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>

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

GeliTextCodec()

Method Summary

GeliTextFeature	decode(java.lang.String line)
GeliTextFeature	decode(java.lang.String[] tokens)
Feature	decodeLoc(java.lang.String line)
java.lang.Object	readActualHeader(LineIterator reader) 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

canDecode, decodeLoc, getFeatureType

Methods inherited from class java.lang.Object

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

Constructor Detail

GeliTextCodec

public GeliTextCodec()

Method Detail

decodeLoc

public Feature decodeLoc(java.lang.String line)

decode

public GeliTextFeature decode(java.lang.String line)

Specified by:

decode in class AsciiFeatureCodec<GeliTextFeature>

See Also:

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

readActualHeader

public java.lang.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<GeliTextFeature>

Returns:

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

decode

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