htsjdk.tribble.gelitext

Class GeliTextCodec

java.lang.Object

htsjdk.tribble.AbstractFeatureCodec<T,LineIterator>

htsjdk.tribble.AsciiFeatureCodec<GeliTextFeature>

htsjdk.tribble.gelitext.GeliTextCodec

All Implemented Interfaces:

FeatureCodec<GeliTextFeature,LineIterator>

Deprecated.

This is deprecated and unsupported.

@Deprecated
public class GeliTextCodec
extends AsciiFeatureCodec<GeliTextFeature>

A codec for parsing geli text files, which is the text version of the geli binary format.

GELI text has the following tab-seperated fields: contig the contig (string) position the position on the contig (long) refBase the reference base (char) depthOfCoverage the depth of coverage at this position (int) maximumMappingQual the maximum mapping quality of a read at this position (int) genotype the called genotype (string) LODBestToReference the LOD score of the best to the reference (double) LODBestToNext the LOD score of the best to the next best genotype (double) likelihoods the array of all genotype likelihoods, in ordinal ordering (array of 10 doubles, in ordinal order)

Constructor Summary

Constructors

Constructor and Description
GeliTextCodec() Deprecated.

Method Summary

Modifier and Type	Method and Description
boolean	canDecode(java.lang.String path) Deprecated. This function returns true iff the File potentialInput can be parsed by this codec.
GeliTextFeature	decode(java.lang.String line) Deprecated.
GeliTextFeature	decode(java.lang.String[] tokens) Deprecated.
Feature	decodeLoc(java.lang.String line) Deprecated.
java.lang.Object	readActualHeader(LineIterator reader) Deprecated. Read and return the header, or null if there is no header.

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

getTabixFormat

Constructor Detail

GeliTextCodec

public GeliTextCodec()

Deprecated.

Method Detail

decodeLoc

public Feature decodeLoc(java.lang.String line)

Deprecated.

decode

public GeliTextFeature decode(java.lang.String line)

Deprecated.

Specified by:

decode in class AsciiFeatureCodec<GeliTextFeature>

See Also:

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

canDecode

public boolean canDecode(java.lang.String path)

Deprecated.

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:

path - the file to test for parsability with this codec

Returns:

true if potentialInput can be parsed, false otherwise

readActualHeader

public java.lang.Object readActualHeader(LineIterator reader)

Deprecated.

Description copied from class: AsciiFeatureCodec

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

Specified by:

readActualHeader in class AsciiFeatureCodec<GeliTextFeature>

Returns:

the actual header data in the file, or null if none is available

decode

public GeliTextFeature decode(java.lang.String[] tokens)

Deprecated.