org.broadinstitute.hellbender.utils.recalibration

Class RecalUtils

java.lang.Object

org.broadinstitute.hellbender.utils.recalibration.RecalUtils

public final class RecalUtils
extends java.lang.Object

This helper class holds the data HashMap as well as submaps that represent the marginal distributions collapsed over all needed dimensions. It also has static methods that are used to perform the various solid recalibration modes that attempt to correct the reference bias. This class holds the parsing methods that are shared between BaseRecalibrator and PrintReads.

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	ALL_COVARIATES_REPORT_TABLE_TITLE
static java.lang.String	ARGUMENT_COLUMN_NAME
static java.lang.String	ARGUMENT_REPORT_TABLE_TITLE
static java.lang.String	ARGUMENT_VALUE_COLUMN_NAME
static java.lang.String	COVARIATE_NAME_COLUMN_NAME
static java.lang.String	COVARIATE_VALUE_COLUMN_NAME
static int	EMPIRICAL_Q_REPORTED_DECIMAL_PLACES
static int	EMPIRICAL_QUAL_DECIMAL_PLACES
static java.lang.String	EMPIRICAL_QUALITY_COLUMN_NAME
static java.lang.String	ESTIMATED_Q_REPORTED_COLUMN_NAME
static java.lang.String	EVENT_TYPE_COLUMN_NAME
static java.lang.String	NUMBER_ERRORS_COLUMN_NAME
static int	NUMBER_ERRORS_DECIMAL_PLACES
static java.lang.String	NUMBER_OBSERVATIONS_COLUMN_NAME
static java.lang.String	QUALITY_SCORE_COLUMN_NAME
static java.lang.String	QUALITY_SCORE_REPORT_TABLE_TITLE
static java.lang.String	QUANTIZED_COUNT_COLUMN_NAME
static java.lang.String	QUANTIZED_REPORT_TABLE_TITLE
static java.lang.String	QUANTIZED_VALUE_COLUMN_NAME
static java.lang.String	READGROUP_COLUMN_NAME
static java.lang.String	READGROUP_REPORT_TABLE_TITLE

Constructor Summary

Constructors

Constructor and Description
RecalUtils()

Method Summary

Modifier and Type	Method and Description
static void	combineTables(NestedIntegerArray<RecalDatum> table1, NestedIntegerArray<RecalDatum> table2) Combines the recalibration data for table1 and table2 into table1 Note that table1 is the destination, so it is modified
static ReadCovariates	computeCovariates(GATKRead read, htsjdk.samtools.SAMFileHeader header, StandardCovariateList covariates, boolean recordIndelValues, CovariateKeyCache keyCache) Computes all requested covariates for every offset in the given read by calling covariate.getValues(..).
static void	computeCovariates(GATKRead read, htsjdk.samtools.SAMFileHeader header, StandardCovariateList covariates, ReadCovariates resultsStorage, boolean recordIndelValues) Computes all requested covariates for every offset in the given read by calling covariate.getValues(..).
static GATKReport	createRecalibrationGATKReport(GATKReportTable argumentTable, GATKReportTable quantizationTable, java.util.List<GATKReportTable> recalTables) Creates a consolidated GATK report from the tables.
static GATKReport	createRecalibrationGATKReport(GATKReportTable argumentTable, QuantizationInfo quantizationInfo, RecalibrationTables recalibrationTables, StandardCovariateList covariates) Creates a consolidated GATK report, first generating report tables.
static RecalibrationReport	createRecalibrationReport(GATKReportTable argumentTable, GATKReportTable quantizationTable, java.util.List<GATKReportTable> recalTables) Creates a consolidated RecalibrationReport report from the tables.
protected static org.broadinstitute.hellbender.utils.recalibration.RecalUtils.CsvPrinter	csvPrinter(java.io.File out, StandardCovariateList covs) Returns a csv output printer.
static void	generateCsv(java.io.File out, java.util.Map<java.lang.String,RecalibrationReport> reports) Prints out a collection of reports into a file in Csv format in a way that can be used by R scripts (such as the plot generator script).
static void	generatePlots(java.io.File csvFile, java.io.File maybeGzipedExampleReportFile, java.io.File output) s Write recalibration plots into a file
static java.util.List<GATKReportTable>	generateReportTables(RecalibrationTables recalibrationTables, StandardCovariateList covariates)
static void	incrementDatumOrPutIfNecessary2keys(NestedIntegerArray<RecalDatum> table, byte qual, double isError, int key0, int key1) Increments the RecalDatum at the specified position in the specified table, or put a new item there if there isn't already one.
static void	incrementDatumOrPutIfNecessary3keys(NestedIntegerArray<RecalDatum> table, byte qual, double isError, int key0, int key1, int key2) Increments the RecalDatum at the specified position in the specified table, or put a new item there if there isn't already one.
static void	incrementDatumOrPutIfNecessary4keys(NestedIntegerArray<RecalDatum> table, byte qual, double isError, int key0, int key1, int key2, int key3) Increments the RecalDatum at the specified position in the specified table, or put a new item there if there isn't already one.
protected static Resource	loadBQSRScriptResource() Retrieve the BQSR.R script
static void	outputRecalibrationReport(java.io.PrintStream recalTableStream, RecalibrationArgumentCollection RAC, QuantizationInfo quantizationInfo, RecalibrationTables recalibrationTables, StandardCovariateList covariates) Outputs the GATK report to RAC.RECAL_TABLE.
static void	parsePlatformForRead(GATKRead read, htsjdk.samtools.SAMFileHeader header, RecalibrationArgumentCollection RAC) Section of code shared between the two recalibration walkers which uses the command line arguments to adjust attributes of the read such as quals or platform string

Methods inherited from class java.lang.Object

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

Field Detail

ARGUMENT_REPORT_TABLE_TITLE

public static final java.lang.String ARGUMENT_REPORT_TABLE_TITLE

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Constant Field Values

QUANTIZED_REPORT_TABLE_TITLE

public static final java.lang.String QUANTIZED_REPORT_TABLE_TITLE

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READGROUP_REPORT_TABLE_TITLE

public static final java.lang.String READGROUP_REPORT_TABLE_TITLE

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QUALITY_SCORE_REPORT_TABLE_TITLE

public static final java.lang.String QUALITY_SCORE_REPORT_TABLE_TITLE

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ALL_COVARIATES_REPORT_TABLE_TITLE

public static final java.lang.String ALL_COVARIATES_REPORT_TABLE_TITLE

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ARGUMENT_COLUMN_NAME

public static final java.lang.String ARGUMENT_COLUMN_NAME

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ARGUMENT_VALUE_COLUMN_NAME

public static final java.lang.String ARGUMENT_VALUE_COLUMN_NAME

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QUANTIZED_VALUE_COLUMN_NAME

public static final java.lang.String QUANTIZED_VALUE_COLUMN_NAME

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QUANTIZED_COUNT_COLUMN_NAME

public static final java.lang.String QUANTIZED_COUNT_COLUMN_NAME

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READGROUP_COLUMN_NAME

public static final java.lang.String READGROUP_COLUMN_NAME

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EVENT_TYPE_COLUMN_NAME

public static final java.lang.String EVENT_TYPE_COLUMN_NAME

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EMPIRICAL_QUALITY_COLUMN_NAME

public static final java.lang.String EMPIRICAL_QUALITY_COLUMN_NAME

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ESTIMATED_Q_REPORTED_COLUMN_NAME

public static final java.lang.String ESTIMATED_Q_REPORTED_COLUMN_NAME

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QUALITY_SCORE_COLUMN_NAME

public static final java.lang.String QUALITY_SCORE_COLUMN_NAME

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COVARIATE_VALUE_COLUMN_NAME

public static final java.lang.String COVARIATE_VALUE_COLUMN_NAME

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COVARIATE_NAME_COLUMN_NAME

public static final java.lang.String COVARIATE_NAME_COLUMN_NAME

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NUMBER_OBSERVATIONS_COLUMN_NAME

public static final java.lang.String NUMBER_OBSERVATIONS_COLUMN_NAME

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NUMBER_ERRORS_COLUMN_NAME

public static final java.lang.String NUMBER_ERRORS_COLUMN_NAME

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EMPIRICAL_QUAL_DECIMAL_PLACES

public static final int EMPIRICAL_QUAL_DECIMAL_PLACES

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EMPIRICAL_Q_REPORTED_DECIMAL_PLACES

public static final int EMPIRICAL_Q_REPORTED_DECIMAL_PLACES

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Constant Field Values

NUMBER_ERRORS_DECIMAL_PLACES

public static final int NUMBER_ERRORS_DECIMAL_PLACES

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Constant Field Values

Constructor Detail

RecalUtils

public RecalUtils()

Method Detail

csvPrinter

protected static org.broadinstitute.hellbender.utils.recalibration.RecalUtils.CsvPrinter csvPrinter(java.io.File out,
                                                                                                    StandardCovariateList covs)
                                                                                             throws java.io.FileNotFoundException

Returns a csv output printer.

Parameters:

out - the output file. It will be overridden

covs - list of covariates to print out.

Returns:

never null

Throws:

java.io.FileNotFoundException - if out could not be created anew.

generateCsv

public static void generateCsv(java.io.File out,
                               java.util.Map<java.lang.String,RecalibrationReport> reports)
                        throws java.io.FileNotFoundException

Prints out a collection of reports into a file in Csv format in a way that can be used by R scripts (such as the plot generator script).

The set of covariates is take as the minimum common set from all reports.

Parameters:

out - the output file. It will be overridden.

reports - map where keys are the unique 'mode' (ORIGINAL, RECALIBRATED, ...) of each report and the corresponding value the report itself.

Throws:

java.io.FileNotFoundException - if out could not be created anew.

generateReportTables

public static java.util.List<GATKReportTable> generateReportTables(RecalibrationTables recalibrationTables,
                                                                   StandardCovariateList covariates)

outputRecalibrationReport

public static void outputRecalibrationReport(java.io.PrintStream recalTableStream,
                                             RecalibrationArgumentCollection RAC,
                                             QuantizationInfo quantizationInfo,
                                             RecalibrationTables recalibrationTables,
                                             StandardCovariateList covariates)

Outputs the GATK report to RAC.RECAL_TABLE.

Parameters:

RAC - The list of shared command line arguments

quantizationInfo - Quantization info

recalibrationTables - Recalibration tables

covariates - The list of requested covariates

createRecalibrationReport

public static RecalibrationReport createRecalibrationReport(GATKReportTable argumentTable,
                                                            GATKReportTable quantizationTable,
                                                            java.util.List<GATKReportTable> recalTables)

Creates a consolidated RecalibrationReport report from the tables.

Parameters:

argumentTable - Argument table

quantizationTable - Quantization Table

recalTables - Other recal tables

Returns:

RecalibrationReport report

createRecalibrationGATKReport

public static GATKReport createRecalibrationGATKReport(GATKReportTable argumentTable,
                                                       QuantizationInfo quantizationInfo,
                                                       RecalibrationTables recalibrationTables,
                                                       StandardCovariateList covariates)

Creates a consolidated GATK report, first generating report tables. Report can then be written to a stream via GATKReport.print(PrintStream).

Parameters:

argumentTable - Argument table

quantizationInfo - Quantization info

recalibrationTables - Recalibration tables

covariates - The list of covariates

Returns:

GATK report

createRecalibrationGATKReport

public static GATKReport createRecalibrationGATKReport(GATKReportTable argumentTable,
                                                       GATKReportTable quantizationTable,
                                                       java.util.List<GATKReportTable> recalTables)

Creates a consolidated GATK report from the tables. Report can then be written to a stream via GATKReport.print(PrintStream).

Parameters:

argumentTable - Argument table

quantizationTable - Quantization Table

recalTables - Other recal tables

Returns:

GATK report

generatePlots

public static void generatePlots(java.io.File csvFile,
                                 java.io.File maybeGzipedExampleReportFile,
                                 java.io.File output)

s Write recalibration plots into a file

Parameters:

csvFile - location of the intermediary file

maybeGzipedExampleReportFile - where the report arguments are collected from.

output - result plot file name.

parsePlatformForRead

public static void parsePlatformForRead(GATKRead read,
                                        htsjdk.samtools.SAMFileHeader header,
                                        RecalibrationArgumentCollection RAC)

Section of code shared between the two recalibration walkers which uses the command line arguments to adjust attributes of the read such as quals or platform string

Parameters:

read - The read to adjust

RAC - The list of shared command line arguments

computeCovariates

public static ReadCovariates computeCovariates(GATKRead read,
                                               htsjdk.samtools.SAMFileHeader header,
                                               StandardCovariateList covariates,
                                               boolean recordIndelValues,
                                               CovariateKeyCache keyCache)

Computes all requested covariates for every offset in the given read by calling covariate.getValues(..). It populates an array of covariate values where result[i][j] is the covariate value for the ith position in the read and the jth covariate in reqeustedCovariates list.

Parameters:

read - The read for which to compute covariate values.

header - SAM header for the read

covariates - The list of requested covariates.

recordIndelValues - should we compute covariates for indel BQSR?

Returns:

a matrix with all the covariates calculated for every base in the read

computeCovariates

public static void computeCovariates(GATKRead read,
                                     htsjdk.samtools.SAMFileHeader header,
                                     StandardCovariateList covariates,
                                     ReadCovariates resultsStorage,
                                     boolean recordIndelValues)

Computes all requested covariates for every offset in the given read by calling covariate.getValues(..). It populates an array of covariate values where result[i][j] is the covariate value for the ith position in the read and the jth covariate in covariates list.

Parameters:

read - The read for which to compute covariate values.

header - SAM header for the read

covariates - The list of covariates.

resultsStorage - The object to store the covariate values

recordIndelValues - should we compute covariates for indel BQSR?

combineTables

public static void combineTables(NestedIntegerArray<RecalDatum> table1,
                                 NestedIntegerArray<RecalDatum> table2)

Combines the recalibration data for table1 and table2 into table1 Note that table1 is the destination, so it is modified

Parameters:

table1 - the destination table to merge table2 into

table2 - the source table to merge into table1

incrementDatumOrPutIfNecessary2keys

public static void incrementDatumOrPutIfNecessary2keys(NestedIntegerArray<RecalDatum> table,
                                                       byte qual,
                                                       double isError,
                                                       int key0,
                                                       int key1)

Increments the RecalDatum at the specified position in the specified table, or put a new item there if there isn't already one. Note: we intentionally do not use varargs here to avoid the performance cost of allocating an array on every call. It showed on the profiler.

Parameters:

table - the table that holds/will hold our item

qual - qual for this event

isError - error value for this event

key0, - key1 location in table of our item

incrementDatumOrPutIfNecessary3keys

public static void incrementDatumOrPutIfNecessary3keys(NestedIntegerArray<RecalDatum> table,
                                                       byte qual,
                                                       double isError,
                                                       int key0,
                                                       int key1,
                                                       int key2)

Increments the RecalDatum at the specified position in the specified table, or put a new item there if there isn't already one. Note: we intentionally do not use varargs here to avoid the performance cost of allocating an array on every call. It showed on the profiler.

Parameters:

table - the table that holds/will hold our item

qual - qual for this event

isError - error value for this event

key0, - key1, key2 location in table of our item

incrementDatumOrPutIfNecessary4keys

public static void incrementDatumOrPutIfNecessary4keys(NestedIntegerArray<RecalDatum> table,
                                                       byte qual,
                                                       double isError,
                                                       int key0,
                                                       int key1,
                                                       int key2,
                                                       int key3)

Increments the RecalDatum at the specified position in the specified table, or put a new item there if there isn't already one. Note: we intentionally do not use varargs here to avoid the performance cost of allocating an array on every call. It showed on the profiler.

Parameters:

table - the table that holds/will hold our item

qual - qual for this event

isError - error value for this event

key0, - key1, key2, key3 location in table of our item

loadBQSRScriptResource

protected static Resource loadBQSRScriptResource()

Retrieve the BQSR.R script

Returns:

Resource representing the R script