parse

Returns:

a set of the filters applied

parseHeaderFromLines

protected VCFHeader parseHeaderFromLines(java.util.List<java.lang.String> headerStrings,
                                         VCFHeaderVersion version)

create a VCF header from a set of header record lines

Parameters:

headerStrings - a list of strings that represent all the ## and # entries

Returns:

a VCFHeader object

setVCFHeader

public VCFHeader setVCFHeader(VCFHeader header,
                              VCFHeaderVersion version)

Explicitly set the VCFHeader on this codec. This will overwrite the header read from the file and the version state stored in this instance; conversely, reading the header from a file will overwrite whatever is set here. The returned header may not be identical to the header argument since the header lines may be "repaired" (i.e., rewritten) if doOnTheFlyModifications is set.

decodeLoc

public Feature decodeLoc(java.lang.String line)

the fast decode function

Parameters:

line - the line of text for the record

Returns:

a feature, (not guaranteed complete) that has the correct start and stop

decode

public VariantContext decode(java.lang.String line)

decode the line into a feature (VariantContext)

Specified by:

decode in class AsciiFeatureCodec<VariantContext>

Parameters:

line - the line

Returns:

a VariantContext

See Also:

AsciiFeatureCodec.decode(htsjdk.tribble.readers.LineIterator)

getName

public java.lang.String getName()

get the name of this codec

Specified by:

getName in interface NameAwareCodec

Returns:

our set name

setName

public void setName(java.lang.String name)

set the name of this codec

Specified by:

setName in interface NameAwareCodec

Parameters:

name - new name

getCachedString

protected java.lang.String getCachedString(java.lang.String str)

Return a cached copy of the supplied string.

Parameters:

str - string

Returns:

interned string

oneAllele

protected static Allele oneAllele(java.lang.String index,
                                  java.util.List<Allele> alleles)

create a an allele from an index and an array of alleles

Parameters:

index - the index

alleles - the alleles

Returns:

an Allele

parseGenotypeAlleles

protected static java.util.List<Allele> parseGenotypeAlleles(java.lang.String GT,
                                                             java.util.List<Allele> alleles,
                                                             java.util.Map<java.lang.String,java.util.List<Allele>> cache)

parse genotype alleles from the genotype string

Parameters:

GT - GT string

alleles - list of possible alleles

cache - cache of alleles for GT

Returns:

the allele list for the GT string

parseQual

protected static java.lang.Double parseQual(java.lang.String qualString)

parse out the qual value

Parameters:

qualString - the quality string

Returns:

return a double

parseAlleles

protected static java.util.List<Allele> parseAlleles(java.lang.String ref,
                                                     java.lang.String alts,
                                                     int lineNo)

parse out the alleles

Parameters:

ref - the reference base

alts - a string of alternates to break into alleles

lineNo - the line number for this record

Returns:

a list of alleles, and a pair of the shortest and longest sequence

canDecodeFile

public static boolean canDecodeFile(java.lang.String potentialInput,
                                    java.lang.String MAGIC_HEADER_LINE)

createGenotypeMap

public LazyGenotypesContext.LazyData createGenotypeMap(java.lang.String str,
                                                       java.util.List<Allele> alleles,
                                                       java.lang.String chr,
                                                       int pos)

create a genotype map

Parameters:

str - the string

alleles - the list of alleles

Returns:

a mapping of sample name to genotype object

disableOnTheFlyModifications

public final void disableOnTheFlyModifications()

Forces all VCFCodecs to not perform any on the fly modifications to the VCF header of VCF records. Useful primarily for raw comparisons such as when comparing raw VCF records

setRemappedSampleName

public void setRemappedSampleName(java.lang.String remappedSampleName)

Replaces the sample name read from the VCF header with the remappedSampleName. Works only for single-sample VCFs -- attempting to perform sample name remapping for multi-sample VCFs will produce an Exception.

Parameters:

remappedSampleName - replacement sample name for the sample specified in the VCF header

generateException

protected void generateException(java.lang.String message)

generateException

protected static void generateException(java.lang.String message,
                                        int lineNo)