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kachuliskachulis
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-3
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9 files changed

+19
-3
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‎src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -246,7 +246,7 @@ public void apply(VariantContext vc, ReadsContext readsContext, ReferenceContext
246246
"Indel is too long", indelLength, splitVariant.getContig(), splitVariant.getStart(), indelLength));
247247
realignedVariants.add(splitVariant);
248248
} else {
249-
final int distanceToLastVariant = (lastVariantWritten != null && splitVariant.contigsMatch(lastVariantWritten)) ? splitVariant.getStart() - lastVariantWritten.getEnd() : Integer.MAX_VALUE;
249+
final int distanceToLastVariant = (lastVariantWritten != null && splitVariant.contigsMatch(lastVariantWritten)) ? splitVariant.getStart() - lastVariantWritten.getStart() : Integer.MAX_VALUE;
250250
realignedVariants.add(GATKVariantContextUtils.leftAlignAndTrim(splitVariant, ref, Math.min(maxLeadingBases, distanceToLastVariant), !dontTrimAlleles));
251251
}
252252
}

‎src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38.vcf‎

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -44,3 +44,5 @@ chr21 39586243 . TAAAA T 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
4444
chr21 39586243 . TA T 30 . AC=1;AF=0.250;AN=4 GT 0/0 0/1
4545
chr21 39586243 . T TA 30 . AC=1;AF=0.250;AN=4 GT 0/0 0/1
4646
chr21 39586245 . A G 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
47+
chr21 39586743 . TACC T 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
48+
chr21 39586744 . AC A 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0

‎src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_maxIndelSize296.vcf‎

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -44,3 +44,5 @@ chr21 39586243 . TAAAA T 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
4444
chr21 39586243 . TA T 30 . AC=1;AF=0.250;AN=4 GT 0/0 0/1
4545
chr21 39586243 . T TA 30 . AC=1;AF=0.250;AN=4 GT 0/0 0/1
4646
chr21 39586245 . A G 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
47+
chr21 39586743 . TACC T 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
48+
chr21 39586744 . AC A 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0

‎src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_maxIndelSize342.vcf‎

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -44,3 +44,5 @@ chr21 39586243 . TAAAA T 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
4444
chr21 39586243 . TA T 30 . AC=1;AF=0.250;AN=4 GT 0/0 0/1
4545
chr21 39586243 . T TA 30 . AC=1;AF=0.250;AN=4 GT 0/0 0/1
4646
chr21 39586245 . A G 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
47+
chr21 39586743 . TACC T 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
48+
chr21 39586744 . AC A 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0

‎src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_notrim.vcf‎

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -44,3 +44,5 @@ chr21 39586239 . CAATT CAATTA 30 . AC=1;AF=0.250;AN=4 GT 0/0 0/1
4444
chr21 39586240 . AATTA AATT 30 . AC=1;AF=0.250;AN=4 GT 0/0 0/1
4545
chr21 39586243 . TAAAA TAGAA 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
4646
chr21 39586243 . TAAAA T 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
47+
chr21 39586743 . TACC T 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
48+
chr21 39586744 . AC A 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0

‎src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_notrim_split_multiallelics.vcf‎

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -47,4 +47,6 @@ chr21 39584953 . AA AG 30 . AC=2;AF=0.500;AN=4 GT 1/1 0/0
4747
chr21 39586239 . CAATT CAATTA 30 . AC=1;AF=0.250;AN=4 GT 0/0 0/1
4848
chr21 39586240 . AATTA AATT 30 . AC=1;AF=0.250;AN=4 GT 0/0 0/1
4949
chr21 39586243 . TAAAA TAGAA 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
50-
chr21 39586243 . TAAAA T 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
50+
chr21 39586243 . TAAAA T 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
51+
chr21 39586743 . TACC T 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
52+
chr21 39586744 . AC A 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0

‎src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_split_multiallelics.vcf‎

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -47,4 +47,6 @@ chr21 39584954 . A G 30 . AC=2;AF=0.500;AN=4 GT 1/1 0/0
4747
chr21 39586243 . TAAAA T 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
4848
chr21 39586243 . TA T 30 . AC=1;AF=0.250;AN=4 GT 0/0 0/1
4949
chr21 39586243 . T TA 30 . AC=1;AF=0.250;AN=4 GT 0/0 0/1
50-
chr21 39586245 . A G 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
50+
chr21 39586245 . A G 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
51+
chr21 39586743 . TACC T 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
52+
chr21 39586744 . AC A 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0

‎src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_split_multiallelics_keepOrigAC.vcf‎

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -51,3 +51,5 @@ chr21 39586243 . TAAAA T 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
5151
chr21 39586243 . TA T 30 . AC=1;AF=0.250;AN=4 GT 0/0 0/1
5252
chr21 39586243 . T TA 30 . AC=1;AF=0.250;AN=4 GT 0/0 0/1
5353
chr21 39586245 . A G 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
54+
chr21 39586743 . TACC T 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
55+
chr21 39586744 . AC A 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0

‎src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/test_left_align_hg38.vcf‎

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -44,3 +44,5 @@ chr21 39586243 . TAAAA TAGAA 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
4444
chr21 39586243 . TAAAA T 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
4545
chr21 39586243 . TAAAA TAAA 30 . AC=1;AF=0.250;AN=4 GT 0/0 0/1
4646
chr21 39586243 . TAAAA TAAAAA 30 . AC=1;AF=0.250;AN=4 GT 0/0 0/1
47+
chr21 39586743 . TACC T 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
48+
chr21 39586745 . CC C 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0

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