zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

1) Revert previous change - indel recalibration is turned on by default and users of the Lite version will need to turn it off to avoid a User Error. 2) Implemented the engine.isGATKLite() method.

This commit is contained in:
Eric Banks 2012-07-17 12:23:40 -04:00
parent 40618ac471
commit 62c5228048
6 changed files with 67 additions and 21 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

34
protected/java/src/org/broadinstitute/sting/utils/DummyProtectedClass.java 100644
View File

@ -0,0 +1,34 @@
package org.broadinstitute.sting.utils;
/*
* Copyright (c) 2009 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
import org.broadinstitute.sting.utils.classloader.ProtectedPackageSource;
public class DummyProtectedClass implements ProtectedPackageSource {
// THIS CLASS IS USED JUST SO THAT WE CAN TEST WHETHER WE ARE USING THE LITE OR FULL VERSION OF THE GATK
}

8
protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java
View File

@ -104,10 +104,10 @@ public class BQSRIntegrationTest extends WalkerTest {
@DataProvider(name = "PRTest")
public Object[][] createPRTestData() {
return new Object[][]{
{new PRTest("", "66aa65223f192ee39c1773aa187fd493")},
{new PRTest(" -qq -1 -IQ", "b7053d3d67aba6d8892f0a60f0ded338")},
{new PRTest(" -qq 6 -IQ", "bfbf0855185b2b70aa35237fb71e4487")},
{new PRTest(" -IQ", "d2d6ed8667cdba7e56f5db97d6262676")}
{new PRTest("", "d2d6ed8667cdba7e56f5db97d6262676")},
{new PRTest(" -qq -1", "b7053d3d67aba6d8892f0a60f0ded338")},
{new PRTest(" -qq 6", "bfbf0855185b2b70aa35237fb71e4487")},
{new PRTest(" -DIQ", "66aa65223f192ee39c1773aa187fd493")}
};
}

22
public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
View File

@ -51,6 +51,7 @@ import org.broadinstitute.sting.gatk.samples.SampleDBBuilder;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
import org.broadinstitute.sting.utils.collections.Pair;
@ -197,17 +198,28 @@ public class GenomeAnalysisEngine {
private BaseRecalibration baseRecalibration = null;
public BaseRecalibration getBaseRecalibration() { return baseRecalibration; }
public boolean hasBaseRecalibration() { return baseRecalibration != null; }
public void setBaseRecalibration(final File recalFile, final int quantizationLevels, final boolean useIndelQuals, final int preserveQLessThan) {
baseRecalibration = new BaseRecalibration(recalFile, quantizationLevels, useIndelQuals, preserveQLessThan, isGATKLite());
public void setBaseRecalibration(final File recalFile, final int quantizationLevels, final boolean disableIndelQuals, final int preserveQLessThan) {
baseRecalibration = new BaseRecalibration(recalFile, quantizationLevels, disableIndelQuals, preserveQLessThan, isGATKLite());
}
/**
* Utility method to determine whether this is the lite version of the GATK
*/
public boolean isGATKLite() {
// TODO -- this is just a place holder for now
return false;
if ( isLiteVersion == null ) {
final List<Class<? extends Object>> classes = new PluginManager<Object>(Object.class).getPlugins();
isLiteVersion = true;
for ( Class c : classes ) {
if ( c.getSimpleName().equals(DummyProtectedClassName)) {
isLiteVersion = false;
break;
}
}
}
return isLiteVersion;
}
private static final String DummyProtectedClassName = "DummyProtectedClass";
private static Boolean isLiteVersion = null;
/**
* Actually run the GATK with the specified walker.
@ -239,7 +251,7 @@ public class GenomeAnalysisEngine {
// if the use specified an input BQSR recalibration table then enable on the fly recalibration
if (args.BQSR_RECAL_FILE != null)
setBaseRecalibration(args.BQSR_RECAL_FILE, args.quantizationLevels, args.enableIndelQuals, args.PRESERVE_QSCORES_LESS_THAN);
setBaseRecalibration(args.BQSR_RECAL_FILE, args.quantizationLevels, args.disableIndelQuals, args.PRESERVE_QSCORES_LESS_THAN);
// Determine how the threads should be divided between CPU vs. IO.
determineThreadAllocation();

6
public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
View File

@ -215,10 +215,10 @@ public class GATKArgumentCollection {
public int quantizationLevels = 0;
/**
* Turns on printing of the base insertion and base deletion tags when using the -BQSR argument. By default, only the base substitution qualities will be produced.
* Turns off printing of the base insertion and base deletion tags when using the -BQSR argument and only the base substitution qualities will be produced.
*/
@Argument(fullName="enable_indel_quals", shortName = "IQ", doc = "If true, enables printing of base insertion and base deletion tags (with -BQSR)", required=false)
public boolean enableIndelQuals = false;
@Argument(fullName="disable_indel_quals", shortName = "DIQ", doc = "If true, disables printing of base insertion and base deletion tags (with -BQSR)", required=false)
public boolean disableIndelQuals = false;
/**
* Do not modify quality scores less than this value but rather just write them out unmodified in the recalibrated BAM file.

4
public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
View File

@ -79,8 +79,8 @@ public class UserException extends ReviewedStingException {
}
public static class NotSupportedInGATKLite extends UserException {
public NotSupportedInGATKLite(String argument) {
super(String.format("Unfortunately, the argument %s is not supported in the Lite version of the GATK", argument));
public NotSupportedInGATKLite(String message) {
super(String.format("GATK Lite does support all of the features of the full version: %s", message));
}
}

14
public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
View File

@ -50,7 +50,7 @@ public class BaseRecalibration {
private final RecalibrationTables recalibrationTables;
private final Covariate[] requestedCovariates; // list of all covariates to be used in this calculation
private final boolean emitIndelQuals;
private final boolean disableIndelQuals;
private final int preserveQLessThan;
private static final NestedHashMap[] qualityScoreByFullCovariateKey = new NestedHashMap[EventType.values().length]; // Caches the result of performSequentialQualityCalculation(..) for all sets of covariate values.
@ -64,14 +64,14 @@ public class BaseRecalibration {
*
* @param RECAL_FILE a GATK Report file containing the recalibration information
* @param quantizationLevels number of bins to quantize the quality scores
* @param emitIndelQuals if true, emit base indel qualities
* @param disableIndelQuals if true, do not emit base indel qualities
* @param preserveQLessThan preserve quality scores less than this value
* @param isGATKLite is this being called from the full or Lite version of the GATK
*/
public BaseRecalibration(final File RECAL_FILE, final int quantizationLevels, final boolean emitIndelQuals, final int preserveQLessThan, final boolean isGATKLite) {
public BaseRecalibration(final File RECAL_FILE, final int quantizationLevels, final boolean disableIndelQuals, final int preserveQLessThan, final boolean isGATKLite) {
// check for unsupported access
if (isGATKLite && emitIndelQuals)
throw new UserException.NotSupportedInGATKLite("enable_indel_quals");
if (isGATKLite && !disableIndelQuals)
throw new UserException.NotSupportedInGATKLite("base insertion/deletion recalibration is not supported, please use the --disable_indel_quals argument");
RecalibrationReport recalibrationReport = new RecalibrationReport(RECAL_FILE);
@ -84,7 +84,7 @@ public class BaseRecalibration {
quantizationInfo.quantizeQualityScores(quantizationLevels);
readCovariates = new ReadCovariates(MAXIMUM_RECALIBRATED_READ_LENGTH, requestedCovariates.length);
this.emitIndelQuals = emitIndelQuals;
this.disableIndelQuals = disableIndelQuals;
this.preserveQLessThan = preserveQLessThan;
}
@ -98,7 +98,7 @@ public class BaseRecalibration {
public void recalibrateRead(final GATKSAMRecord read) {
RecalDataManager.computeCovariates(read, requestedCovariates, readCovariates); // compute all covariates for the read
for (final EventType errorModel : EventType.values()) { // recalibrate all three quality strings
if (!emitIndelQuals && errorModel != EventType.BASE_SUBSTITUTION) {
if (disableIndelQuals && errorModel != EventType.BASE_SUBSTITUTION) {
read.setBaseQualities(null, errorModel);
continue;
}