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VariantsToTable now supports wildcard captures. -F PREFIX* now captures all fields that begin with PREFIX, output as a comma-separated list of unique values. Added integration test for VariantsToTable since I find it so useful. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4706 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-11-18 18:54:59 +00:00
parent 302cc13735
commit 721e8cb679
2 changed files with 65 additions and 1 deletions
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18
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
View File

@ -119,7 +119,6 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
for ( VariantContext vc : vcs) {
if ( (! ignoreMultiAllelic || vc.isBiallelic()) && ( showFiltered || vc.isNotFiltered() ) ) {
List<String> vals = extractFields(vc, fieldsToTake);
out.println(Utils.join("\t", vals));
}
}
@ -134,6 +133,10 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
}
}
private static final boolean isWildCard(String s) {
return s.endsWith("*");
}
public static List<String> extractFields(VariantContext vc, List<String> fields) {
List<String> vals = new ArrayList<String>();
@ -144,6 +147,19 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
val = getters.get(field).get(vc);
} else if ( vc.hasAttribute(field) ) {
val = vc.getAttributeAsString(field);
} else if ( isWildCard(field) ) {
Set<String> wildVals = new HashSet<String>();
for ( Map.Entry<String,Object> elt : vc.getAttributes().entrySet()) {
if ( elt.getKey().startsWith(field.substring(0, field.length() - 1)) ) {
wildVals.add(elt.getValue().toString());
}
}
if ( wildVals.size() > 0 ) {
List<String> toVal = new ArrayList<String>(wildVals);
Collections.sort(toVal);
val = Utils.join(",", toVal);
}
}
vals.add(val);

48
java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantToTableIntegrationTest.java 100644
View File

@ -0,0 +1,48 @@
/*
* Copyright (c) 2010, 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.
*/
package org.broadinstitute.sting.gatk.walkers.variantutils;
import org.broadinstitute.sting.WalkerTest;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.testng.annotations.Test;
import org.testng.annotations.DataProvider;
import java.util.*;
import java.io.File;
public class VariantToTableIntegrationTest extends WalkerTest {
@Test(enabled = true)
public void testComplexVariantsToTable() {
// functional class is a wild card operator
WalkerTestSpec spec = new WalkerTestSpec(
"-R " + hg18Reference +
" -B:eval,vcf " + validationDataLocation + "/soap_gatk_annotated.vcf" +
" -T VariantsToTable" +
" -F CHROM,POS,ID,REF,ALT,QUAL,FILTER,TRANSITION,DP,SB,set,RankSumP,refseq.functionalClass*" +
" -L chr1 -o %s",
Arrays.asList("b2a3712c1bfad8f1383ffada8b5017ba"));
executeTest("testComplexVariantsToTable", spec).getFirst();
}
}