org.molgenis.gavin.job.input

Class Parser

java.lang.Object

org.molgenis.gavin.job.input.Parser

@Component
public class Parser
extends Object

Parses input lines. Two formats are supported, the output from the online CADD webtool and a VCF of which only the first five columns are read.

Field Summary

Fields

Modifier and Type	Field and Description
static int	MAX_LINES

Constructor Summary

Constructors

Constructor and Description
Parser()

Method Summary

Modifier and Type	Method and Description
boolean	isComment(String line) Determines if a line is a comment line.
LineType	transformLine(String line, int numLines, int numValidLines, LineSink outputSink, LineSink errorSink) Transforms a single line.
Variant	tryParseVariant(String line) Parses a line into a Variant.
com.google.common.collect.Multiset<LineType>	tryTransform(File inputFile, File output, File error) Transforms gavin input file.

Methods inherited from class java.lang.Object

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

Field Detail

MAX_LINES

public static final int MAX_LINES

See Also:

Constant Field Values

Constructor Detail

Parser

public Parser()

Method Detail

tryTransform

public com.google.common.collect.Multiset<LineType> tryTransform(File inputFile,
                                                                 File output,
                                                                 File error)
                                                          throws IOException

Transforms gavin input file.

Parameters:

inputFile - the file to transform

output - the file to output parsed variants to

error - the file to output error lines to

Returns:

Multiset counting the LineTypes of the input file's lines

Throws:

IOException - if the file interaction fails

transformLine

public LineType transformLine(String line,
                              int numLines,
                              int numValidLines,
                              LineSink outputSink,
                              LineSink errorSink)

Transforms a single line.

Parameters:

line - the line to parse

numValidLines - the number of valid lines already parsed

outputSink - LineSink to write parsed variants to

errorSink - LineSink to write lines to that we cannot parse

Returns:

LineType of the parsed line

isComment

public boolean isComment(String line)

Determines if a line is a comment line. Comment lines start with "#".

Parameters:

line - the line that may be a comment line

Returns:

true if the line is a comment line

tryParseVariant

public Variant tryParseVariant(String line)

Parses a line into a Variant. It may be one of two formats, CADD output or five VCF columns.

Parameters:

line - the line to parse

Returns:

parsed Variant, or null if the line could not be parsed