Fix coordinate conversion for BEDPE files

src/main/scala/com/fulcrumgenomics/sv/BreakpointPileup.scala

@@ -11,11 +11,11 @@ import com.fulcrumgenomics.util.Metric
  *
  * @param id            an ID assigned to the breakpoint that can be used to lookup supporting reads in the BAM.
  * @param left_contig   the contig of chromosome on which the left hand side of the breakpoint exists.
- * @param left_pos      the position (possibly imprecise) of the left-hand breakend.
+ * @param left_pos      the position (possibly imprecise) of the left-hand breakend (1-based).
  * @param left_strand   the strand of the left-hand breakend; sequence reads would traverse this strand
  *                      in order to arrive at the breakend and transit into the right-hand side of the breakpoint.
  * @param right_contig  the contig of chromosome on which the left hand side of the breakpoint exists.
- * @param right_pos     the position (possibly imprecise) of the right-hand breakend.
+ * @param right_pos     the position (possibly imprecise) of the right-hand breakend (1-based).
  * @param right_strand  the strand of the right-hand breakend;. sequence reads would continue reading onto
  *                      this strand after transiting the breakpoint from the left breakend
  * @param split_reads   the number of templates/inserts with split-read alignments that identified this breakpoint.

src/main/scala/com/fulcrumgenomics/sv/tools/AggregateSvPileup.scala

@@ -46,7 +46,7 @@ import scala.collection.mutable
     |The output file is a tab-delimited table with one record per aggregated cluster of pileups. Aggregated
     |pileups are reported with the minimum and maximum (inclusive) coordinates of all pileups in the cluster, a
     |possible putative structural variant event type supported by the pileups, and the sum of read support from all
-    |pileups in the cluster.
+    |pileups in the cluster. Positions in this file are 1-based positions.
     |""")
 class AggregateSvPileup
 (@arg(flag='i', doc="Input text file of pileups generated by SvPileup") input: FilePath,
@@ -230,12 +230,12 @@ object BreakpointCategory extends Enumeration {
  * @param id                    Combined ID retaining the IDs of all constituent breakpoints
  * @param category              Breakpoint category
  * @param left_contig           Contig name for left side of breakpoint
- * @param left_min_pos          Minimum coordinate of left breakends
- * @param left_max_pos          Maximum coordinate of left breakends
+ * @param left_min_pos          Minimum coordinate of left breakends (1-based)
+ * @param left_max_pos          Maximum coordinate of left breakends (1-based)
  * @param left_strand           Strand at left breakends
  * @param right_contig          Contig name for right side of breakpoint
- * @param right_min_pos         Minimum coordinate of right breakends
- * @param right_max_pos         Maximum coordinate of right breakends
+ * @param right_min_pos         Minimum coordinate of right breakends (1-based)
+ * @param right_max_pos         Maximum coordinate of right breakends (1-based)
  * @param right_strand          Strand at right breakends
  * @param split_reads           Total number of split reads supporting the breakpoints in the cluster
  * @param read_pairs            Total number of read pairs supporting the breakpoints in the cluster

src/main/scala/com/fulcrumgenomics/sv/tools/AggregateSvPileupToBedPE.scala

@@ -73,11 +73,11 @@ object AggregateSvPileupToBedPE {
     def apply(pileup: AggregatedBreakpointPileup): BedPE = {
       new BedPE(
         chrom1  = pileup.left_contig,
-        start1  = pileup.left_min_pos,
-        end1    = pileup.left_max_pos + 1,
+        start1  = pileup.left_min_pos - 1,
+        end1    = pileup.left_max_pos,
         chrom2  = pileup.right_contig,
-        start2  = pileup.right_min_pos,
-        end2    = pileup.right_max_pos + 1,
+        start2  = pileup.right_min_pos - 1,
+        end2    = pileup.right_max_pos,
         name    = pileup.id,
         score   = pileup.total,
         strand1 = Strand.decode(pileup.left_strand),

src/main/scala/com/fulcrumgenomics/sv/tools/SvPileup.scala

@@ -47,9 +47,9 @@ object TargetBedRequirement extends FgBioEnum[TargetBedRequirement] {
     |
     |1. `<output-prefix>.txt`: a tab-delimited file describing SV pileups, one line per breakpoint event.  The returned
     |   breakpoint will be canonicalized such that the "left" side of the breakpoint will have the lower (or equal to)
-    |   position on the genome vs. the "right"s side.
+    |   position on the genome vs. the "right"s side. Positions in this file are 1-based positions.
     |2. `<output-prefix>.bam`: a SAM/BAM file containing reads that contain SV breakpoint evidence annotated with SAM
-    |  tag.
+    |   tag.
     |
     |The `be` SAM tag contains a comma-delimited list of breakpoints to which a given alignment belongs.  Each element is
     |semi-colon delimited, with four fields: