refinements and unit tests

* add TSS_DUP annotation category
* fix TSS and promoter inference and overlap determination
* handle 2nd breakpoint for BNDs in GATK-SV VCF format
* handle BND representation of CPX and CTX events for spec-compliant VCF format
* add option to annotate BNDs under a specified length as DEL or DUP if applicable
* style edits
* add unit tests for TSS, promoter, annotation of all SV types, and add toy GTF file for testing

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

@@ -74,6 +74,7 @@ public final class GATKSVVCFConstants {
     public static final String CPX_SV_REF_SEGMENTS = "SEGMENTS";
     public static final String CPX_EVENT_KEY = "CPX_EVENT";
     public static final String CPX_INTERVALS = "CPX_INTERVALS";
+    public static final String CPX_TYPE = "CPX_TYPE";
 
     // not defined in output vcf header but used in internal id that is currently output in the ID column
     public static final String INTERVAL_VARIANT_ID_FIELD_SEPARATOR = "_";
@@ -87,6 +88,8 @@ public final class GATKSVVCFConstants {
     public static final String DEPTH_ALGORITHM = "depth";
     public static final String END_CONTIG_ATTRIBUTE = "CHR2";
     public static final String END_CONTIG_POSITION = "END2";
+    public static final String BND_DELETION_STRANDS = "+-";
+    public static final String BND_DUPLICATION_STRANDS = "-+";
 
     // format block
     public static final String COPY_NUMBER_FORMAT = "CN";
@@ -114,6 +117,7 @@ public final class GATKSVVCFConstants {
     public static final String NONCODING_SPAN = "PREDICTED_NONCODING_SPAN";
     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";
 
     ///////////////////////////////////////////////////////////////////////////////////////////////////////////////////