Package org.broadinstitute.hellbender.utils.smithwaterman

Class SmithWatermanJavaAligner

java.lang.Object

org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanJavaAligner

All Implemented Interfaces:

Closeable, AutoCloseable, SmithWatermanAligner

public final class SmithWatermanJavaAligner
extends Object
implements SmithWatermanAligner

Pairwise discrete smith-waterman alignment implemented in pure java ************************************************************************ **** IMPORTANT NOTE: **** **** This class assumes that all bytes come from UPPERCASED chars! **** ************************************************************************

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
protected static enum	SmithWatermanJavaAligner.State	The state of a trace step through the matrix

Nested classes/interfaces inherited from interface org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanAligner

SmithWatermanAligner.Implementation

Field Summary

Fields inherited from interface org.broadinstitute.hellbender.utils.smithwaterman.SmithWatermanAligner

logger

Method Summary

Modifier and Type	Method	Description
SmithWatermanAlignment	align(byte[] reference, byte[] alternate, org.broadinstitute.gatk.nativebindings.smithwaterman.SWParameters parameters, org.broadinstitute.gatk.nativebindings.smithwaterman.SWOverhangStrategy overhangStrategy)	Aligns the alternate sequence to the reference sequence
void	close()	Implementations may optionally implement close in order to release any resources that they are holding.
static SmithWatermanJavaAligner	getInstance()	return the stateless singleton instance of SmithWatermanJavaAligner

Methods inherited from class java.lang.Object

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

Method Details

getInstance

public static SmithWatermanJavaAligner getInstance()

return the stateless singleton instance of SmithWatermanJavaAligner

align

public SmithWatermanAlignment align(byte[] reference,
 byte[] alternate,
 org.broadinstitute.gatk.nativebindings.smithwaterman.SWParameters parameters,
 org.broadinstitute.gatk.nativebindings.smithwaterman.SWOverhangStrategy overhangStrategy)

Aligns the alternate sequence to the reference sequence

Specified by:

align in interface SmithWatermanAligner

Parameters:

reference - ref sequence

alternate - alt sequence

parameters - a set of weights to use when performing the alignment

overhangStrategy - how to treat overhangs during alignment

close

public void close()

Description copied from interface: SmithWatermanAligner

Implementations may optionally implement close in order to release any resources that they are holding. Calling SmithWatermanAligner.align(byte[], byte[], SWParameters, SWOverhangStrategy) after close must not return an incorrect or invalid alignment, but otherwise the behavior is undefined. If a subclass implements close it's recommended that subsequent calls to align after a call to close should throw IllegalStateException

Specified by:

close in interface AutoCloseable

Specified by:

close in interface Closeable

Specified by:

close in interface SmithWatermanAligner