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package org.broadinstitute.hellbender.utils.recalibration;
import org.broadinstitute.barclay.argparser.Argument;
import org.broadinstitute.barclay.argparser.Hidden;
import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
import org.broadinstitute.hellbender.utils.QualityUtils;
import org.broadinstitute.hellbender.utils.baq.BAQ;
import org.broadinstitute.hellbender.utils.report.GATKReportTable;
import java.io.File;
import java.io.Serializable;
import java.util.LinkedHashMap;
import java.util.Map;
/**
* A collection of the arguments that are used for BQSR. Used to be common to both CovariateCounterWalker and TableRecalibrationWalker.
* This set of arguments will also be passed to the constructor of every Covariate when it is instantiated.
*/
public final class RecalibrationArgumentCollection implements Serializable {
private static final long serialVersionUID = 1L;
// We always use the same covariates. The field is retained for compatibility with GATK3 reports.
public static final boolean DO_NOT_USE_STANDARD_COVARIATES = false;
//We don't support SOLID. The field is retained for compatibility with GATK3 reports.
public static final String SOLID_RECAL_MODE = "SET_Q_ZERO";
public static final String SOLID_NOCALL_STRATEGY = "THROW_EXCEPTION";
//It makes no sense to run BQSR without sites. so we remove this option.
public static final boolean RUN_WITHOUT_DBSNP = false;
/**
* The context covariate will use a context of this size to calculate its covariate value for base mismatches. Must be between 1 and 13 (inclusive). Note that higher values will increase runtime and required java heap size.
*/
@Argument(fullName = "mismatches-context-size", shortName = "mcs", doc = "Size of the k-mer context to be used for base mismatches", optional = true)
public int MISMATCHES_CONTEXT_SIZE = 2;
/**
* The context covariate will use a context of this size to calculate its covariate value for base insertions and deletions. Must be between 1 and 13 (inclusive). Note that higher values will increase runtime and required java heap size.
*/
@Argument(fullName = "indels-context-size", shortName = "ics", doc = "Size of the k-mer context to be used for base insertions and deletions", optional = true)
public int INDELS_CONTEXT_SIZE = 3;
/**
* The cycle covariate will generate an error if it encounters a cycle greater than this value.
* This argument is ignored if the Cycle covariate is not used.
*/
@Argument(fullName = "maximum-cycle-value", shortName = "max-cycle", doc = "The maximum cycle value permitted for the Cycle covariate", optional = true)
public int MAXIMUM_CYCLE_VALUE = 500;
/**
* A default base qualities to use as a prior (reported quality) in the mismatch covariate model. This value will replace all base qualities in the read for this default value. Negative value turns it off. [default is off]
*/
@Argument(fullName = "mismatches-default-quality", doc = "default quality for the base mismatches covariate", optional = true)
public byte MISMATCHES_DEFAULT_QUALITY = -1;
/**
* A default base qualities to use as a prior (reported quality) in the insertion covariate model. This parameter is used for all reads without insertion quality scores for each base. [default is on]
*/
@Argument(fullName = "insertions-default-quality", doc = "default quality for the base insertions covariate", optional = true)
public byte INSERTIONS_DEFAULT_QUALITY = 45;
/**
* A default base qualities to use as a prior (reported quality) in the mismatch covariate model. This value will replace all base qualities in the read for this default value. Negative value turns it off. [default is on]
*/
@Argument(fullName = "deletions-default-quality", doc = "default quality for the base deletions covariate", optional = true)
public byte DELETIONS_DEFAULT_QUALITY = 45;
/**
* Reads with low quality bases on either tail (beginning or end) will not be considered in the context. This parameter defines the quality below which (inclusive) a tail is considered low quality
*/
@Argument(fullName = "low-quality-tail", doc = "minimum quality for the bases in the tail of the reads to be considered", optional = true)
public byte LOW_QUAL_TAIL = 2;
/**
* BQSR generates a quantization table for quick quantization later by subsequent tools. BQSR does not quantize the base qualities, this is done by the engine with the -qq or -bqsr options.
* This parameter tells BQSR the number of levels of quantization to use to build the quantization table.
*/
@Argument(fullName = "quantizing-levels", optional = true, doc = "number of distinct quality scores in the quantized output")
public int QUANTIZING_LEVELS = 16;
/**
* The tag name for the binary tag covariate (if using it)
*/
@Argument(fullName = "binary-tag-name", optional = true, doc = "the binary tag covariate name if using it")
public String BINARY_TAG_NAME = null;
@Argument(fullName = "bqsr-baq-gap-open-penalty", doc="BQSR BAQ gap open penalty (Phred Scaled). Default value is 40. 30 is perhaps better for whole genome call sets", optional = true)
public double BAQGOP = BAQ.DEFAULT_GOP;
/**
* This flag tells GATK not to modify quality scores less than this value. Instead they will be written out unmodified in the recalibrated BAM file.
* In general it's unsafe to change qualities scores below < 6, since base callers use these values to indicate random or bad bases.
* For example, Illumina writes Q2 bases when the machine has really gone wrong. This would be fine in and of itself,
* but when you select a subset of these reads based on their ability to align to the reference and their dinucleotide effect,
* your Q2 bin can be elevated to Q8 or Q10, leading to issues downstream.
*/
@Argument(fullName = "preserve-qscores-less-than", doc = "Don't recalibrate bases with quality scores less than this threshold (with -" + StandardArgumentDefinitions.BQSR_TABLE_SHORT_NAME + ")", optional = true)
public int PRESERVE_QSCORES_LESS_THAN = QualityUtils.MIN_USABLE_Q_SCORE;
@Hidden
@Argument(fullName = "enable-baq", doc = "do BAQ correction")
public boolean enableBAQ = false;
@Hidden
@Argument(fullName = "compute-indel-bqsr-tables", shortName = "indels", doc = "compute indel BQSR tables")
public boolean computeIndelBQSRTables = false;
// --------------------------------------------------------------------------------------------------------------
//
// quality encoding checking arguments
//
// --------------------------------------------------------------------------------------------------------------
/**
* This flag tells GATK to use the original base qualities (that were in the data before BQSR/recalibration) which
* are stored in the OQ tag, if they are present, rather than use the post-recalibration quality scores. If no OQ
* tag is present for a read, the standard qual score will be used.
*/
@Argument(fullName="use-original-qualities", shortName = "OQ", doc = "Use the base quality scores from the OQ tag", optional = true)
public Boolean useOriginalBaseQualities = false;
/**
* If reads are missing some or all base quality scores, this value will be used for all base quality scores.
* By default this is set to -1 to disable default base quality assignment.
*/
//TODO: minValue = 0, maxValue = Byte.MAX_VALUE)
@Argument(fullName="default-base-qualities", doc = "Assign a default base quality", optional = true)
public byte defaultBaseQualities = -1;
/////////////////////////////
// Debugging-only Arguments
/////////////////////////////
@Hidden
@Argument(fullName = "default-platform", optional = true, doc = "If a read has no platform then default to the provided String. Valid options are illumina, 454, and solid.")
public String DEFAULT_PLATFORM = null;
@Hidden
@Argument(fullName = "force-platform", optional = true, doc = "If provided, the platform of EVERY read will be forced to be the provided String. Valid options are illumina, 454, and solid.")
public String FORCE_PLATFORM = null;
public File existingRecalibrationReport = null;
public GATKReportTable generateReportTable(final String covariateNames) {
GATKReportTable argumentsTable;
argumentsTable = new GATKReportTable("Arguments", "Recalibration argument collection values used in this run", 2, GATKReportTable.Sorting.SORT_BY_COLUMN);
argumentsTable.addColumn("Argument", "%s");
argumentsTable.addColumn(RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, "");
argumentsTable.addRowID("covariate", true);
argumentsTable.set("covariate", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, covariateNames);
argumentsTable.addRowID("no_standard_covs", true);
argumentsTable.set("no_standard_covs", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, DO_NOT_USE_STANDARD_COVARIATES);
argumentsTable.addRowID("run_without_dbsnp", true);
argumentsTable.set("run_without_dbsnp", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, RUN_WITHOUT_DBSNP);
argumentsTable.addRowID("solid_recal_mode", true);
argumentsTable.set("solid_recal_mode", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, SOLID_RECAL_MODE);
argumentsTable.addRowID("solid_nocall_strategy", true);
argumentsTable.set("solid_nocall_strategy", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, SOLID_NOCALL_STRATEGY);
argumentsTable.addRowID("mismatches_context_size", true);
argumentsTable.set("mismatches_context_size", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, MISMATCHES_CONTEXT_SIZE);
argumentsTable.addRowID("indels_context_size", true);
argumentsTable.set("indels_context_size", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, INDELS_CONTEXT_SIZE);
argumentsTable.addRowID("mismatches_default_quality", true);
argumentsTable.set("mismatches_default_quality", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, MISMATCHES_DEFAULT_QUALITY);
argumentsTable.addRowID("deletions_default_quality", true);
argumentsTable.set("deletions_default_quality", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, DELETIONS_DEFAULT_QUALITY);
argumentsTable.addRowID("insertions_default_quality", true);
argumentsTable.set("insertions_default_quality", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, INSERTIONS_DEFAULT_QUALITY);
argumentsTable.addRowID("maximum_cycle_value", true);
argumentsTable.set("maximum_cycle_value", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, MAXIMUM_CYCLE_VALUE);
argumentsTable.addRowID("low_quality_tail", true);
argumentsTable.set("low_quality_tail", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, LOW_QUAL_TAIL);
argumentsTable.addRowID("default_platform", true);
argumentsTable.set("default_platform", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, DEFAULT_PLATFORM);
argumentsTable.addRowID("force_platform", true);
argumentsTable.set("force_platform", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, FORCE_PLATFORM);
argumentsTable.addRowID("quantizing_levels", true);
argumentsTable.set("quantizing_levels", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, QUANTIZING_LEVELS);
argumentsTable.addRowID("recalibration_report", true);
argumentsTable.set("recalibration_report", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, existingRecalibrationReport == null ? "null" : existingRecalibrationReport.getAbsolutePath());
argumentsTable.addRowID("binary_tag_name", true);
argumentsTable.set("binary_tag_name", RecalUtils.ARGUMENT_VALUE_COLUMN_NAME, BINARY_TAG_NAME == null ? "null" : BINARY_TAG_NAME);
return argumentsTable;
}
/**
* Returns a map with the arguments that differ between this an
* another {@link RecalibrationArgumentCollection} instance.
*
* The key is the name of that argument in the report file. The value is a message
* that explains the difference to the end user.
*
* Thus, a empty map indicates that there is no differences between both argument collection that
* is relevant to report comparison.
*
* This method should not throw any exception.
*
* @param other the argument-collection to compare against.
* @param thisRole the name used to refer to this RAC report that makes sense to the end user.
* @param otherRole the name used to refer to the other RAC report that makes sense to the end user.
*
* @return never null, but a zero-size collection if there are no differences.
*/
public Map compareReportArguments(final RecalibrationArgumentCollection other,final String thisRole, final String otherRole) {
final Map result = new LinkedHashMap<>(15);
compareSimpleReportArgument(result,"no_standard_covs", DO_NOT_USE_STANDARD_COVARIATES, DO_NOT_USE_STANDARD_COVARIATES, thisRole, otherRole);
compareSimpleReportArgument(result,"run_without_dbsnp",RUN_WITHOUT_DBSNP, RUN_WITHOUT_DBSNP,thisRole,otherRole);
compareSimpleReportArgument(result,"solid_recal_mode", SOLID_RECAL_MODE, SOLID_RECAL_MODE,thisRole,otherRole);
compareSimpleReportArgument(result,"solid_nocall_strategy", SOLID_NOCALL_STRATEGY, SOLID_NOCALL_STRATEGY,thisRole,otherRole);
compareSimpleReportArgument(result,"mismatches_context_size", MISMATCHES_CONTEXT_SIZE,other.MISMATCHES_CONTEXT_SIZE,thisRole,otherRole);
compareSimpleReportArgument(result,"mismatches_default_quality", MISMATCHES_DEFAULT_QUALITY, other.MISMATCHES_DEFAULT_QUALITY,thisRole,otherRole);
compareSimpleReportArgument(result,"deletions_default_quality", DELETIONS_DEFAULT_QUALITY, other.DELETIONS_DEFAULT_QUALITY,thisRole,otherRole);
compareSimpleReportArgument(result,"insertions_default_quality", INSERTIONS_DEFAULT_QUALITY, other.INSERTIONS_DEFAULT_QUALITY,thisRole,otherRole);
compareSimpleReportArgument(result,"maximum_cycle_value", MAXIMUM_CYCLE_VALUE, other.MAXIMUM_CYCLE_VALUE,thisRole,otherRole);
compareSimpleReportArgument(result,"low_quality_tail", LOW_QUAL_TAIL, other.LOW_QUAL_TAIL,thisRole,otherRole);
compareSimpleReportArgument(result,"default_platform", DEFAULT_PLATFORM, other.DEFAULT_PLATFORM,thisRole,otherRole);
compareSimpleReportArgument(result,"force_platform", FORCE_PLATFORM, other.FORCE_PLATFORM,thisRole,otherRole);
compareSimpleReportArgument(result,"quantizing_levels", QUANTIZING_LEVELS, other.QUANTIZING_LEVELS,thisRole,otherRole);
compareSimpleReportArgument(result,"binary_tag_name", BINARY_TAG_NAME, other.BINARY_TAG_NAME,thisRole,otherRole);
return result;
}
/**
* Annotates a map with any difference encountered in a simple value report argument that differs between this an
* another {@link RecalibrationArgumentCollection} instance.
*
* The key of the new entry would be the name of that argument in the report file. The value is a message
* that explains the difference to the end user.
*
*
*
* This method should not return any exception.
*
* @param diffs where to annotate the differences.
* @param name the name of the report argument to compare.
* @param thisValue this argument collection value for that argument.
* @param otherValue the other collection value for that argument.
* @param thisRole the name used to refer to this RAC report that makes sense to the end user.
* @param otherRole the name used to refer to the other RAC report that makes sense to the end user.
*
* @type T the argument Object value type.
*
* @return true if a difference has been spotted, thus diff has been modified.
*/
private boolean compareSimpleReportArgument(final Map diffs,
final String name, final T thisValue, final T otherValue, final String thisRole, final String otherRole) {
if (thisValue == null && otherValue == null) {
return false;
} else if (thisValue != null && thisValue.equals(otherValue)) {
return false;
} else {
diffs.put(name,
String.format("differences between '%s' {%s} and '%s' {%s}.",
thisRole, thisValue == null ? "" : thisValue,
otherRole, otherValue == null ? "" : otherValue));
return true;
}
}
}
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