storage: Fix junit tests. #TASK-6765

opencb · Sep 9, 2024 · 53bf816 · 53bf816
1 parent 717beac
commit 53bf816
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Showing 2 changed files with 7 additions and 13 deletions.
diff --git a/...org/opencb/opencga/storage/hadoop/variant/index/sample/SampleIndexVariantBiConverter.java b/...org/opencb/opencga/storage/hadoop/variant/index/sample/SampleIndexVariantBiConverter.java
@@ -118,17 +118,15 @@ protected int toBytes(int relativeStart, String reference, String alternate, byt
     }
 
     public Variant toVariant(String chromosome, int batchStart, byte[] bytes) {
-        return toVariant(chromosome, batchStart, bytes, 0, bytes.length);
+        return toVariant(chromosome, batchStart, bytes, 0);
     }
 
-    public Variant toVariant(String chromosome, int batchStart, byte[] bytes, int offset, int length) {
+    public Variant toVariant(String chromosome, int batchStart, byte[] bytes, int offset) {
         if (hasEncodedAlleles(bytes, offset)) {
             return toVariantEncodedAlleles(chromosome, batchStart, bytes, offset);
         } else {
-            int currentOffset = INT24_LENGTH;
-            int referenceLength = readNextSeparator(bytes, offset + currentOffset, length - currentOffset);
-            currentOffset += referenceLength + SEPARATOR_LENGTH;
-            int alternateLength = readNextSeparator(bytes, offset + currentOffset, length - currentOffset);
+            int referenceLength = readNextSeparator(bytes, offset + INT24_LENGTH);
+            int alternateLength = readNextSeparator(bytes, offset + INT24_LENGTH + referenceLength + SEPARATOR_LENGTH);
             return toVariant(chromosome, batchStart, bytes, offset, referenceLength, alternateLength);
         }
     }
@@ -704,16 +702,12 @@ private Variant toVariant(String chromosome, int batchStart, byte[] bytes, int o
     }
 
     private int readNextSeparator(byte[] bytes, int offset) {
-        return readNextSeparator(bytes, offset, bytes.length - offset);
-    }
-
-    private int readNextSeparator(byte[] bytes, int offset, int length) {
-        for (int i = offset; i < (offset + length); i++) {
+        for (int i = offset; i < bytes.length; i++) {
             if (bytes[i] == 0) {
                 return i - offset;
             }
         }
-        return length - offset;
+        return bytes.length - offset;
     }
 
     protected int getRelativeStart(Variant variant) {

diff --git a/...rg/opencb/opencga/storage/hadoop/variant/archive/mr/VariantLocalConflictResolverTest.java b/...rg/opencb/opencga/storage/hadoop/variant/archive/mr/VariantLocalConflictResolverTest.java
@@ -169,7 +169,7 @@ public void resolveConflictIndelCase1() throws Exception {
         se.setSampleDataKeys(Arrays.asList(GENOTYPE_KEY, GENOTYPE_FILTER_KEY));
         se.setSamplesPosition(asMap("S1", 0));
         se.addSampleData("S1", Arrays.asList("1/2", "LowGQXHetDel"));
-        se.getSecondaryAlternates().add(new AlternateCoordinate(null, null, 328, "CTT", "CTTTC", INDEL));
+        se.getSecondaryAlternates().add(new AlternateCoordinate(null, 328, 330, "CTT", "CTTTC", INDEL));
         addAttribute(v1, FILTER, "LowGQXHetDel");