org.dishevelled.bio.tools

Class FilterSam

java.lang.Object

org.dishevelled.bio.tools.AbstractFilter

org.dishevelled.bio.tools.FilterSam

All Implemented Interfaces:

Callable<Integer>

public final class FilterSam
extends AbstractFilter

Filter alignments in SAM format.

Since:

1.1

Author:

Michael Heuer

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
(package private) static interface	FilterSam.Filter Filter.
static class	FilterSam.MapqFilter MAPQ filter.
static class	FilterSam.RangeFilter Range filter.
static class	FilterSam.ScriptFilter Script filter.

Constructor Summary

Constructors

Constructor and Description
FilterSam(List<FilterSam.Filter> filters, File inputSamFile, File outputSamFile) Filter alignments in SAM format.
FilterSam(List<FilterSam.Filter> filters, Path inputSamPath, File outputSamFile) Filter alignments in SAM format.

Method Summary

Modifier and Type	Method and Description
Integer	call()
static void	main(String[] args) Main.

Methods inherited from class org.dishevelled.bio.tools.AbstractFilter

createScriptEngine

Methods inherited from class java.lang.Object

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

Constructor Detail

FilterSam

public FilterSam(List<FilterSam.Filter> filters,
                 File inputSamFile,
                 File outputSamFile)

Filter alignments in SAM format.

Parameters:

filters - list of filters, must not be null

inputSamFile - input SAM file, if any

outputSamFile - output SAM file, if any

FilterSam

public FilterSam(List<FilterSam.Filter> filters,
                 Path inputSamPath,
                 File outputSamFile)

Filter alignments in SAM format.

Parameters:

filters - list of filters, must not be null

inputSamPath - input SAM path, if any

outputSamFile - output SAM file, if any

Since:

2.1

Method Detail

call

public Integer call()
             throws Exception

Throws:

Exception

main

public static void main(String[] args)

Main.

Parameters:

args - command line args