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Usability cleanup for BQSR 

-- I'm seeing a lot of people trying to use BinaryTagCovariate in the community.  They really shouldn't do this, so I moved it to private.
-- Throw an exception if its required bintag argument is missing
-- Check explicitly if user is requesting DinucCovariate and tell them that its been retired in favor of ContextCovariate
-- Show the type (Required, Experimental, Standard) of the covariates when running --list
This commit is contained in:
Mark DePristo 2012-08-25 14:53:00 -04:00
parent e5cfdb4811
commit dcc972a557
3 changed files with 31 additions and 72 deletions
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15
public/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java
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@ -25,12 +25,14 @@
package org.broadinstitute.sting.utils.classloader;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.StingException;
import org.reflections.util.ClasspathHelper;
import java.io.File;
import java.io.IOException;
import java.lang.annotation.Annotation;
import java.lang.reflect.*;
import java.net.URL;
import java.util.*;
@ -234,4 +236,17 @@ public class JVMUtils {
} else
throw new ReviewedStingException("BUG: could not find generic type on class " + t);
}
/**
* Returns a comma-separated list of the names of the interfaces implemented by this class
*
* @param covClass
* @return
*/
public static String classInterfaces(final Class covClass) {
final List<String> interfaces = new ArrayList<String>();
for ( final Class interfaceClass : covClass.getInterfaces() )
interfaces.add(interfaceClass.getSimpleName());
return Utils.join(", ", interfaces);
}
}

25
public/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java
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@ -29,6 +29,7 @@ import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.report.GATKReport;
import org.broadinstitute.sting.gatk.report.GATKReportTable;
import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection;
import org.broadinstitute.sting.utils.classloader.JVMUtils;
import org.broadinstitute.sting.utils.recalibration.covariates.*;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.R.RScriptExecutor;
@ -117,6 +118,12 @@ public class RecalUtils {
if (argumentCollection.COVARIATES != null) { // parse the -cov arguments that were provided, skipping over the ones already specified
for (String requestedCovariateString : argumentCollection.COVARIATES) {
// help the transition from BQSR v1 to BQSR v2
if ( requestedCovariateString.equals("DinucCovariate") )
throw new UserException.CommandLineException("DinucCovariate has been retired. Please use its successor covariate " +
"ContextCovariate instead, which includes the 2 bp (dinuc) substitution model of the retired DinucCovariate " +
"as well as an indel context to model the indel error rates");
boolean foundClass = false;
for (Class<? extends Covariate> covClass : covariateClasses) {
if (requestedCovariateString.equalsIgnoreCase(covClass.getSimpleName())) { // -cov argument matches the class name for an implementing class
@ -178,18 +185,18 @@ public class RecalUtils {
return dest;
}
public static void listAvailableCovariates(Logger logger) {
// Get a list of all available covariates
final List<Class<? extends Covariate>> covariateClasses = new PluginManager<Covariate>(Covariate.class).getPlugins();
// Print and exit if that's what was requested
/**
* Print a list of all available covariates to logger as info
*
* @param logger
*/
public static void listAvailableCovariates(final Logger logger) {
logger.info("Available covariates:");
for (Class<?> covClass : covariateClasses)
logger.info(covClass.getSimpleName());
logger.info("");
for (final Class<? extends Covariate> covClass : new PluginManager<Covariate>(Covariate.class).getPlugins()) {
logger.info(String.format("\t%30s\t%s", covClass.getSimpleName(), JVMUtils.classInterfaces(covClass)));
}
}
public enum SOLID_RECAL_MODE {
/**
* Treat reference inserted bases as reference matching bases. Very unsafe!

63
public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/BinaryTagCovariate.java
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@ -1,63 +0,0 @@
package org.broadinstitute.sting.utils.recalibration.covariates;
import org.broadinstitute.sting.utils.recalibration.ReadCovariates;
import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
/**
* Binary covariate allows BQSR to recalibrate based on a binary covariate in the BAM file. This covariate should assume values of 1 and 0.
*
* @author Mauricio Carneiro
* @since 7/6/12
*/
public class BinaryTagCovariate implements ExperimentalCovariate {
private String tag;
@Override
public void initialize(RecalibrationArgumentCollection RAC) {
tag = RAC.BINARY_TAG_NAME;
}
@Override
public void recordValues(GATKSAMRecord read, ReadCovariates values) {
final Object tagObject = read.getAttribute(tag);
byte[] binaryTag;
if (tagObject instanceof byte[])
binaryTag = (byte[]) tagObject;
else if (tagObject instanceof String) {
int readLength = ((String) tagObject).length();
binaryTag = new byte[readLength];
for (int i = 0; i<readLength; i++)
binaryTag[i] = Byte.decode(((String) tagObject).substring(i, i+1));
}
else
throw new UserException("Binary tag is not a byte array (fast) or a string (slow). Type not supported");
for (int i = 0; i < read.getReadLength(); i++) {
values.addCovariate((int) binaryTag[i], (int) binaryTag[i], (int) binaryTag[i], i);
}
}
@Override
public Object getValue(String str) {
return Integer.decode(str);
}
@Override
public String formatKey(int key) {
return String.format("%d", key);
}
@Override
public int keyFromValue(Object value) {
return Integer.decode((String) value);
}
@Override
public int maximumKeyValue() {
return 1;
}
}