Rewrite complex SV functional annotation in SVAnnotate

src/main/java/org/broadinstitute/hellbender/tools/spark/sv/utils/GATKSVVCFConstants.java

@@ -89,7 +89,9 @@ public enum ComplexVariantSubtype {
         piDUP_RF,
         dDUP,
         dDUP_iDEL,
-        INS_iDEL
+        INS_iDEL,
+        CTX_PP_QQ,
+        CTX_PQ_QP
     }
 
     // not defined in output vcf header but used in internal id that is currently output in the ID column
@@ -163,6 +165,7 @@ public enum ComplexVariantSubtype {
     public static final String NONCODING_BREAKPOINT = "PREDICTED_NONCODING_BREAKPOINT";
     public static final String NEAREST_TSS = "PREDICTED_NEAREST_TSS";
     public static final String TSS_DUP = "PREDICTED_TSS_DUP";
+    public static final String PARTIAL_DISPERSED_DUP = "PREDICTED_PARTIAL_DISPERSED_DUP";
 
     // SVTYPE classes
     public enum StructuralVariantAnnotationType {

src/main/java/org/broadinstitute/hellbender/tools/walkers/sv/SVAnnotate.java

@@ -123,6 +123,11 @@
  *     duplicated. The partial duplication occurs when a duplication has one breakpoint within the transcript and one
  *     breakpoint after the end of the transcript. When the duplication is in tandem, the result is that there is one
  *     intact copy of the full endogenous gene.</p></li>
+ *     <li><p><i>PREDICTED_PARTIAL_DISPERSED_DUP</i><br />
+ *     Gene(s) which are partially overlapped by the duplicated segment involved in an SV's dispersed duplication.
+ *     This annotation is applied to a dispersed (non-tandem) duplication segment that is part of a complex SV if the
+ *     duplicated segment overlaps part of a transcript but not the entire transcript (which would be a
+ *     PREDICTED_COPY_GAIN event).</p></li>
  *     <li><p><i>PREDICTED_INV_SPAN</i><br />
  *     Gene(s) which are entirely spanned by an SV's inversion. A whole-gene inversion occurs when an inversion spans
  *     the entire transcript, from the first base of the 5' UTR to the last base of the 3' UTR. </p></li>
@@ -354,6 +359,7 @@ private void addAnnotationInfoKeysToHeader(final VCFHeader header) {
         header.addMetaDataLine(new VCFInfoHeaderLine(GATKSVVCFConstants.NONCODING_SPAN, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "Class(es) of noncoding elements spanned by SV."));
         header.addMetaDataLine(new VCFInfoHeaderLine(GATKSVVCFConstants.NONCODING_BREAKPOINT, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "Class(es) of noncoding elements disrupted by SV breakpoint."));
         header.addMetaDataLine(new VCFInfoHeaderLine(GATKSVVCFConstants.NEAREST_TSS, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "Nearest transcription start site to an intergenic variant."));
+        header.addMetaDataLine(new VCFInfoHeaderLine(GATKSVVCFConstants.PARTIAL_DISPERSED_DUP, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "Gene(s) overlapped partially by the duplicated interval involved in a dispersed duplication event in a complex SV."));
 
     }
 

src/main/java/org/broadinstitute/hellbender/utils/SimpleInterval.java

@@ -1,6 +1,7 @@
  package org.broadinstitute.hellbender.utils;
 
 
+import com.google.common.annotations.VisibleForTesting;
 import htsjdk.samtools.SAMSequenceDictionary;
 import htsjdk.samtools.SAMSequenceRecord;
 import htsjdk.samtools.util.Locatable;
@@ -275,6 +276,25 @@ public SimpleInterval intersect( final Locatable that ) {
                  Math.min( getEnd(), that.getEnd()) );
      }
 
+     /**
+      * Get section of starting interval (this) that is not overlapped by the other interval (that)
+      * @param that - interval to subtract from starting interval. Must overlap (but not fully contain) starting interval
+      * @return - SimpleInterval representing the portion of starting interval (this) not overlapped by other interval (that)
+      */
+     @VisibleForTesting
+     public SimpleInterval subtract(final Locatable that) {
+         Utils.validateArg(this.overlaps(that), () ->
+                 "SimpleIntervaL::subtract(): The two intervals need to overlap: " + this + ", " + that);
+         Utils.validateArg(!that.contains(this), () ->
+                 "SimpleIntervaL::subtract(): Interval to subtract " + that + " cannot contain starting interval " + this);
+         if (this.getStart() < that.getStart()) {
+             return new SimpleInterval(this.getContig(), this.getStart(), that.getStart());
+         }
+         else {
+             return new SimpleInterval(this.getContig(), that.getEnd(), this.getEnd());
+         }
+     }
+
      /**
       * Returns a new SimpleInterval that represents the entire span of this and that.  Requires that
       * this and that SimpleInterval are contiguous.