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After dicussion with Ryan/Eric, the Structural_Indel variant type is now gone, and has been entirely replaced with the access pattern .isStructuralIndel(). This makes it a strict subtype of indel. I agree that this method is a bit more sensible. 

In addition, fix for GSA-310. If supplied -rf argument does not match a known read filter, the list of read filters will be printed, and users directed to the documentation for more information.
This commit is contained in:
Christopher Hartl 2012-08-30 17:57:31 -04:00
parent 82b2845b9f
commit 5a142fe265
4 changed files with 49 additions and 12 deletions
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26
public/java/src/org/broadinstitute/sting/gatk/filters/FilterManager.java
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@ -25,9 +25,13 @@
package org.broadinstitute.sting.gatk.filters;
import com.google.common.base.Function;
import com.google.common.collect.Collections2;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.classloader.PluginManager;
import java.util.Collection;
import java.util.List;
/**
* Manage filters and filter options. Any requests for basic filtering classes
@ -54,4 +58,26 @@ public class FilterManager extends PluginManager<ReadFilter> {
public Collection<Class<? extends ReadFilter>> getValues() {
return this.getPlugins();
}
/**
* Rather than use the default error message, print out a list of read filters as well.
* @param pluginCategory - string, the category of the plugin (e.g. read filter)
* @param pluginName - string, what we were trying to match (but failed to)
* @return - A wall of text with the default message, followed by a listing of available read filters
*/
@Override
protected String formatErrorMessage(String pluginCategory, String pluginName) {
List<Class<? extends ReadFilter>> availableFilters = this.getPluginsImplementing(ReadFilter.class);
Collection<String> availableFilterNames = Collections2.transform(availableFilters, new Function<Class<? extends ReadFilter>,String>(){
@Override
public String apply(final Class<? extends ReadFilter> input) {
return getName(input);
}
});
return String.format("Read filter %s not found. Available read filters:%n%s.%n%n%s",pluginName,
Utils.join(String.format(", "),availableFilterNames),
"Please consult the GATK Documentation (http://www.broadinstitute.org/gatk/gatkdocs/) for more information.");
}
}

1
public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
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@ -286,7 +286,6 @@ public class VariantDataManager {
case INDEL:
case MIXED:
case SYMBOLIC:
case STRUCTURAL_INDEL:
return checkVariationClass( evalVC, VariantRecalibratorArgumentCollection.Mode.INDEL );
default:
return false;

12
public/java/src/org/broadinstitute/sting/utils/classloader/PluginManager.java
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@ -277,7 +277,7 @@ public class PluginManager<PluginType> {
public PluginType createByName(String pluginName) {
Class<? extends PluginType> plugin = pluginsByName.get(pluginName);
if( plugin == null )
throw new UserException(String.format("Could not find %s with name: %s", pluginCategory,pluginName));
throw new UserException(formatErrorMessage(pluginCategory,pluginName));
try {
return plugin.newInstance();
} catch (Exception e) {
@ -330,4 +330,14 @@ public class PluginManager<PluginType> {
return pluginName;
}
/**
* Generate the error message for the plugin manager. The message is allowed to depend on the class.
* @param pluginCategory - string, the category of the plugin (e.g. read filter)
* @param pluginName - string, what we were trying to match (but failed to)
* @return error message text describing the error
*/
protected String formatErrorMessage(String pluginCategory, String pluginName ) {
return String.format("Could not find %s with name: %s", pluginCategory,pluginName);
}
}

22
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
View File

@ -457,7 +457,6 @@ public class VariantContext implements Feature { // to enable tribble integratio
SNP,
MNP, // a multi-nucleotide polymorphism
INDEL,
STRUCTURAL_INDEL,
SYMBOLIC,
MIXED,
}
@ -531,7 +530,17 @@ public class VariantContext implements Feature { // to enable tribble integratio
}
public boolean isStructuralIndel() {
return getType() == Type.STRUCTURAL_INDEL;
if ( getType() == Type.INDEL ) {
List<Integer> sizes = getIndelLengths();
if ( sizes != null ) {
for ( Integer length : sizes ) {
if ( length > MAX_ALLELE_SIZE_FOR_NON_SV ) {
return true;
}
}
}
}
return false;
}
/**
@ -716,7 +725,7 @@ public class VariantContext implements Feature { // to enable tribble integratio
* @return a list of indel lengths ( null if not of type indel or mixed )
*/
public List<Integer> getIndelLengths() {
if ( getType() != Type.INDEL && getType() != Type.MIXED && getType() != Type.STRUCTURAL_INDEL ) {
if ( getType() != Type.INDEL && getType() != Type.MIXED ) {
return null;
}
@ -1263,13 +1272,6 @@ public class VariantContext implements Feature { // to enable tribble integratio
// is reserved for cases of multiple alternate alleles of different types). Therefore, if we've reached this point
// in the code (so we're not a SNP, MNP, or symbolic allele), we absolutely must be an INDEL.
// Because a number of structural variation callers write the whole alternate allele into the VCF where possible,
// this can result in insertion/deletion alleles of structural variant size, e.g. 151+. As of July 2012, we now
// classify these as structural events, rather than indel events, as we think differently about the mechanism,
// representation, and handling of these events. Check for this case here:
if ( ref.length() > MAX_ALLELE_SIZE_FOR_NON_SV || allele.length() > MAX_ALLELE_SIZE_FOR_NON_SV )
return Type.STRUCTURAL_INDEL;
return Type.INDEL;
// old incorrect logic: