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Added function to gatkdocs to specify what VCF field an annotation goes in (INFO or FORMAT)

This commit is contained in:
Geraldine Van der Auwera 2013-07-25 13:58:54 -04:00
parent edbd17b8e0
commit 0ea3f8ca58
2 changed files with 35 additions and 4 deletions
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32
public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java
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@ -1,6 +1,6 @@
/*
* Copyright (c) 2012 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
@ -9,10 +9,10 @@
* 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
@ -37,6 +37,8 @@ import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.classloader.JVMUtils;
import org.broadinstitute.sting.utils.collections.Pair;
@ -295,6 +297,8 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
// Get annotation info (what type of annotation, standard etc.)
final HashSet<String> annotInfo = getAnnotInfo(myClass, new HashSet<String>());
root.put("annotinfo", StringUtils.join(annotInfo, ", "));
// Get annotation field (whether it goes in INFO or FORMAT)
root.put("annotfield", getAnnotField(myClass));
// Get walker type if applicable
root.put("walkertype", getWalkerType(myClass));
// Get partition type if applicable
@ -316,6 +320,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
// put empty items to avoid blowups
root.put("parallel", new HashSet<String>());
root.put("annotinfo", "");
root.put("annotfield", "");
root.put("walkertype", "");
root.put("partitiontype", "");
root.put("readfilters", new HashSet<HashMap<String, Object>>());
@ -359,6 +364,27 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
return getParallelism(mySuperClass, parallelOptions);
}
/**
* Utility function that looks up whether the annotation goes in INFO or FORMAT field.
*
* @param myClass the class to query for the interfaces
* @return a String specifying the annotation field
*/
private final String getAnnotField(Class myClass) {
//
// Look up superclasses recursively until we find either
// GenotypeAnnotation or InfoFieldAnnotation
final Class mySuperClass = myClass.getSuperclass();
if (mySuperClass == InfoFieldAnnotation.class) {
return "INFO (variant-level)";
} else if (mySuperClass == GenotypeAnnotation.class) {
return "FORMAT (sample genotype-level)";
} else if (mySuperClass.getSimpleName().equals("Object")) {
return "";
}
return getAnnotField(mySuperClass);
}
/**
* Utility function that determines the annotation type for an instance of class c.
*

7
settings/helpTemplates/generic.template.html
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@ -123,8 +123,13 @@
<small>${partitiontype}</small>
</h3>
</#if>
<#if annotfield != "" >
<h3>VCF Field
<small>${annotfield}</small>
</h3>
</#if>
<#if annotinfo != "" >
<h3>Annotation type
<h3>Type
<small>${annotinfo}</small>
</h3>
</#if>