org.broadinstitute.hellbender.tools.validation

Class CompareBaseQualities

java.lang.Object

org.broadinstitute.hellbender.cmdline.CommandLineProgram

org.broadinstitute.hellbender.cmdline.PicardCommandLineProgram

org.broadinstitute.hellbender.tools.validation.CompareBaseQualities

All Implemented Interfaces:

org.broadinstitute.barclay.argparser.CommandLinePluginProvider

@DocumentedFeature
public final class CompareBaseQualities
extends PicardCommandLineProgram

Compares the base qualities of two SAM/BAM/CRAM files. The reads in the two files must have exactly the same names and appear in the same order. The two files are each specified without a flag. The tool summarizes the results in a text file.

Usage example

 gatk CompareBaseQualities \
   input_1.bam \
   input_2.bam \
   -O diff.txt
 

An example result with identical base qualities between two inputs

 -----------CompareMatrix summary------------
 all 10000 quality scores are the same

 ---------CompareMatrix full matrix (non-zero entries) ----------
 QRead1 QRead2  diff    count
 40     40      0       10000
 -----------CompareMatrix-binned summary------------
 all 10000 quality scores are the same

 ---------CompareMatrix-binned full matrix (non-zero entries) ----------
 QRead1 QRead2  diff    count
 40     40      0       10000
 

Field Summary

Fields

Modifier and Type	Field and Description
protected java.lang.String	outputFilename
static java.lang.String	ROUND_DOWN_QUANTIZED_LONG_NAME
boolean	roundDown Round down quantized only works with the STATIC_QUANTIZED_QUALS_LONG_NAME option.
java.util.List<java.io.File>	samFiles
static java.lang.String	STATIC_QUANTIZED_QUALS_LONG_NAME
java.util.List<java.lang.Integer>	staticQuantizationQuals Return value is 0 if the two files have identical base qualities and non-zero otherwise.
static java.lang.String	THROW_ON_DIFF_LONG_NAME
protected boolean	throwOnDiff

Fields inherited from class org.broadinstitute.hellbender.cmdline.PicardCommandLineProgram

COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, MAX_RECORDS_IN_RAM, REFERENCE_SEQUENCE, VALIDATION_STRINGENCY

Fields inherited from class org.broadinstitute.hellbender.cmdline.CommandLineProgram

GATK_CONFIG_FILE, logger, NIO_MAX_REOPENS, QUIET, specialArgumentsCollection, TMP_DIR, useJdkDeflater, useJdkInflater, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
CompareBaseQualities()

Method Summary

Modifier and Type	Method and Description
protected java.lang.Object	doWork() Do the work after command line has been parsed.

Methods inherited from class org.broadinstitute.hellbender.cmdline.PicardCommandLineProgram

createSAMWriter, instanceMain

Methods inherited from class org.broadinstitute.hellbender.cmdline.CommandLineProgram

customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getPluginDescriptors, getSupportInformation, getToolkitName, getToolStatusWarning, getUsage, getVersion, instanceMainPostParseArgs, isBetaFeature, isExperimentalFeature, onShutdown, onStartup, parseArgs, printLibraryVersions, printSettings, printStartupMessage, runTool, setDefaultHeaders, warnOnToolStatus

Methods inherited from class java.lang.Object

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

Field Detail

samFiles

@PositionalArguments(minElements=2,
                     maxElements=2)
public java.util.List<java.io.File> samFiles

THROW_ON_DIFF_LONG_NAME

public static final java.lang.String THROW_ON_DIFF_LONG_NAME

See Also:

Constant Field Values

STATIC_QUANTIZED_QUALS_LONG_NAME

public static final java.lang.String STATIC_QUANTIZED_QUALS_LONG_NAME

See Also:

Constant Field Values

ROUND_DOWN_QUANTIZED_LONG_NAME

public static final java.lang.String ROUND_DOWN_QUANTIZED_LONG_NAME

See Also:

Constant Field Values

outputFilename

@Argument(doc="Summary output file.",
          shortName="O",
          fullName="output",
          optional=true)
protected java.lang.String outputFilename

throwOnDiff

@Argument(doc="Throw exception on difference.",
          fullName="throw-on-diff",
          optional=true)
protected boolean throwOnDiff

staticQuantizationQuals

@Advanced
 @Argument(doc="Use static quantized quality scores to a given number of levels (with --bqsr-recal-file)",
          fullName="static-quantized-quals",
          optional=true)
public java.util.List<java.lang.Integer> staticQuantizationQuals

Return value is 0 if the two files have identical base qualities and non-zero otherwise. Use static quantized quality scores to a given number of levels.

roundDown

@Advanced
 @Argument(doc="Round down quality scores to nearest quantized value.",
          fullName="round-down-quantized",
          optional=true)
public boolean roundDown

Round down quantized only works with the STATIC_QUANTIZED_QUALS_LONG_NAME option. If enabled, rounding is done in probability space to the nearest bin. Otherwise, the value is rounded to the nearest bin that is smaller than the current bin. Note: this option only works when STATIC_QUANTIZED_QUALS_LONG_NAME is set.

Constructor Detail

CompareBaseQualities

public CompareBaseQualities()

Method Detail

doWork

protected java.lang.Object doWork()

Description copied from class: CommandLineProgram

Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.

Specified by:

doWork in class CommandLineProgram

Returns:

the return value or null is there is none.