Linx:

- filter out any SV filter except PASS, INFERRED or empty
hartwigmedical · Sep 13, 2019 · 1de2538 · 1de2538
1 parent 565358e
commit 1de2538
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Showing 3 changed files with 13 additions and 10 deletions.
diff --git a/...rc/main/java/com/hartwig/hmftools/common/variant/structural/StructuralVariantFactory.java b/...rc/main/java/com/hartwig/hmftools/common/variant/structural/StructuralVariantFactory.java
@@ -33,6 +33,7 @@ public class StructuralVariantFactory {
     public final static String RECOVERED = "RECOVERED";
     public final static String RECOVERY_METHOD = "RECOVERY_METHOD";
     public final static String RECOVERY_FILTER = "RECOVERY_FILTER";
+    public static final String PASS = "PASS";
     public static final String INFERRED = "INFERRED";
     public final static String CIPOS = "CIPOS";
     public final static String SVTYPE = "SVTYPE";
@@ -449,10 +450,10 @@ private static String filters(@NotNull VariantContext context, @Nullable Variant
         }
         if (filters.size() > 1) {
             // Doesn't pass if a filter is applied to either of the two records
-            filters.remove("PASS");
+            filters.remove(PASS);
         }
         if (filters.size() == 0) {
-            filters.add("PASS");
+            filters.add(PASS);
         }
         return filters.stream().sorted().collect(Collectors.joining(";"));
     }

diff --git a/sv-linx/src/main/java/com/hartwig/hmftools/linx/SvLinxApplication.java b/sv-linx/src/main/java/com/hartwig/hmftools/linx/SvLinxApplication.java
@@ -1,5 +1,7 @@
 package com.hartwig.hmftools.linx;
 
+import static com.hartwig.hmftools.common.variant.structural.StructuralVariantFactory.INFERRED;
+import static com.hartwig.hmftools.common.variant.structural.StructuralVariantFactory.PASS;
 import static com.hartwig.hmftools.common.variant.structural.StructuralVariantFactory.PON_FILTER_PON;
 import static com.hartwig.hmftools.linx.LinxConfig.DB_PASS;
 import static com.hartwig.hmftools.linx.LinxConfig.DB_URL;
@@ -259,13 +261,12 @@ private static List<SvVarData> createSvData(List<StructuralVariantData> svRecord
     {
         List<SvVarData> svVarDataItems = Lists.newArrayList();
 
-        for (final StructuralVariantData svRecord : svRecords) {
-
-            if(svRecord.filter().equals(PON_FILTER_PON))
-                continue;
-
-            // all others (currently PASS or blank) are accepted
-            svVarDataItems.add(new SvVarData(svRecord));
+        for (final StructuralVariantData svRecord : svRecords)
+        {
+            if(svRecord.filter().isEmpty() || svRecord.filter().equals(PASS) || svRecord.filter().equals(INFERRED))
+            {
+                svVarDataItems.add(new SvVarData(svRecord));
+            }
         }
 
         return svVarDataItems;

diff --git a/sv-linx/src/test/java/com/hartwig/hmftools/linx/utils/SvTestUtils.java b/sv-linx/src/test/java/com/hartwig/hmftools/linx/utils/SvTestUtils.java
@@ -1,5 +1,6 @@
 package com.hartwig.hmftools.linx.utils;
 
+import static com.hartwig.hmftools.common.variant.structural.StructuralVariantFactory.PASS;
 import static com.hartwig.hmftools.common.variant.structural.StructuralVariantType.BND;
 import static com.hartwig.hmftools.common.variant.structural.StructuralVariantType.DEL;
 import static com.hartwig.hmftools.common.variant.structural.StructuralVariantType.DUP;
@@ -85,7 +86,7 @@ public static SvVarData createTestSv(final int varId, final String chrStart, fin
             long posStart, long posEnd, int orientStart, int orientEnd, StructuralVariantType type,
             double cnStart, double cnEnd, double cnChgStart, double cnChgEnd, double ploidy, final String insertSeq)
     {
-        return createTestSv(varId, chrStart, chrEnd, posStart, posEnd, orientStart, orientEnd, type, cnStart, cnEnd, cnChgStart, cnChgEnd, ploidy, insertSeq, "PASS");
+        return createTestSv(varId, chrStart, chrEnd, posStart, posEnd, orientStart, orientEnd, type, cnStart, cnEnd, cnChgStart, cnChgEnd, ploidy, insertSeq, PASS);
     }
 
     public static SvVarData createTestSv(final int varId, final String chrStart, final String chrEnd,