Merge pull request #105 from yunfeiguo/quick_fix_distance_metric

Quick fix distance metric

pom.xml

@@ -95,6 +95,11 @@
             <artifactId>htsjdk</artifactId>
             <version>2.7.0</version>
         </dependency>
+	<dependency>
+	    <groupId>org.jgrapht</groupId>
+	    <artifactId>jgrapht-core</artifactId>
+	    <version>1.0.1</version>
+	</dependency>
         <dependency>
             <groupId>args4j</groupId>
             <artifactId>args4j</artifactId>
@@ -115,6 +120,11 @@
             <artifactId>commons-lang3</artifactId>
             <version>3.3.1</version>
         </dependency>
+        <dependency>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-math3</artifactId>
+            <version>3.6.1</version>
+        </dependency>
         <dependency>
             <groupId>org.apache.commons</groupId>
             <artifactId>commons-io</artifactId>

src/main/java/com/bina/varsim/types/variant/Variant.java

@@ -45,6 +45,11 @@ public class Variant implements Comparable<Variant>{
     private volatile int hashCode; //caching hashcode
     private List<Variant> compositions; //when this variant is a composite variant, this field will store constitutional variants
 
+    //additional INFO fields
+    private int threePrimeDistance = -1; //3' end distance with a matching variant
+    private int fivePrimeDistance = -1;//5' end distance with a matching variant
+    private int lengthDifference = -1; //length difference with a matching variant
+
 
     public List<Variant> getCompositions() {
         return compositions;
@@ -90,7 +95,6 @@ public static class Builder {
         private ChrString[] chr2;
         private int[] pos2;
         private int[] end2;
-        private int end;
         private Boolean isinv; //is sequence inverted? useful for interspersed dup, translocation dup
         private String traid; //translocation ID
         private List<Variant> compositions;
@@ -156,10 +160,6 @@ public Builder pos2(final int[] pos2) {
             this.pos2 = pos2;
             return this;
         }
-        public Builder end(final int end) {
-            this.end = end;
-            return this;
-        }
         public Builder end2(final int[] end2) {
             this.end2 = end2;
             return this;
@@ -197,7 +197,6 @@ private Variant(Builder builder) {
         this.paternal = builder.paternal;
         this.maternal = builder.maternal;
         this.isPhased = builder.isPhased;
-        this.end = builder.end;
         this.traid = builder.traid;
         this.isinv = builder.isinv;
         this.compositions = builder.compositions;
@@ -234,7 +233,6 @@ public Variant(final Variant var) {
         this.chr2 = var.chr2;
         this.pos2 = var.pos2;
         this.end2 = var.end2;
-        this.end = var.end;
         paternal = var.paternal;
         maternal = var.maternal;
         isPhased = var.isPhased;
@@ -388,8 +386,24 @@ public int[] getAllEnd2() {
         return this.end2;
     }
 
+    /**
+     * return 1-based end of variant depending on overall type of the variant
+     * for insertion, SNP, interspersed duplication, tandem duplication
+     * and translocation duplication, return 3' end
+     * otherwise, return 3' end plus length
+     * @return
+     */
     public int getEnd() {
-        return this.end;
+        switch(getType()) {
+            case Insertion:
+            case SNP:
+            case InterDup:
+            case TandemDup:
+            case TransDup:
+                return pos;
+            default:
+                return pos + maxLen() - 1;
+        }
     }
 
     public String getTraid() {
@@ -748,6 +762,18 @@ public void setAlt(final int ind, Alt alt) {
             alts[ind - 1] = alt;
     }
 
+    public void setThreePrimeDistance(int threePrimeDistance) {
+        this.threePrimeDistance = threePrimeDistance;
+    }
+
+    public void setFivePrimeDistance(int fivePrimeDistance) {
+        this.fivePrimeDistance = fivePrimeDistance;
+    }
+
+    public void setLengthDifference(int lengthDifference) {
+        this.lengthDifference = lengthDifference;
+    }
+
     public String getFilter() {
         return filter;
     }
@@ -1005,6 +1031,7 @@ public void calculateExtraBase(final Sequence refSeq) {
     /**
      * @return a VCF record of the variant
      */
+    @Override
     public String toString() {
         return toString(getGoodPaternal(), getGoodMaternal());
     }
@@ -1085,6 +1112,24 @@ public String toString(final int paternal, final int maternal) {
             sbStr.append("SVLEN=");
             sbStr.append(getLengthString());
         }
+        /*
+        checking -1 is for backward compatibility
+        if output_distance_metric is disabled,
+        then these INFO fields will not be set
+        nor reported.
+         */
+        if (threePrimeDistance != -1) {
+            sbStr.append(";3PrimeDistance=");
+            sbStr.append(threePrimeDistance);
+        }
+        if (fivePrimeDistance != -1) {
+            sbStr.append(";5PrimeDistance=");
+            sbStr.append(fivePrimeDistance);
+        }
+        if (lengthDifference != -1) {
+            sbStr.append(";LengthDifference=");
+            sbStr.append(lengthDifference);
+        }
         sbStr.append("\t");
 
         // label (GT)

src/test/java/com/bina/varsim/tools/evaluation/VCFCompareTest.java

@@ -219,4 +219,54 @@ public void breakendEvaluationDifferentDuplicationOrientations() throws IOExcept
   public void breakendEvaluationNonReciprocalBalancedWithLargeWiggle() throws IOException {
     universalTestMethod("src/test/resources/validationTest/breakendTests/nonreciprocalBalancedWithLargeWiggle", new String[]{"-wig", "10"});
   }
+  /******tests for distance-based metrics**************/
+  /**
+   * 1 SNP in TP, 1 SNP in compare, with 1-bp distance
+   *
+   */
+  @Test
+  public void distanceSNPTest() throws IOException {
+    universalTestMethod("src/test/resources/validationTest/distanceMetricTests/snpDistance", new String[]{"-output_distance_metric"});
+  }
+  /**
+   * 1 INS in TP, 1 INS in compare, with 100-bp 3' distance, 100-bp 5' distance, 100bp length difference
+   *
+   */
+  @Test
+  public void distanceINSTest() throws IOException {
+    universalTestMethod("src/test/resources/validationTest/distanceMetricTests/insDistance", new String[]{"-wig", "150","-over","0.5","-output_distance_metric"});
+  }
+  /**
+   * 1 INV in TP, 1 INV in compare, with 1000-bp 3' distance, 11000-bp 5' distance, 100bp length difference
+   *
+   */
+  @Test
+  public void distanceINVTest() throws IOException {
+    universalTestMethod("src/test/resources/validationTest/distanceMetricTests/invDistance", new String[]{"-wig", "2000","-over","0.55","-output_distance_metric"});
+  }
+  /**
+   * 1 DEL in TP with 2 ALTs, 1 DEL in compare with 1 ALT, matching only one of the 2 ALTS in TP
+   *
+   */
+  @Test
+  public void distanceDELTest() throws IOException {
+    universalTestMethod("src/test/resources/validationTest/distanceMetricTests/delDistance", new String[]{"-wig", "10","-over","0.5","-output_distance_metric"});
+  }
+  /**
+   * 1 DUP in TP, 1 DUP in compare, length the same, distance 10bp
+   *
+   */
+  @Test
+  public void distanceDUPTest() throws IOException {
+    universalTestMethod("src/test/resources/validationTest/distanceMetricTests/dupDistance", new String[]{"-wig", "20","-over","0.7","-output_distance_metric"});
+  }
+  /**
+   * 1 DEL in TP, 2 DEL in compare, length the same, distance 30bp,10bp, respectively
+   * wiggle=50bp, both DEL in compare can match, but we only match the closest one
+   */
+  @Test
+  public void distanceMultipleMatchingTest() throws IOException {
+    //disabled until global matching is implemented
+    //universalTestMethod("src/test/resources/validationTest/distanceMetricTests/multipleMatchingDistance", new String[]{"-wig", "50","-over","0.7","-output_distance_metric"});
+  }
 }

src/test/resources/validationTest/distanceMetricTests/delDistance/compare.vcf

@@ -0,0 +1 @@
+chrX	976	.	N	<DEL>	.	.	SVTYPE=DEL;SVLEN=-200	GT	1/0

src/test/resources/validationTest/distanceMetricTests/delDistance/test_TP.vcf

@@ -0,0 +1 @@
+X	876	.	N	<DEL>,<DEL>	.	.	SVTYPE=DEL;SVLEN=-200,-200;3PrimeDistance=100;5PrimeDistance=100;LengthDifference=0	GT	1|2

src/test/resources/validationTest/distanceMetricTests/delDistance/test_report.json

@@ -0,0 +1 @@
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