From 6b8bed34d01856b4ae4fb45154b1f9fd3c9dba64 Mon Sep 17 00:00:00 2001
From: Guillermo del Angel <delangel@broadinstitute.org>
Date: Sat, 30 Mar 2013 19:05:04 -0400
Subject: [PATCH] Big bad bug fix: feature added to LeftAlignAndTrimVariants to
 left align multiallelic records didn't work. -- Corrected logic to pick
 biallelic vc to left align. -- Added integration test to make sure this
 feature is tested and feature to trim bases is also tested.

---
 ...ftAlignAndTrimVariantsIntegrationTest.java | 10 ++++++++++
 .../LeftAlignAndTrimVariants.java             | 20 +++++++++++--------
 2 files changed, 22 insertions(+), 8 deletions(-)

diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java
index 0b3d9c930..a7d32d43b 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java
@@ -64,4 +64,14 @@ public class LeftAlignAndTrimVariantsIntegrationTest extends WalkerTest {
                  Arrays.asList("bcf05f56adbb32a47b6d6b27b327d5c2"));
          executeTest("test left alignment", spec);
     }
+
+    @Test
+    public void testLeftAlignmentWithTrimmingAndMultialleliecs() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "forHardLeftAlignVariantsTest.vcf --no_cmdline_in_header -trim -split",
+                1,
+                Arrays.asList("4ae03954f8bd66e73fd005c49ea301db"));
+        executeTest("test left alignment with trimming and hard multiple alleles", spec);
+
+    }
 }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignAndTrimVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignAndTrimVariants.java
index 25e3e9857..9168d17f0 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignAndTrimVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignAndTrimVariants.java
@@ -138,18 +138,22 @@ public class LeftAlignAndTrimVariants extends RodWalker<Integer, Integer> {
             if (splitMultiallelics) {
                 final List<VariantContext> vcList = GATKVariantContextUtils.splitVariantContextToBiallelics( vc);
                 for (final VariantContext biallelicVC: vcList) {
-                    final VariantContext v = (trimAlleles ? GATKVariantContextUtils.trimAlleles(vc,true,true):biallelicVC);
+                    final VariantContext v = (trimAlleles ? GATKVariantContextUtils.trimAlleles(biallelicVC,true,true):biallelicVC);
                     result = alignAndWrite(v, ref);
-
+                    writer.add(result.first);
+                    changedSites += result.second;
                 }
             }
-            else if (trimAlleles)
-                result = alignAndWrite(GATKVariantContextUtils.trimAlleles(vc,true,true), ref);
-            else
-                result = alignAndWrite(vc,ref);
+            else {
+                if (trimAlleles)
+                    result = alignAndWrite(GATKVariantContextUtils.trimAlleles(vc,true,true), ref);
+                else
+                    result = alignAndWrite(vc,ref);
+                writer.add(result.first);
+                changedSites += result.second;
+
+            }
 
-            writer.add(result.first);
-            changedSites += result.second;
         }
 
         return changedSites;