From a7734b8abd262122043f6a0f12faae853baad8da Mon Sep 17 00:00:00 2001
From: Chris Kachulis <ckachuli@broadinstitute.org>
Date: Fri, 19 Dec 2025 14:18:02 -0500
Subject: [PATCH 1/6] fix bugs

---
 .../LeftAlignAndTrimVariants.java             | 34 ++++++++++++++-----
 .../variant/GATKVariantContextUtils.java      | 11 +++---
 .../expected_left_align_hg38.vcf              |  9 ++++-
 ...pected_left_align_hg38_maxIndelSize296.vcf |  9 ++++-
 ...pected_left_align_hg38_maxIndelSize342.vcf |  9 ++++-
 .../expected_left_align_hg38_notrim.vcf       |  9 ++++-
 ..._align_hg38_notrim_split_multiallelics.vcf | 11 +++++-
 ...ed_left_align_hg38_split_multiallelics.vcf | 11 +++++-
 ...gn_hg38_split_multiallelics_keepOrigAC.vcf | 11 +++++-
 .../test_left_align_hg38.vcf                  |  7 ++++
 10 files changed, 99 insertions(+), 22 deletions(-)

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants.java
index 70c4c46b724..fa6e5ca4a24 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants.java
@@ -28,11 +28,11 @@
  * Left-align indels in a variant callset
  *
  * <p>
- * This tool takes a VCF file, left-aligns the indels and trims common bases from indels,
+ * This tool takes a VCF file, left-aligns the indels and trims common bases from all variants,
  * leaving them with a minimum representation. The same indel can often be placed at multiple positions and still
  * represent the same haplotype. While the standard convention with VCF is to place an indel at the left-most position
  * this isn't always done, so this tool can be used to left-align them. This tool optionally splits multiallelic
- * sites into biallelics and left-aligns individual alleles. Optionally, the tool will not trim common bases from indels.
+ * sites into biallelics and left-aligns individual alleles. Optionally, the tool will not trim common bases from variants.
  * </p>
  *
  * <h3>Input</h3>
@@ -172,8 +172,10 @@ public class LeftAlignAndTrimVariants extends VariantWalker {
     private VariantContextWriter vcfWriter = null;
     private VCFHeader vcfHeader = null;
 
-    VariantContext lastVariant;
-
+    private int thisVariantGroupStart = 0;
+    private String thisVariantGroupContig = null;
+    private VariantContext lastVariantWritten = null;
+    private final List<VariantContext> realignedVariants = new ArrayList<>();
     @Override
     public void onTraversalStart() {
         final Map<String, VCFHeader> vcfHeaders = Collections.singletonMap(getDrivingVariantsFeatureInput().getName(), getHeaderForVariants());
@@ -213,6 +215,17 @@ private Set<VCFHeaderLine> createVCFHeaderLineList(Map<String, VCFHeader> vcfHea
      */
     @Override
     public void apply(VariantContext vc, ReadsContext readsContext, ReferenceContext ref, FeatureContext featureContext) {
+        if (vc.getContig() != thisVariantGroupContig || vc.getStart() > thisVariantGroupStart) {
+            realignedVariants.sort(Comparator.comparingInt(VariantContext::getStart));
+            for (VariantContext realignedVariant : realignedVariants) {
+                vcfWriter.add(realignedVariant);
+            }
+            thisVariantGroupStart = vc.getStart();
+            thisVariantGroupContig = vc.getContig();
+            lastVariantWritten = realignedVariants.isEmpty() ? lastVariantWritten : realignedVariants.get(realignedVariants.size() - 1);
+            realignedVariants.clear();
+        }
+
         final List<VariantContext> vcList;
         if (splitMultiallelics) {
             if (vc.getGenotypes().stream().anyMatch(g -> g.hasAnyAttribute(GATKVCFConstants.ALLELE_FRACTION_KEY))) {
@@ -231,12 +244,10 @@ public void apply(VariantContext vc, ReadsContext readsContext, ReferenceContext
             if (indelLength > maxIndelSize) {
                 logger.info(String.format("%s (%d) at position %s:%d; skipping that record. Set --max-indel-length >= %d",
                         "Indel is too long", indelLength, splitVariant.getContig(), splitVariant.getStart(), indelLength));
-                lastVariant = splitVariant;
-                vcfWriter.add(splitVariant);
+                realignedVariants.add(splitVariant);
             } else {
-                final int distanceToLastVariant = (lastVariant != null && splitVariant.contigsMatch(lastVariant)) ? splitVariant.getStart() - lastVariant.getEnd() : Integer.MAX_VALUE;
-                lastVariant = GATKVariantContextUtils.leftAlignAndTrim(splitVariant, ref, Math.min(maxLeadingBases, distanceToLastVariant - 1), !dontTrimAlleles);
-                vcfWriter.add(lastVariant);
+                final int distanceToLastVariant = (lastVariantWritten != null && splitVariant.contigsMatch(lastVariantWritten)) ? splitVariant.getStart() - lastVariantWritten.getEnd() : Integer.MAX_VALUE;
+                realignedVariants.add(GATKVariantContextUtils.leftAlignAndTrim(splitVariant, ref, Math.min(maxLeadingBases, distanceToLastVariant), !dontTrimAlleles));
             }
         }
     }
@@ -256,6 +267,11 @@ public boolean requiresReference() {
      */
     @Override
     public Object onTraversalSuccess() {
+        //write out remaining variants
+        realignedVariants.sort(Comparator.comparingInt(VariantContext::getStart));
+        for (VariantContext realignedVariant : realignedVariants) {
+            vcfWriter.add(realignedVariant);
+        }
         return "SUCCESS";
     }
 
diff --git a/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVariantContextUtils.java b/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVariantContextUtils.java
index 2df684087e4..6dd20811d72 100644
--- a/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVariantContextUtils.java
+++ b/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVariantContextUtils.java
@@ -2220,15 +2220,13 @@ public static <T> List<T> removeItemsByIndex(List<T> data, List<Integer> indexes
      * By definition, it will only take biallelic vc's. Splitting into multiple alleles has to be
      * handled by calling routine.
      *
-     * @param vc  Input VC with variants to left align
+     * @param vc  Input VC with variants to left align and trim
      * @param ref Reference context
      * @return new VC.
      */
-    public static VariantContext leftAlignAndTrim(final VariantContext vc, final ReferenceContext ref, final int maxLeadingBases, final boolean trim) {
-        if (!vc.isIndel() || maxLeadingBases <= 0) {
-            return vc;
-        }
+    public static VariantContext leftAlignAndTrim(final VariantContext vc, final ReferenceContext ref, final int maxLeadingBasesIndel, final boolean trim) {
 
+        final int maxLeadingBases = vc.isIndel() ? maxLeadingBasesIndel : 0;
 
         for(int leadingBases = Math.min(maxLeadingBases, 10); leadingBases <= maxLeadingBases; leadingBases = Math.min(2*leadingBases, maxLeadingBases)) {
             final int refStart = Math.max(vc.getStart() - leadingBases, 1);
@@ -2245,8 +2243,9 @@ public static VariantContext leftAlignAndTrim(final VariantContext vc, final Ref
                 return result;
             }).collect(Collectors.toList());
 
+            final int boundStart = vc.isSNP() || vc.isMNP() ? variantOffsetInRef : variantOffsetInRef + 1; // +1 to ignore the shared base in front for indels
             final List<IndexRange> alleleRanges = vc.getAlleles().stream()
-                    .map(a -> new IndexRange(variantOffsetInRef + 1, variantOffsetInRef + a.length()))  // +1 to ignore the shared base in front
+                    .map(a -> new IndexRange(boundStart, variantOffsetInRef + a.length()))
                     .collect(Collectors.toList());
 
             // note that this also shifts the index ranges as a side effect, so below they can be used to output allele bases
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38.vcf
index 05df02709e0..5b3ab8afcc9 100755
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38.vcf
@@ -35,5 +35,12 @@ chr21	10382389	.	A	ATT	30	.	AC=2;AF=0.500;AN=2	GT	1/1	./.
 chr21	10388233	.	GGAA	G	30	.	AC=1;AF=0.250;AN=2	GT	0/1	./.
 chr21	10804284	.	T	TGC	30	.	AC=1;AF=0.250;AN=2	GT	0/1	./.
 chr21	13255296	.	A	G	30	.	AC=2;AF=0.500;AN=2	GT	1/1	./.
-chr21	13255297	.	AAA	A	30	.	AC=2;AF=0.500;AN=2	GT	1/1	./.
+chr21	13255296	.	AAA	A	30	.	AC=2;AF=0.500;AN=2	GT	1/1	./.
 chr21	39583817	.	CTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCT	C	30	.	AC=3;AF=0.750;AN=4	GT	1/1	0/1
+chr21	39584859	.	C	G	30	.	AC=3;AF=0.750;AN=4	GT	1/1	0/1
+chr21	39584950	.	C	G,CC	30	.	AC=2,1;AF=0.500,0.250;AN=4	GT	1/1	0/2
+chr21	39584953	.	AA	AG,A	30	.	AC=2,1;AF=0.500,0.250;AN=4	GT	1/1	0/2
+chr21	39586243	.	TAAAA	T	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
+chr21	39586243	.	TA	T	30	.	AC=1;AF=0.250;AN=4	GT	0/0	0/1
+chr21	39586243	.	T	TA	30	.	AC=1;AF=0.250;AN=4	GT	0/0	0/1
+chr21	39586245	.	A	G	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_maxIndelSize296.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_maxIndelSize296.vcf
index ee3325842fd..94be82d58e5 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_maxIndelSize296.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_maxIndelSize296.vcf
@@ -35,5 +35,12 @@ chr21	10382389	.	A	ATT	30	.	AC=2;AF=0.500;AN=2	GT	1/1	./.
 chr21	10388233	.	GGAA	G	30	.	AC=1;AF=0.250;AN=2	GT	0/1	./.
 chr21	10804284	.	T	TGC	30	.	AC=1;AF=0.250;AN=2	GT	0/1	./.
 chr21	13255296	.	A	G	30	.	AC=2;AF=0.500;AN=2	GT	1/1	./.
-chr21	13255297	.	AAA	A	30	.	AC=2;AF=0.500;AN=2	GT	1/1	./.
+chr21	13255296	.	AAA	A	30	.	AC=2;AF=0.500;AN=2	GT	1/1	./.
 chr21	39583817	.	CTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCT	C	30	.	AC=3;AF=0.750;AN=4	GT	1/1	0/1
+chr21	39584859	.	C	G	30	.	AC=3;AF=0.750;AN=4	GT	1/1	0/1
+chr21	39584950	.	C	G,CC	30	.	AC=2,1;AF=0.500,0.250;AN=4	GT	1/1	0/2
+chr21	39584953	.	AA	AG,A	30	.	AC=2,1;AF=0.500,0.250;AN=4	GT	1/1	0/2
+chr21	39586243	.	TAAAA	T	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
+chr21	39586243	.	TA	T	30	.	AC=1;AF=0.250;AN=4	GT	0/0	0/1
+chr21	39586243	.	T	TA	30	.	AC=1;AF=0.250;AN=4	GT	0/0	0/1
+chr21	39586245	.	A	G	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_maxIndelSize342.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_maxIndelSize342.vcf
index 107ff0811e9..4ccb33ea38a 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_maxIndelSize342.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_maxIndelSize342.vcf
@@ -35,5 +35,12 @@ chr21	10382389	.	A	ATT	30	.	AC=2;AF=0.500;AN=2	GT	1/1	./.
 chr21	10388233	.	GGAA	G	30	.	AC=1;AF=0.250;AN=2	GT	0/1	./.
 chr21	10804284	.	T	TGC	30	.	AC=1;AF=0.250;AN=2	GT	0/1	./.
 chr21	13255296	.	A	G	30	.	AC=2;AF=0.500;AN=2	GT	1/1	./.
-chr21	13255297	.	AAA	A	30	.	AC=2;AF=0.500;AN=2	GT	1/1	./.
+chr21	13255296	.	AAA	A	30	.	AC=2;AF=0.500;AN=2	GT	1/1	./.
 chr21	39583817	.	CTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCT	C	30	.	AC=3;AF=0.750;AN=4	GT	1/1	0/1
+chr21	39584859	.	C	G	30	.	AC=3;AF=0.750;AN=4	GT	1/1	0/1
+chr21	39584950	.	C	G,CC	30	.	AC=2,1;AF=0.500,0.250;AN=4	GT	1/1	0/2
+chr21	39584953	.	AA	AG,A	30	.	AC=2,1;AF=0.500,0.250;AN=4	GT	1/1	0/2
+chr21	39586243	.	TAAAA	T	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
+chr21	39586243	.	TA	T	30	.	AC=1;AF=0.250;AN=4	GT	0/0	0/1
+chr21	39586243	.	T	TA	30	.	AC=1;AF=0.250;AN=4	GT	0/0	0/1
+chr21	39586245	.	A	G	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_notrim.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_notrim.vcf
index 3c5f0086bf6..cfd092b0892 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_notrim.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_notrim.vcf
@@ -35,5 +35,12 @@ chr21	10382389	.	A	ATT	30	.	AC=2;AF=0.500;AN=2	GT	1/1	./.
 chr21	10388233	.	GGAA	G	30	.	AC=1;AF=0.250;AN=2	GT	0/1	./.
 chr21	10804284	.	T	TGC	30	.	AC=1;AF=0.250;AN=2	GT	0/1	./.
 chr21	13255296	.	A	G	30	.	AC=2;AF=0.500;AN=2	GT	1/1	./.
-chr21	13255297	.	AAA	A	30	.	AC=2;AF=0.500;AN=2	GT	1/1	./.
+chr21	13255296	.	AAA	A	30	.	AC=2;AF=0.500;AN=2	GT	1/1	./.
 chr21	39583817	.	CTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCT	C	30	.	AC=3;AF=0.750;AN=4	GT	1/1	0/1
+chr21	39584859	.	CAA	GAA	30	.	AC=3;AF=0.750;AN=4	GT	1/1	0/1
+chr21	39584950	.	C	G,CC	30	.	AC=2,1;AF=0.500,0.250;AN=4	GT	1/1	0/2
+chr21	39584953	.	AA	AG,A	30	.	AC=2,1;AF=0.500,0.250;AN=4	GT	1/1	0/2
+chr21	39586239	.	CAATT	CAATTA	30	.	AC=1;AF=0.250;AN=4	GT	0/0	0/1
+chr21	39586240	.	AATTA	AATT	30	.	AC=1;AF=0.250;AN=4	GT	0/0	0/1
+chr21	39586243	.	TAAAA	TAGAA	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
+chr21	39586243	.	TAAAA	T	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_notrim_split_multiallelics.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_notrim_split_multiallelics.vcf
index 80ea5bb296d..d88b09e05ff 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_notrim_split_multiallelics.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_notrim_split_multiallelics.vcf
@@ -37,5 +37,14 @@ chr21	10382389	.	A	ATT	30	.	AC=2;AF=0.500;AN=2	GT	1/1	./.
 chr21	10388233	.	GGAA	G	30	.	AC=1;AF=0.250;AN=2	GT	0/1	./.
 chr21	10804284	.	T	TGC	30	.	AC=1;AF=0.250;AN=2	GT	0/1	./.
 chr21	13255296	.	A	G	30	.	AC=2;AF=0.500;AN=2	GT	1/1	./.
-chr21	13255297	.	AAA	A	30	.	AC=2;AF=0.500;AN=2	GT	1/1	./.
+chr21	13255296	.	AAA	A	30	.	AC=2;AF=0.500;AN=2	GT	1/1	./.
 chr21	39583817	.	CTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCT	C	30	.	AC=3;AF=0.750;AN=4	GT	1/1	0/1
+chr21	39584859	.	CAA	GAA	30	.	AC=3;AF=0.750;AN=4	GT	1/1	0/1
+chr21	39584948	.	A	AC	30	.	AC=1;AF=0.250;AN=4	GT	0/0	0/1
+chr21	39584950	.	C	G	30	.	AC=2;AF=0.500;AN=4	GT	1/1	0/0
+chr21	39584951	.	CA	C	30	.	AC=1;AF=0.250;AN=4	GT	0/0	0/1
+chr21	39584953	.	AA	AG	30	.	AC=2;AF=0.500;AN=4	GT	1/1	0/0
+chr21	39586239	.	CAATT	CAATTA	30	.	AC=1;AF=0.250;AN=4	GT	0/0	0/1
+chr21	39586240	.	AATTA	AATT	30	.	AC=1;AF=0.250;AN=4	GT	0/0	0/1
+chr21	39586243	.	TAAAA	TAGAA	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
+chr21	39586243	.	TAAAA	T	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
\ No newline at end of file
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_split_multiallelics.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_split_multiallelics.vcf
index 52f63f0419b..7d3b81cc99f 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_split_multiallelics.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_split_multiallelics.vcf
@@ -37,5 +37,14 @@ chr21	10382389	.	A	ATT	30	.	AC=2;AF=0.500;AN=2	GT	1/1	./.
 chr21	10388233	.	GGAA	G	30	.	AC=1;AF=0.250;AN=2	GT	0/1	./.
 chr21	10804284	.	T	TGC	30	.	AC=1;AF=0.250;AN=2	GT	0/1	./.
 chr21	13255296	.	A	G	30	.	AC=2;AF=0.500;AN=2	GT	1/1	./.
-chr21	13255297	.	AAA	A	30	.	AC=2;AF=0.500;AN=2	GT	1/1	./.
+chr21	13255296	.	AAA	A	30	.	AC=2;AF=0.500;AN=2	GT	1/1	./.
 chr21	39583817	.	CTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCT	C	30	.	AC=3;AF=0.750;AN=4	GT	1/1	0/1
+chr21	39584859	.	C	G	30	.	AC=3;AF=0.750;AN=4	GT	1/1	0/1
+chr21	39584948	.	A	AC	30	.	AC=1;AF=0.250;AN=4	GT	0/0	0/1
+chr21	39584950	.	C	G	30	.	AC=2;AF=0.500;AN=4	GT	1/1	0/0
+chr21	39584951	.	CA	C	30	.	AC=1;AF=0.250;AN=4	GT	0/0	0/1
+chr21	39584954	.	A	G	30	.	AC=2;AF=0.500;AN=4	GT	1/1	0/0
+chr21	39586243	.	TAAAA	T	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
+chr21	39586243	.	TA	T	30	.	AC=1;AF=0.250;AN=4	GT	0/0	0/1
+chr21	39586243	.	T	TA	30	.	AC=1;AF=0.250;AN=4	GT	0/0	0/1
+chr21	39586245	.	A	G	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
\ No newline at end of file
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_split_multiallelics_keepOrigAC.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_split_multiallelics_keepOrigAC.vcf
index 4007fb39696..59491829659 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_split_multiallelics_keepOrigAC.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_split_multiallelics_keepOrigAC.vcf
@@ -40,5 +40,14 @@ chr21	10382389	.	A	ATT	30	.	AC=2;AF=0.500;AN=2	GT	1/1	./.
 chr21	10388233	.	GGAA	G	30	.	AC=1;AF=0.250;AN=2	GT	0/1	./.
 chr21	10804284	.	T	TGC	30	.	AC=1;AF=0.250;AN=2	GT	0/1	./.
 chr21	13255296	.	A	G	30	.	AC=2;AF=0.500;AN=2	GT	1/1	./.
-chr21	13255297	.	AAA	A	30	.	AC=2;AF=0.500;AN=2	GT	1/1	./.
+chr21	13255296	.	AAA	A	30	.	AC=2;AF=0.500;AN=2	GT	1/1	./.
 chr21	39583817	.	CTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCT	C	30	.	AC=3;AF=0.750;AN=4	GT	1/1	0/1
+chr21	39584859	.	C	G	30	.	AC=3;AF=0.750;AN=4	GT	1/1	0/1
+chr21	39584948	.	A	AC	30	.	AC=1;AC_Orig=1;AF=0.250;AF_Orig=0.250;AN=4;AN_Orig=4	GT	0/0	0/1
+chr21	39584950	.	C	G	30	.	AC=2;AC_Orig=2;AF=0.500;AF_Orig=0.500;AN=4;AN_Orig=4	GT	1/1	0/0
+chr21	39584951	.	CA	C	30	.	AC=1;AC_Orig=1;AF=0.250;AF_Orig=0.250;AN=4;AN_Orig=4	GT	0/0	0/1
+chr21	39584954	.	A	G	30	.	AC=2;AC_Orig=2;AF=0.500;AF_Orig=0.500;AN=4;AN_Orig=4	GT	1/1	0/0
+chr21	39586243	.	TAAAA	T	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
+chr21	39586243	.	TA	T	30	.	AC=1;AF=0.250;AN=4	GT	0/0	0/1
+chr21	39586243	.	T	TA	30	.	AC=1;AF=0.250;AN=4	GT	0/0	0/1
+chr21	39586245	.	A	G	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/test_left_align_hg38.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/test_left_align_hg38.vcf
index 410fa01cd77..87e4f647d85 100755
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/test_left_align_hg38.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/test_left_align_hg38.vcf
@@ -37,3 +37,10 @@ chr21	10804284	.	T	TGC	30	.	AC=1;AF=0.250;AN=2	GT	0/1	./.
 chr21	13255296	.	A	G	30	.	AC=2;AF=0.500;AN=2	GT	1/1	./.
 chr21	13255301	.	AAA	A	30	.	AC=2;AF=0.500;AN=2	GT	1/1	./.
 chr21	39584006	.	CTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCC	C	30	.	AC=3;AF=0.750;AN=4	GT	1/1	0/1
+chr21	39584859	.	CAA	GAA	30	.	AC=3;AF=0.750;AN=4	GT	1/1	0/1
+chr21	39584950	.	C	G,CC	30	.	AC=2,1;AF=0.500,0.250;AN=4	GT	1/1	0/2
+chr21	39584953	.	AA	AG,A	30	.	AC=2,1;AF=0.500,0.250;AN=4	GT	1/1	0/2
+chr21	39586243	.	TAAAA	TAGAA	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
+chr21	39586243	.	TAAAA	T	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
+chr21	39586243	.	TAAAA	TAAA	30	.	AC=1;AF=0.250;AN=4	GT	0/0	0/1
+chr21	39586243	.	TAAAA	TAAAAA	30	.	AC=1;AF=0.250;AN=4	GT	0/0	0/1

From 554373afa1bc371b907b4fca9995a9a86ede2f0e Mon Sep 17 00:00:00 2001
From: Chris Kachulis <ckachuli@broadinstitute.org>
Date: Fri, 19 Dec 2025 21:33:31 -0500
Subject: [PATCH 2/6] .

---
 .../tools/walkers/variantutils/LeftAlignAndTrimVariants.java  | 2 +-
 .../LeftAlignAndTrimVariants/expected_left_align_hg38.vcf     | 2 ++
 .../expected_left_align_hg38_maxIndelSize296.vcf              | 2 ++
 .../expected_left_align_hg38_maxIndelSize342.vcf              | 2 ++
 .../expected_left_align_hg38_notrim.vcf                       | 2 ++
 .../expected_left_align_hg38_notrim_split_multiallelics.vcf   | 4 +++-
 .../expected_left_align_hg38_split_multiallelics.vcf          | 4 +++-
 ...xpected_left_align_hg38_split_multiallelics_keepOrigAC.vcf | 2 ++
 .../LeftAlignAndTrimVariants/test_left_align_hg38.vcf         | 2 ++
 9 files changed, 19 insertions(+), 3 deletions(-)

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants.java
index fa6e5ca4a24..b38853e6134 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants.java
@@ -246,7 +246,7 @@ public void apply(VariantContext vc, ReadsContext readsContext, ReferenceContext
                         "Indel is too long", indelLength, splitVariant.getContig(), splitVariant.getStart(), indelLength));
                 realignedVariants.add(splitVariant);
             } else {
-                final int distanceToLastVariant = (lastVariantWritten != null && splitVariant.contigsMatch(lastVariantWritten)) ? splitVariant.getStart() - lastVariantWritten.getEnd() : Integer.MAX_VALUE;
+                final int distanceToLastVariant = (lastVariantWritten != null && splitVariant.contigsMatch(lastVariantWritten)) ? splitVariant.getStart() - lastVariantWritten.getStart() : Integer.MAX_VALUE;
                 realignedVariants.add(GATKVariantContextUtils.leftAlignAndTrim(splitVariant, ref, Math.min(maxLeadingBases, distanceToLastVariant), !dontTrimAlleles));
             }
         }
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38.vcf
index 5b3ab8afcc9..d87372b77ca 100755
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38.vcf
@@ -44,3 +44,5 @@ chr21	39586243	.	TAAAA	T	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
 chr21	39586243	.	TA	T	30	.	AC=1;AF=0.250;AN=4	GT	0/0	0/1
 chr21	39586243	.	T	TA	30	.	AC=1;AF=0.250;AN=4	GT	0/0	0/1
 chr21	39586245	.	A	G	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
+chr21	39586743	.	TACC	T	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
+chr21	39586744	.	AC	A	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_maxIndelSize296.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_maxIndelSize296.vcf
index 94be82d58e5..20289443963 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_maxIndelSize296.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_maxIndelSize296.vcf
@@ -44,3 +44,5 @@ chr21	39586243	.	TAAAA	T	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
 chr21	39586243	.	TA	T	30	.	AC=1;AF=0.250;AN=4	GT	0/0	0/1
 chr21	39586243	.	T	TA	30	.	AC=1;AF=0.250;AN=4	GT	0/0	0/1
 chr21	39586245	.	A	G	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
+chr21	39586743	.	TACC	T	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
+chr21	39586744	.	AC	A	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_maxIndelSize342.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_maxIndelSize342.vcf
index 4ccb33ea38a..4d533e66553 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_maxIndelSize342.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_maxIndelSize342.vcf
@@ -44,3 +44,5 @@ chr21	39586243	.	TAAAA	T	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
 chr21	39586243	.	TA	T	30	.	AC=1;AF=0.250;AN=4	GT	0/0	0/1
 chr21	39586243	.	T	TA	30	.	AC=1;AF=0.250;AN=4	GT	0/0	0/1
 chr21	39586245	.	A	G	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
+chr21	39586743	.	TACC	T	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
+chr21	39586744	.	AC	A	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_notrim.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_notrim.vcf
index cfd092b0892..bc3b85de197 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_notrim.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_notrim.vcf
@@ -44,3 +44,5 @@ chr21	39586239	.	CAATT	CAATTA	30	.	AC=1;AF=0.250;AN=4	GT	0/0	0/1
 chr21	39586240	.	AATTA	AATT	30	.	AC=1;AF=0.250;AN=4	GT	0/0	0/1
 chr21	39586243	.	TAAAA	TAGAA	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
 chr21	39586243	.	TAAAA	T	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
+chr21	39586743	.	TACC	T	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
+chr21	39586744	.	AC	A	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_notrim_split_multiallelics.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_notrim_split_multiallelics.vcf
index d88b09e05ff..75d2f190dd8 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_notrim_split_multiallelics.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_notrim_split_multiallelics.vcf
@@ -47,4 +47,6 @@ chr21	39584953	.	AA	AG	30	.	AC=2;AF=0.500;AN=4	GT	1/1	0/0
 chr21	39586239	.	CAATT	CAATTA	30	.	AC=1;AF=0.250;AN=4	GT	0/0	0/1
 chr21	39586240	.	AATTA	AATT	30	.	AC=1;AF=0.250;AN=4	GT	0/0	0/1
 chr21	39586243	.	TAAAA	TAGAA	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
-chr21	39586243	.	TAAAA	T	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
\ No newline at end of file
+chr21	39586243	.	TAAAA	T	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
+chr21	39586743	.	TACC	T	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
+chr21	39586744	.	AC	A	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
\ No newline at end of file
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_split_multiallelics.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_split_multiallelics.vcf
index 7d3b81cc99f..7721f6271a1 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_split_multiallelics.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_split_multiallelics.vcf
@@ -47,4 +47,6 @@ chr21	39584954	.	A	G	30	.	AC=2;AF=0.500;AN=4	GT	1/1	0/0
 chr21	39586243	.	TAAAA	T	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
 chr21	39586243	.	TA	T	30	.	AC=1;AF=0.250;AN=4	GT	0/0	0/1
 chr21	39586243	.	T	TA	30	.	AC=1;AF=0.250;AN=4	GT	0/0	0/1
-chr21	39586245	.	A	G	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
\ No newline at end of file
+chr21	39586245	.	A	G	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
+chr21	39586743	.	TACC	T	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
+chr21	39586744	.	AC	A	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
\ No newline at end of file
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_split_multiallelics_keepOrigAC.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_split_multiallelics_keepOrigAC.vcf
index 59491829659..80194bc7d8c 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_split_multiallelics_keepOrigAC.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_split_multiallelics_keepOrigAC.vcf
@@ -51,3 +51,5 @@ chr21	39586243	.	TAAAA	T	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
 chr21	39586243	.	TA	T	30	.	AC=1;AF=0.250;AN=4	GT	0/0	0/1
 chr21	39586243	.	T	TA	30	.	AC=1;AF=0.250;AN=4	GT	0/0	0/1
 chr21	39586245	.	A	G	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
+chr21	39586743	.	TACC	T	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
+chr21	39586744	.	AC	A	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/test_left_align_hg38.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/test_left_align_hg38.vcf
index 87e4f647d85..26690f59eaf 100755
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/test_left_align_hg38.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/test_left_align_hg38.vcf
@@ -44,3 +44,5 @@ chr21	39586243	.	TAAAA	TAGAA	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
 chr21	39586243	.	TAAAA	T	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
 chr21	39586243	.	TAAAA	TAAA	30	.	AC=1;AF=0.250;AN=4	GT	0/0	0/1
 chr21	39586243	.	TAAAA	TAAAAA	30	.	AC=1;AF=0.250;AN=4	GT	0/0	0/1
+chr21	39586743	.	TACC	T	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0
+chr21	39586745	.	CC	C	30	.	AC=1;AF=0.250;AN=4	GT	0/1	0/0

From 3a390fa1d9171269896a50614a8c359366bc56aa Mon Sep 17 00:00:00 2001
From: Chris Kachulis <ckachuli@broadinstitute.org>
Date: Mon, 5 Jan 2026 12:18:11 -0500
Subject: [PATCH 3/6] ubuntu-slim

---
 .github/workflows/gatk-tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/gatk-tests.yml b/.github/workflows/gatk-tests.yml
index 54f0945106c..18b21f6680f 100644
--- a/.github/workflows/gatk-tests.yml
+++ b/.github/workflows/gatk-tests.yml
@@ -288,7 +288,7 @@ jobs:
 
   #Run our various targeted medium scale wdl wiring tests
   wdlTests:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-slim
     strategy:
       matrix:
         wdlTest: [ 'RUN_CNV_GERMLINE_COHORT_WDL', 'RUN_CNV_GERMLINE_CASE_WDL', 'RUN_CNV_SOMATIC_WDL', 'RUN_M2_WDL', 'RUN_VCF_SITE_LEVEL_FILTERING_WDL' ]

From 4375c5a699006407a52a9631a3102c9769ba4f1e Mon Sep 17 00:00:00 2001
From: Chris Kachulis <ckachuli@broadinstitute.org>
Date: Mon, 5 Jan 2026 12:29:24 -0500
Subject: [PATCH 4/6] purge more disk

---
 .github/actions/purge-runner-disk/action.yml | 3 +++
 .github/workflows/gatk-tests.yml             | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/actions/purge-runner-disk/action.yml b/.github/actions/purge-runner-disk/action.yml
index d9bd987bbe9..12b69a88923 100644
--- a/.github/actions/purge-runner-disk/action.yml
+++ b/.github/actions/purge-runner-disk/action.yml
@@ -9,4 +9,7 @@ runs:
       run: |
         sudo rm -rf /usr/share/dotnet
         sudo rm -rf "$AGENT_TOOLSDIRECTORY"
+        sudo rm -rf /usr/local/lib/android
+        sudo rm -rf /opt/ghc
+        sudo docker image prune --all --force
       shell: bash
diff --git a/.github/workflows/gatk-tests.yml b/.github/workflows/gatk-tests.yml
index 18b21f6680f..54f0945106c 100644
--- a/.github/workflows/gatk-tests.yml
+++ b/.github/workflows/gatk-tests.yml
@@ -288,7 +288,7 @@ jobs:
 
   #Run our various targeted medium scale wdl wiring tests
   wdlTests:
-    runs-on: ubuntu-slim
+    runs-on: ubuntu-latest
     strategy:
       matrix:
         wdlTest: [ 'RUN_CNV_GERMLINE_COHORT_WDL', 'RUN_CNV_GERMLINE_CASE_WDL', 'RUN_CNV_SOMATIC_WDL', 'RUN_M2_WDL', 'RUN_VCF_SITE_LEVEL_FILTERING_WDL' ]

From 9278074eed5826bdc6754e34b522578357101a66 Mon Sep 17 00:00:00 2001
From: Chris Kachulis <ckachuli@broadinstitute.org>
Date: Mon, 5 Jan 2026 13:20:28 -0500
Subject: [PATCH 5/6] debug purge-runner-disk

---
 .github/actions/purge-runner-disk/action.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/actions/purge-runner-disk/action.yml b/.github/actions/purge-runner-disk/action.yml
index 12b69a88923..dc86fbd7794 100644
--- a/.github/actions/purge-runner-disk/action.yml
+++ b/.github/actions/purge-runner-disk/action.yml
@@ -7,9 +7,12 @@ runs:
     #https://github.com/actions/runner-images/issues/2840
     - name: Reclaim some runner disk space
       run: |
+        sudo df -h
+        echo "$AGENT_TOOLSDIRECTORY"
         sudo rm -rf /usr/share/dotnet
         sudo rm -rf "$AGENT_TOOLSDIRECTORY"
         sudo rm -rf /usr/local/lib/android
         sudo rm -rf /opt/ghc
         sudo docker image prune --all --force
+        sudo df -h
       shell: bash

From ca6a6c7a04dfa26536ecffb83da574388f2c165b Mon Sep 17 00:00:00 2001
From: Chris Kachulis <ckachuli@broadinstitute.org>
Date: Wed, 7 Jan 2026 09:31:54 -0500
Subject: [PATCH 6/6] debug

---
 .../germline/run_cnv_germline_workflows.sh                 | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/scripts/cnv_cromwell_tests/germline/run_cnv_germline_workflows.sh b/scripts/cnv_cromwell_tests/germline/run_cnv_germline_workflows.sh
index 97305996d54..50dd3bcd1f0 100644
--- a/scripts/cnv_cromwell_tests/germline/run_cnv_germline_workflows.sh
+++ b/scripts/cnv_cromwell_tests/germline/run_cnv_germline_workflows.sh
@@ -1,5 +1,5 @@
 #!/bin/bash -l
-set -e
+#set -e
 
 MODE=$1
 # We split up the test into CASE in COHORT to reduce overall test runtime
@@ -42,7 +42,10 @@ echo "Running ========"
 # Cohort WES w/ explicit GC correction
 if [[ "$MODE" == "COHORT" ]]; then
   java -jar ${CROMWELL_JAR} run $WORKING_DIR/gatk/scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl -i cnv_germline_cohort_workflow_mod.json ;
-  find /home/runner/work/gatk/gatk/scripts/cnv_cromwell_tests/germline/cromwell-executions/CNVGermlineCohortWorkflow/ | grep 'stdout\|stderr' | xargs cat ;
+  if [[ "$?" != 0 ]]; then
+    find /home/runner/work/gatk/gatk/scripts/cnv_cromwell_tests/germline/cromwell-executions/CNVGermlineCohortWorkflow/ | grep 'stdout\|stderr' | xargs cat ;
+    exit 1 ;
+  fi
 fi
 
 # Scattered case WES w/ explicit GC correction