org.broadinstitute.hellbender.utils.smithwaterman

Interface SmithWatermanAligner

All Superinterfaces:

java.lang.AutoCloseable, java.io.Closeable

All Known Implementing Classes:

SmithWatermanIntelAligner, SmithWatermanJavaAligner, SWNativeAlignerWrapper

public interface SmithWatermanAligner
extends java.io.Closeable

Interface and factory for Smith-Waterman aligners

Nested Class Summary

Nested Classes

Modifier and Type	Interface and Description
static class	SmithWatermanAligner.Implementation

Field Summary

Fields

Modifier and Type	Field and Description
static org.apache.logging.log4j.Logger	logger
static org.broadinstitute.gatk.nativebindings.smithwaterman.SWParameters	ORIGINAL_DEFAULT
static org.broadinstitute.gatk.nativebindings.smithwaterman.SWParameters	STANDARD_NGS

Method Summary

Modifier and Type	Method and Description
SmithWatermanAlignment	align(byte[] ref, byte[] alt, org.broadinstitute.gatk.nativebindings.smithwaterman.SWParameters parameters, org.broadinstitute.gatk.nativebindings.smithwaterman.SWOverhangStrategy overhangStrategy) perform a Smith-Waterman alignment of alt against ref
default void	close() Implementations may optionally implement close in order to release any resources that they are holding.
static SmithWatermanAligner	getAligner(SmithWatermanAligner.Implementation type) Factory method to get an instance of an aligner corresponding to the given implementation

Field Detail

logger

static final org.apache.logging.log4j.Logger logger

ORIGINAL_DEFAULT

static final org.broadinstitute.gatk.nativebindings.smithwaterman.SWParameters ORIGINAL_DEFAULT

STANDARD_NGS

static final org.broadinstitute.gatk.nativebindings.smithwaterman.SWParameters STANDARD_NGS

Method Detail

align

SmithWatermanAlignment align(byte[] ref,
                             byte[] alt,
                             org.broadinstitute.gatk.nativebindings.smithwaterman.SWParameters parameters,
                             org.broadinstitute.gatk.nativebindings.smithwaterman.SWOverhangStrategy overhangStrategy)

perform a Smith-Waterman alignment of alt against ref

Parameters:

ref - bases to align to, values must be the byte equivalent of uppercase chars

alt - bases to align against ref, values must be the byte equivalent of uppercase chars

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

overhangStrategy - how to treat overhangs during alignment

close

default void close()

Implementations may optionally implement close in order to release any resources that they are holding. Calling 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 java.lang.AutoCloseable

Specified by:

close in interface java.io.Closeable

getAligner

static SmithWatermanAligner getAligner(SmithWatermanAligner.Implementation type)

Factory method to get an instance of an aligner corresponding to the given implementation