org.broadinstitute.hellbender.utils.codecs.table

Class TableCodec

java.lang.Object

htsjdk.tribble.AbstractFeatureCodec<T,htsjdk.tribble.readers.LineIterator>

htsjdk.tribble.AsciiFeatureCodec<TableFeature>

org.broadinstitute.hellbender.utils.codecs.table.TableCodec

All Implemented Interfaces:

htsjdk.tribble.FeatureCodec<TableFeature,htsjdk.tribble.readers.LineIterator>

public final class TableCodec
extends htsjdk.tribble.AsciiFeatureCodec<TableFeature>

Reads tab deliminated tabular text files

• Header: must begin with line HEADER or track (for IGV), followed by any number of column names, separated by whitespace.
• Header: Custom header delimiters can be provided, with a null header line being interpreted as having a non-delimeted header which consists of one line.
• Comment lines starting with # are ignored
• Each non-header and non-comment line is split into parts by whitespace, and these parts are assigned as a map to their corresponding column name in the header. Note that the first element (corresponding to the HEADER column) must be a valid genome loc such as 1, 1:1 or 1:1-10, which is the position of the Table element on the genome. TableCodec requires that there be one value for each column in the header, and no more, on all lines.

File format example 1

     HEADER a b c
     1:1  1   2   3
     1:2  4   5   6
     1:3  7   8   9
 

File format example 2

     a b c
     1:1  1   2   3
     1:2  4   5   6
     1:3  7   8   9
 

Field Summary

Fields

Modifier and Type	Field and Description
protected static java.lang.String	COMMENT_DELIMITER
protected static java.lang.String	DEFAULT_HEADER_DELIMITER
protected java.lang.String	delimiter_regex
protected java.util.List<java.lang.String>	header
protected static java.lang.String	IGV_HEADER_DELIMITER

Constructor Summary

Constructors

Constructor and Description
TableCodec() Create a TableCodec for IGV track data.
TableCodec(java.lang.String headerLineDelimiter) Create a TableCodec with a configured header line delimiter

Method Summary

Modifier and Type	Method and Description
boolean	canDecode(java.lang.String path)
TableFeature	decode(java.lang.String line)
java.util.List<java.lang.String>	readActualHeader(htsjdk.tribble.readers.LineIterator reader)

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, getTabixFormat

Field Detail

DEFAULT_HEADER_DELIMITER

protected static final java.lang.String DEFAULT_HEADER_DELIMITER

See Also:

Constant Field Values

IGV_HEADER_DELIMITER

protected static final java.lang.String IGV_HEADER_DELIMITER

See Also:

Constant Field Values

COMMENT_DELIMITER

protected static final java.lang.String COMMENT_DELIMITER

See Also:

Constant Field Values

delimiter_regex

protected java.lang.String delimiter_regex

header

protected java.util.List<java.lang.String> header

Constructor Detail

TableCodec

public TableCodec(java.lang.String headerLineDelimiter)

Create a TableCodec with a configured header line delimiter

Parameters:

headerLineDelimiter - the delimeter for comment header lines, or null if the header is a single commented line-

TableCodec

public TableCodec()

Create a TableCodec for IGV track data.

Method Detail

decode

public TableFeature decode(java.lang.String line)

Specified by:

decode in class htsjdk.tribble.AsciiFeatureCodec<TableFeature>

readActualHeader

public java.util.List<java.lang.String> readActualHeader(htsjdk.tribble.readers.LineIterator reader)

Specified by:

readActualHeader in class htsjdk.tribble.AsciiFeatureCodec<TableFeature>

canDecode

public boolean canDecode(java.lang.String path)