org.broadinstitute.hellbender.utils.baq

Class BAQ

java.lang.Object

org.broadinstitute.hellbender.utils.baq.BAQ

All Implemented Interfaces:

java.io.Serializable

public final class BAQ
extends java.lang.Object
implements java.io.Serializable

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	BAQ.BAQCalculationResult
static class	BAQ.CalculationMode
static class	BAQ.QualityMode these are features that only the walker can override

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	BAQ_TAG
double	cd
static int	DEFAULT_BANDWIDTH
static double	DEFAULT_GOP

Constructor Summary

Constructors

Constructor and Description
BAQ() Use defaults for everything
BAQ(double gapOpenPenalty) Use defaults for everything
BAQ(double d, double e, int b, byte minBaseQual) Create a new HmmGlocal object with specified parameters

Method Summary

Modifier and Type	Method and Description
static void	addBAQTag(GATKRead read, byte[] baq)
byte[]	baqRead(GATKRead read, ReferenceDataSource refDS, BAQ.CalculationMode calculationType, BAQ.QualityMode qmode) Modifies read in place so that the base quality scores are capped by the BAQ calculation.
BAQ.BAQCalculationResult	calcBAQFromHMM(byte[] ref, byte[] query, byte[] quals, int queryStart, int queryEnd)
BAQ.BAQCalculationResult	calcBAQFromHMM(GATKRead read, byte[] ref, int refOffset)
BAQ.BAQCalculationResult	calcBAQFromHMM(GATKRead read, ReferenceDataSource refDS)
static byte[]	calcBAQFromTag(GATKRead read, boolean overwriteOriginalQuals, boolean useRawQualsIfNoBAQTag) Returns a new qual array for read that includes the BAQ adjustment.
static byte	calcBAQFromTag(GATKRead read, int offset, boolean useRawQualsIfNoBAQTag) Returns the BAQ adjusted quality score for this read at this offset.
protected double	calcEpsilon(byte ref, byte read, byte qualB)
byte	capBaseByBAQ(byte oq, byte bq, int state, int expectedPos)
static java.lang.String	encodeBQTag(GATKRead read, byte[] baq)
boolean	excludeReadFromBAQ(GATKRead read) Returns true if we don't think this read is eligible for the BAQ calculation.
int	getBandWidth()
static byte[]	getBAQTag(GATKRead read) Get the BAQ attribute from the tag in read.
double	getGapExtensionProb()
double	getGapOpenProb()
byte	getMinBaseQual()
static SimpleInterval	getReferenceWindowForRead(GATKRead read, int bandWidth) Given a read, get an interval representing the span of reference bases required by BAQ for that read
static boolean	hasBAQTag(GATKRead read) Returns true if the read has a BAQ tag, or false otherwise
int	hmm_glocal(byte[] ref, byte[] query, int qstart, int l_query, byte[] _iqual, int[] state, byte[] q)
static int	stateAlignedPosition(int state) decode the bit encoded state array values
static boolean	stateIsIndel(int state) decode the bit encoded state array values

Methods inherited from class java.lang.Object

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

Field Detail

BAQ_TAG

public static final java.lang.String BAQ_TAG

See Also:

Constant Field Values

DEFAULT_GOP

public static final double DEFAULT_GOP

See Also:

Constant Field Values

DEFAULT_BANDWIDTH

public static final int DEFAULT_BANDWIDTH

See Also:

Constant Field Values

cd

public double cd

Constructor Detail

BAQ

public BAQ()

Use defaults for everything

BAQ

public BAQ(double gapOpenPenalty)

Use defaults for everything

BAQ

public BAQ(double d,
           double e,
           int b,
           byte minBaseQual)

Create a new HmmGlocal object with specified parameters

Parameters:

d - gap open prob (not phred scaled!).

e - gap extension prob.

b - band width

minBaseQual - All bases with Q < minBaseQual are up'd to this value

Method Detail

getMinBaseQual

public byte getMinBaseQual()

getGapOpenProb

public double getGapOpenProb()

getGapExtensionProb

public double getGapExtensionProb()

getBandWidth

public int getBandWidth()

calcEpsilon

protected double calcEpsilon(byte ref,
                             byte read,
                             byte qualB)

hmm_glocal

public int hmm_glocal(byte[] ref,
                      byte[] query,
                      int qstart,
                      int l_query,
                      byte[] _iqual,
                      int[] state,
                      byte[] q)

stateIsIndel

public static boolean stateIsIndel(int state)

decode the bit encoded state array values

stateAlignedPosition

public static int stateAlignedPosition(int state)

decode the bit encoded state array values

getBAQTag

public static byte[] getBAQTag(GATKRead read)

Get the BAQ attribute from the tag in read. Returns null if no BAQ tag is present.

Parameters:

read -

Returns:

encodeBQTag

public static java.lang.String encodeBQTag(GATKRead read,
                                           byte[] baq)

addBAQTag

public static void addBAQTag(GATKRead read,
                             byte[] baq)

hasBAQTag

public static boolean hasBAQTag(GATKRead read)

Returns true if the read has a BAQ tag, or false otherwise

calcBAQFromTag

public static byte[] calcBAQFromTag(GATKRead read,
                                    boolean overwriteOriginalQuals,
                                    boolean useRawQualsIfNoBAQTag)

Returns a new qual array for read that includes the BAQ adjustment. Does not support on-the-fly BAQ calculation

Parameters:

read - the GATKRead to operate on

overwriteOriginalQuals - If true, we replace the original qualities scores in the read with their BAQ'd version

useRawQualsIfNoBAQTag - If useRawQualsIfNoBAQTag is true, then if there's no BAQ annotation we just use the raw quality scores. Throws IllegalStateException is false and no BAQ tag is present

Returns:

calcBAQFromTag

public static byte calcBAQFromTag(GATKRead read,
                                  int offset,
                                  boolean useRawQualsIfNoBAQTag)

Returns the BAQ adjusted quality score for this read at this offset. Does not support on-the-fly BAQ calculation

Parameters:

read - the GATKRead to operate on

offset - the offset of operate on

useRawQualsIfNoBAQTag - If useRawQualsIfNoBAQTag is true, then if there's no BAQ annotation we just use the raw quality scores. Throws IllegalStateException is false and no BAQ tag is present

Returns:

getReferenceWindowForRead

public static SimpleInterval getReferenceWindowForRead(GATKRead read,
                                                       int bandWidth)

Given a read, get an interval representing the span of reference bases required by BAQ for that read

Parameters:

read - read that is going to be input to BAQ

bandWidth - band width being used by the BAQ algorithm

Returns:

an interval representing the span of reference bases required by BAQ for the given read

calcBAQFromHMM

public BAQ.BAQCalculationResult calcBAQFromHMM(GATKRead read,
                                               ReferenceDataSource refDS)

calcBAQFromHMM

public BAQ.BAQCalculationResult calcBAQFromHMM(byte[] ref,
                                               byte[] query,
                                               byte[] quals,
                                               int queryStart,
                                               int queryEnd)

calcBAQFromHMM

public BAQ.BAQCalculationResult calcBAQFromHMM(GATKRead read,
                                               byte[] ref,
                                               int refOffset)

capBaseByBAQ

public byte capBaseByBAQ(byte oq,
                         byte bq,
                         int state,
                         int expectedPos)

baqRead

public byte[] baqRead(GATKRead read,
                      ReferenceDataSource refDS,
                      BAQ.CalculationMode calculationType,
                      BAQ.QualityMode qmode)

Modifies read in place so that the base quality scores are capped by the BAQ calculation. Uses the BAQ tag if present already and alwaysRecalculate is false, otherwise fires up the HMM and does the BAQ on the fly using the refReader to obtain the reference bases as needed.

Returns:

BQ qualities for use, in case qmode is DONT_MODIFY

excludeReadFromBAQ

public boolean excludeReadFromBAQ(GATKRead read)

Returns true if we don't think this read is eligible for the BAQ calculation. Examples include non-PF reads, duplicates, or unmapped reads. Used by baqRead to determine if a read should fall through the calculation.

Parameters:

read -

Returns: