A B C D E F G H I L M O R S T V

A

alignPairs() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

alignSeqs(List<byte[]>) - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

Just align some sequences.

alignSeqs(Iterable<T>, Function<T, byte[]>) - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

A more abstract version that takes an iterable of things that can be turned into a byte[] of base calls.

average - Variable in class org.broadinstitute.hellbender.utils.bwa.BwaMemPairEndStats

The average insert size.

B

BwaMemAligner - Class in org.broadinstitute.hellbender.utils.bwa

Given an open index, this class lets you do alignment of sequences.

BwaMemAligner(BwaMemIndex) - Constructor for class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

BwaMemAlignment - Class in org.broadinstitute.hellbender.utils.bwa

Info from the Aligner about an alignment to reference that it discovered for some sequence.

BwaMemAlignment(int, int, int, int, int, int, int, int, int, int, String, String, String, int, int, int) - Constructor for class org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment

BwaMemIndex - Class in org.broadinstitute.hellbender.utils.bwa

BwaMemIndex manages the mapping of a bwa index image file into (non-Java) memory.

BwaMemIndex(String) - Constructor for class org.broadinstitute.hellbender.utils.bwa.BwaMemIndex

Loads an index from an image file.

BwaMemIndex.Algorithm - Enum in org.broadinstitute.hellbender.utils.bwa

Indexing algorithms supported by Bwa.

BwaMemPairEndStats - Class in org.broadinstitute.hellbender.utils.bwa

Equivalent to Bwa's mem_pestat_t struct.

BwaMemPairEndStats(double, double) - Constructor for class org.broadinstitute.hellbender.utils.bwa.BwaMemPairEndStats

Composes a new instance given the estimated average and std.

BwaMemPairEndStats(double) - Constructor for class org.broadinstitute.hellbender.utils.bwa.BwaMemPairEndStats

Composes a new instance given the estimated average.

BwaMemPairEndStats(double, double, int, int) - Constructor for class org.broadinstitute.hellbender.utils.bwa.BwaMemPairEndStats

Composes a new instance giving arbitrary (albeit valid and consistent) values to all its numerical fields: BwaMemPairEndStats.average, BwaMemPairEndStats.std, BwaMemPairEndStats.low and BwaMemPairEndStats.high.

C

close() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

close() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemIndex

Close the index and release the (non-Java) memory that's been allocated

CouldNotCreateIndexException - Exception in org.broadinstitute.hellbender.utils.bwa

Created by valentin on 7/29/17.

CouldNotCreateIndexException(String, String, String) - Constructor for exception org.broadinstitute.hellbender.utils.bwa.CouldNotCreateIndexException

CouldNotCreateIndexImageException - Exception in org.broadinstitute.hellbender.utils.bwa

Created by valentin on 7/30/17.

CouldNotCreateIndexImageException(String, String) - Constructor for exception org.broadinstitute.hellbender.utils.bwa.CouldNotCreateIndexImageException

CouldNotCreateIndexImageException(String, String, Throwable) - Constructor for exception org.broadinstitute.hellbender.utils.bwa.CouldNotCreateIndexImageException

CouldNotReadImageException - Exception in org.broadinstitute.hellbender.utils.bwa

Created by valentin on 7/30/17.

CouldNotReadImageException(String, String) - Constructor for exception org.broadinstitute.hellbender.utils.bwa.CouldNotReadImageException

CouldNotReadImageException(String) - Constructor for exception org.broadinstitute.hellbender.utils.bwa.CouldNotReadImageException

CouldNotReadIndexException - Exception in org.broadinstitute.hellbender.utils.bwa

Created by valentin on 7/30/17.

CouldNotReadIndexException(String, String) - Constructor for exception org.broadinstitute.hellbender.utils.bwa.CouldNotReadIndexException

CouldNotReadIndexException(String) - Constructor for exception org.broadinstitute.hellbender.utils.bwa.CouldNotReadIndexException

CouldNotReadReferenceException - Exception in org.broadinstitute.hellbender.utils.bwa

Created by valentin on 7/30/17.

CouldNotReadReferenceException(String, String) - Constructor for exception org.broadinstitute.hellbender.utils.bwa.CouldNotReadReferenceException

CouldNotReadReferenceException(String) - Constructor for exception org.broadinstitute.hellbender.utils.bwa.CouldNotReadReferenceException

createIndexImageFromFastaFile(String) - Static method in class org.broadinstitute.hellbender.utils.bwa.BwaMemIndex

Create the index image file for a fasta file.

createIndexImageFromFastaFile(String, String) - Static method in class org.broadinstitute.hellbender.utils.bwa.BwaMemIndex

Creates the index image file for a reference fasta file.

createIndexImageFromFastaFile(String, String, BwaMemIndex.Algorithm) - Static method in class org.broadinstitute.hellbender.utils.bwa.BwaMemIndex

Creates the index image file for a reference fasta file.

createIndexImageFromIndexFiles(String, String) - Static method in class org.broadinstitute.hellbender.utils.bwa.BwaMemIndex

Create the index image file for a complete set of BWA index files

D

DEFAULT_LOW_AND_HIGH_SIGMA - Static variable in class org.broadinstitute.hellbender.utils.bwa.BwaMemPairEndStats

Default number of std.

DEFAULT_STD_TO_AVERAGE_RATIO - Static variable in class org.broadinstitute.hellbender.utils.bwa.BwaMemPairEndStats

Default std.

deRefIndex() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemIndex

done using the index -- if ref count has fallen to 0, a call to close can be expected to succeed

DO_NOT_INFER - Static variable in class org.broadinstitute.hellbender.utils.bwa.BwaMemPairEndStats

Constant to indicate that pair-end insert size inference failed or hat is should not be inferred depending on the context.

dontInferPairEndStats() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

Tells the aligner to avoid trying to infer inter-size stats and just go with bwamem defaults when that information is not-available.

E

equals(Object) - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemPairEndStats

equals(BwaMemPairEndStats) - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemPairEndStats

F

FAILED - Static variable in class org.broadinstitute.hellbender.utils.bwa.BwaMemPairEndStats

Constant to indicate that pair-end insert size inference failed or that it should not be inferred depending on the context.

failed - Variable in class org.broadinstitute.hellbender.utils.bwa.BwaMemPairEndStats

Depending on the context, indicates iff the insert-size inference failed or if we are requesting not to perform such a inference.

FASTA_FILE_EXTENSIONS - Static variable in class org.broadinstitute.hellbender.utils.bwa.BwaMemIndex

G

getAlignerScore() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment

getBandwidthOption() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

getBWAVersion() - Static method in class org.broadinstitute.hellbender.utils.bwa.BwaMemIndex

returns github GUID for the version of bwa that has been compiled

getChunkSizeOption() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

getCigar() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment

getClip3PenaltyOption() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

getClip5PenaltyOption() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

getDefaultIndexImageNameFromFastaFile(String) - Static method in class org.broadinstitute.hellbender.utils.bwa.BwaMemIndex

Gets the default index image name for the provided FASTA.

getDGapExtendPenaltyOption() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

getDGapOpenPenaltyOption() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

getDropRatioOption() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

getFile() - Method in exception org.broadinstitute.hellbender.utils.bwa.InvalidFileFormatException

getFlagOption() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

getIGapExtendPenaltyOption() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

getIGapOpenPenaltyOption() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

getImage() - Method in exception org.broadinstitute.hellbender.utils.bwa.CouldNotReadImageException

getImage() - Method in exception org.broadinstitute.hellbender.utils.bwa.CouldNotReadIndexException

getIndex() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

getLine() - Method in exception org.broadinstitute.hellbender.utils.bwa.InvalidFileFormatException

getMapQCoefFacOption() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

getMapQCoefLenOption() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

getMapQual() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment

getMaskLevelOption() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

getMaskLevelRedunOption() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

getMatchScoreOption() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

getMateRefId() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment

getMateRefStart() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment

getMaxChainExtendOption() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

getMaxChainGapOption() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

getMaxInsOption() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

getMaxMateSWOption() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

getMaxMemIntvOption() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

getMaxSeedOccurencesOption() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

getMaxXAHitsAltOption() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

getMaxXAHitsOption() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

getMDTag() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment

getMinChainWeightOption() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

getMinSeedLengthOption() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

getMismatchPenaltyOption() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

getNMismatches() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment

getNThreadsOption() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

getOutputScoreThresholdOption() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

getRefEnd() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment

getReference() - Method in exception org.broadinstitute.hellbender.utils.bwa.CouldNotReadReferenceException

getReferenceContigNames() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemIndex

retrieve list of contig names in the reference dictionary

getRefId() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment

getRefStart() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment

getSamFlag() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment

getScoringMatrixOption() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

getSeqEnd() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment

getSeqStart() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment

getSplitFactorOption() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

getSplitWidthOption() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

getSuboptimalScore() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment

getTemplateLen() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment

getUnpairedPenaltyOption() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

getXADropRatio() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

getXATag() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAlignment

getZDropOption() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

H

hashCode() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemPairEndStats

high - Variable in class org.broadinstitute.hellbender.utils.bwa.BwaMemPairEndStats

The longest insert size that is considered normal.

I

IMAGE_FILE_EXTENSION - Static variable in class org.broadinstitute.hellbender.utils.bwa.BwaMemIndex

INDEX_FILE_EXTENSIONS - Static variable in class org.broadinstitute.hellbender.utils.bwa.BwaMemIndex

inferPairEndStats() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

Indicate that we want bwa-mem to infer pair-end inter-size stat from the sequences given.

InvalidFileFormatException - Exception in org.broadinstitute.hellbender.utils.bwa

Created by valentin on 7/28/17.

InvalidFileFormatException(String, OptionalLong, String, Throwable) - Constructor for exception org.broadinstitute.hellbender.utils.bwa.InvalidFileFormatException

InvalidFileFormatException(String, String, Throwable) - Constructor for exception org.broadinstitute.hellbender.utils.bwa.InvalidFileFormatException

InvalidFileFormatException(String, String) - Constructor for exception org.broadinstitute.hellbender.utils.bwa.InvalidFileFormatException

InvalidInputException - Exception in org.broadinstitute.hellbender.utils.bwa

Created by valentin on 7/28/17.

InvalidInputException() - Constructor for exception org.broadinstitute.hellbender.utils.bwa.InvalidInputException

InvalidInputException(String) - Constructor for exception org.broadinstitute.hellbender.utils.bwa.InvalidInputException

InvalidInputException(String, Throwable) - Constructor for exception org.broadinstitute.hellbender.utils.bwa.InvalidInputException

InvalidInputException(Throwable) - Constructor for exception org.broadinstitute.hellbender.utils.bwa.InvalidInputException

InvalidInputException(String, Throwable, boolean, boolean) - Constructor for exception org.broadinstitute.hellbender.utils.bwa.InvalidInputException

isOpen() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

isOpen() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemIndex

true if index has not been closed

L

low - Variable in class org.broadinstitute.hellbender.utils.bwa.BwaMemPairEndStats

The shortest insert size that is considered normal.

M

MEM_F_ALL - Static variable in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

MEM_F_NO_MULTI - Static variable in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

MEM_F_NO_RESCUE - Static variable in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

MEM_F_NOPAIRING - Static variable in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

MEM_F_PE - Static variable in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

MEM_F_PRIMARY5 - Static variable in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

MEM_F_REF_HDR - Static variable in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

MEM_F_SMARTPE - Static variable in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

MEM_F_SOFTCLIP - Static variable in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

O

org.broadinstitute.hellbender.utils.bwa - package org.broadinstitute.hellbender.utils.bwa

R

refIndex() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemIndex

there's someone using the index -- don't allow it to be closed

S

setBandwidthOption(int) - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

setChunkSizeOption(int) - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

setClip3PenaltyOption(int) - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

setClip5PenaltyOption(int) - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

setDGapExtendPenaltyOption(int) - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

setDGapOpenPenaltyOption(int) - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

setDropRatioOption(float) - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

setFlagOption(int) - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

setIGapExtendPenaltyOption(int) - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

setIGapOpenPenaltyOption(int) - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

setIntraCtgOptions() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

setMapQCoefFacOption(int) - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

setMapQCoefLenOption(float) - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

setMaskLevelRedunOption(float) - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

setMatchScoreOption(int) - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

setMaxChainExtendOption(int) - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

setMaxChainGapOption(int) - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

setMaxInsOption(int) - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

setMaxLevelOption(float) - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

setMaxMateSWOption(int) - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

setMaxMemIntvOption(long) - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

setMaxSeedOccurencesOption(int) - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

setMaxXAHitsAltOption(int) - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

setMaxXAHitsOption(int) - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

setMinChainWeightOption(int) - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

setMinSeedLengthOption(int) - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

setMismatchPenaltyOption(int) - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

setNThreadsOption(int) - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

setOutputScoreThresholdOption(int) - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

setProperPairEndStats(BwaMemPairEndStats) - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

Indicate the pair-end inter size stats for "properly" oriented read-pairs.

setScoringMatrixOption(byte[]) - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

setSplitFactorOption(float) - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

setSplitWidthOption(int) - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

setUnpairedPenaltyOption(int) - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

setXADropRatio(float) - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

setZDropOption(int) - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemAligner

std - Variable in class org.broadinstitute.hellbender.utils.bwa.BwaMemPairEndStats

The insert size std.

T

toBwaName() - Method in enum org.broadinstitute.hellbender.utils.bwa.BwaMemIndex.Algorithm

The string name use by the Bwa command line to denote that algorithm.

toString() - Method in class org.broadinstitute.hellbender.utils.bwa.BwaMemPairEndStats

V

valueOf(String) - Static method in enum org.broadinstitute.hellbender.utils.bwa.BwaMemIndex.Algorithm

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.broadinstitute.hellbender.utils.bwa.BwaMemIndex.Algorithm

Returns an array containing the constants of this enum type, in the order they are declared.

A B C D E F G H I L M O R S T V