diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java
index a0e3f862b..4b5d9979f 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java
@@ -51,9 +51,14 @@
package org.broadinstitute.gatk.tools.walkers.variantutils;
+import org.apache.commons.io.FileUtils;
+import org.apache.log4j.Level;
import org.broadinstitute.gatk.engine.walkers.WalkerTest;
+import org.testng.Assert;
import org.testng.annotations.Test;
+import java.io.File;
+import java.io.IOException;
import java.util.Arrays;
/**
@@ -70,6 +75,53 @@ public class LeftAlignAndTrimVariantsIntegrationTest extends WalkerTest {
executeTest("test left alignment", spec);
}
+ @Test
+ public void testLeftAlignmentLongAllelesError() throws IOException {
+
+ // Need to see log INFO messages
+ Level level = logger.getLevel();
+ logger.setLevel(Level.INFO);
+
+ File logFile = createTempFile("testLargeReferenceAlleleError.log", ".tmp");
+ String logFileName = logFile.getAbsolutePath();
+
+ WalkerTestSpec spec = new WalkerTestSpec(
+ "-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "longAlleles.vcf --no_cmdline_in_header -log " + logFileName,
+ 1,
+ Arrays.asList("136f88a5bd07a022a3404089359cb8ee"));
+ executeTest("test left alignment with long alleles with an error", spec);
+
+ // Make sure the "reference allele too long" message is in the log
+ Assert.assertTrue(FileUtils.readFileToString(logFile).contains(ValidateVariants.REFERENCE_ALLELE_TOO_LONG_MSG));
+
+ // Set the log level back
+ logger.setLevel(level);
+ }
+
+ @Test
+ public void testLeftAlignmentLongAllelesFix() throws IOException {
+
+ // Need to see log INFO messages
+ Level level = logger.getLevel();
+ logger.setLevel(Level.INFO);
+
+ File logFile = createTempFile("testLargeReferenceAlleleError.log", ".tmp");
+ String logFileName = logFile.getAbsolutePath();
+
+ WalkerTestSpec spec = new WalkerTestSpec(
+ "-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir +
+ "longAlleles.vcf --no_cmdline_in_header --reference_window_stop 208 -log " + logFileName,
+ 1,
+ Arrays.asList("c4ca5520ee499da171053059e3717b2f"));
+ executeTest("test left alignment with long alleles fix", spec);
+
+ // Make sure the "reference allele too long" message is in the log
+ Assert.assertFalse(FileUtils.readFileToString(logFile).contains(ValidateVariants.REFERENCE_ALLELE_TOO_LONG_MSG));
+
+ // Set the log level back
+ logger.setLevel(level);
+ }
+
@Test
public void testLeftAlignmentDontTrim() {
WalkerTestSpec spec = new WalkerTestSpec(
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariants.java
index d62a944c9..0ba7e1013 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariants.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariants.java
@@ -94,17 +94,27 @@ import java.util.*;
* -T LeftAlignAndTrimVariants \
* -R reference.fasta \
* --variant input.vcf \
- * -o output.vcf
+ * -o output.vcf \
* --dontTrimAlleles
*
*
+ * Left align and trim alleles, process alleles <= 208 bases
+ *
+ * java -jar GenomeAnalysisTK.jar \
+ * -T LeftAlignAndTrimVariants \
+ * -R reference.fasta \
+ * --variant input.vcf \
+ * -o output.vcf \
+ * --reference_window_stop 208
+ *
+ *
* Split multiallics into biallelics, left align and trim alleles
*
* java -jar GenomeAnalysisTK.jar \
* -T LeftAlignAndTrimVariants \
* -R reference.fasta \
* --variant input.vcf \
- * -o output.vcf
+ * -o output.vcf \
* --splitMultiallelics
*
*
@@ -114,8 +124,8 @@ import java.util.*;
* -T LeftAlignAndTrimVariants \
* -R reference.fasta \
* --variant input.vcf \
- * -o output.vcf
- * --splitMultiallelics
+ * -o output.vcf \
+ * --splitMultiallelics \
* --dontTrimAlleles
*
*
@@ -124,6 +134,9 @@ import java.util.*;
@Reference(window=@Window(start=-200,stop=200)) // WARNING: if this changes,MAX_INDEL_LENGTH needs to change as well!
public class LeftAlignAndTrimVariants extends RodWalker {
+ // Log message for a reference allele that is too long
+ protected static final String REFERENCE_ALLELE_TOO_LONG_MSG = "Reference allele is too long";
+
@ArgumentCollection
protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
@@ -147,6 +160,10 @@ public class LeftAlignAndTrimVariants extends RodWalker {
private VariantContextWriter writer;
private static final int MAX_INDEL_LENGTH = 200; // needs to match reference window size!
+
+ // Stop of the expanded window for which the reference context should be provided, relative to the locus.
+ private int referenceWindowStop;
+
public void initialize() {
String trackName = variantCollection.variants.getName();
Set samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(trackName));
@@ -155,7 +172,9 @@ public class LeftAlignAndTrimVariants extends RodWalker {
Set headerLines = vcfHeaders.get(trackName).getMetaDataInSortedOrder();
baseWriter.writeHeader(new VCFHeader(headerLines, samples));
- writer = VariantContextWriterFactory.sortOnTheFly(baseWriter, 200);
+ writer = VariantContextWriterFactory.sortOnTheFly(baseWriter, MAX_INDEL_LENGTH);
+
+ referenceWindowStop = getToolkit().getArguments().reference_window_stop;
}
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
@@ -203,6 +222,15 @@ public class LeftAlignAndTrimVariants extends RodWalker {
@Requires("vc != null")
protected int trimAlignWrite(final VariantContext vc, final ReferenceContext ref, final int numBiallelics ){
+ final int refLength = vc.getReference().length();
+
+ // ignore if the reference length is greater than the reference window stop before and after expansion
+ if ( refLength > MAX_INDEL_LENGTH && refLength > referenceWindowStop ) {
+ logger.info(String.format("%s (%d) at position %s:%d; skipping that record. Set --referenceWindowStop >= %d",
+ REFERENCE_ALLELE_TOO_LONG_MSG, refLength, vc.getChr(), vc.getStart(), refLength));
+ return 0;
+ }
+
// optionally don't trim VC
final VariantContext v = dontTrimAlleles ? vc : GATKVariantContextUtils.trimAlleles(vc, true, true);
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariants.java
index 1bfbf753f..a5b710acc 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariants.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariants.java
@@ -91,7 +91,7 @@ import java.util.*;
* --dbsnp dbsnp.vcf
*
*
- * To perform VCF format tests and all strict validations with the VCFs containing alleles > 208 bases
+ * To perform VCF format tests and all strict validations with the VCFs containing alleles <= 208 bases
*
* java -jar GenomeAnalysisTK.jar \
* -T ValidateVariants \