Package htsjdk.variant.vcf

Class VCF3Codec

java.lang.Object

htsjdk.tribble.AbstractFeatureCodec<T,LineIterator>

htsjdk.tribble.AsciiFeatureCodec<VariantContext>

htsjdk.variant.vcf.AbstractVCFCodec

htsjdk.variant.vcf.VCF3Codec

All Implemented Interfaces:

FeatureCodec<VariantContext,LineIterator>, NameAwareCodec

public class VCF3Codec
extends AbstractVCFCodec

A feature codec for the VCF3 specification, to read older VCF files. VCF3 has been depreciated in favor of VCF4 (See VCF codec for the latest information)

Reads historical VCF3 encoded files (1000 Genomes Pilot results, for example)

See also: @see VCF specification
See also: @see VCF spec. publication

Since:

2010

Field Summary

Fields

Modifier and Type	Field	Description
static final String	VCF3_MAGIC_HEADER

Fields inherited from class htsjdk.variant.vcf.AbstractVCFCodec

alleleMap, doOnTheFlyModifications, filterHash, genotypeParts, header, lineNo, locParts, MAX_ALLELE_SIZE_BEFORE_WARNING, name, NUM_STANDARD_FIELDS, parts, remappedSampleName, stringCache, validate, version, warnedAboutNoEqualsForNonFlag

Constructor Summary

Constructors

Constructor	Description
VCF3Codec()

Method Summary

Modifier and Type	Method	Description
boolean	canDecode(String potentialInput)	This function returns true iff the File potentialInput can be parsed by this codec.
protected List<String>	parseFilters(String filterString)	parse the filter string, first checking to see if we already have parsed it in a previous attempt
Object	readActualHeader(LineIterator reader)	Read and return the header, or null if there is no header.

Methods inherited from class htsjdk.variant.vcf.AbstractVCFCodec

canDecodeFile, createGenotypeMap, decode, decodeLoc, disableOnTheFlyModifications, generateException, generateException, getAltHeaderLine, getCachedString, getHeader, getMetaHeaderLine, getName, getPedigreeHeaderLine, getSampleHeaderLine, getTabixFormat, getVersion, oneAllele, parseAlleles, parseGenotypeAlleles, parseHeaderFromLines, parseQual, setName, setRemappedSampleName, setVCFHeader

Methods inherited from class htsjdk.tribble.AsciiFeatureCodec

close, decode, isDone, makeIndexableSourceFromStream, makeSourceFromStream, 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

getPathToDataFile

Field Details

VCF3_MAGIC_HEADER

public static final String VCF3_MAGIC_HEADER

See Also:

• Constant Field Values

Constructor Details

VCF3Codec

public VCF3Codec()

Method Details

readActualHeader

public Object readActualHeader(LineIterator reader)

Description copied from class: AsciiFeatureCodec

Read and return the header, or null if there is no header.

Specified by:

readActualHeader in class AsciiFeatureCodec<VariantContext>

Parameters:

reader - the line reader to take header lines from

Returns:

the number of header lines

parseFilters

protected List<String> parseFilters(String filterString)

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

Specified by:

parseFilters in class AbstractVCFCodec

Parameters:

filterString - the string to parse

Returns:

a set of the filters applied

canDecode

public boolean canDecode(String potentialInput)

Description copied from interface: FeatureCodec

This function returns true iff the File potentialInput can be parsed by this codec. Note that checking the file's extension is a perfectly acceptable implementation of this method and file contents only rarely need to be checked.

There is an assumption that there's never a situation where two different Codecs return true for the same file. If this occurs, the recommendation would be to error out.

Note this function must never throw an error. All errors should be trapped and false returned.

Parameters:

potentialInput - the file to test for parsability with this codec

Returns:

true if potentialInput can be parsed, false otherwise