Fix coordinate conversion for BEDPE files

docs/04_Metrics.md

@@ -29,12 +29,12 @@ Aggregated cluster of breakpoint pileups
 |id|String|Combined ID retaining the IDs of all constituent breakpoints|
 |category|BreakpointCategory|Breakpoint category|
 |left_contig|String|Contig name for left side of breakpoint|
-|left_min_pos|Int|Minimum coordinate of left breakends|
-|left_max_pos|Int|Maximum coordinate of left breakends|
+|left_min_pos|Int|Minimum coordinate of left breakends (1-based)|
+|left_max_pos|Int|Maximum coordinate of left breakends (1-based)|
 |left_strand|Char|Strand at left breakends|
 |right_contig|String|Contig name for right side of breakpoint|
-|right_min_pos|Int|Minimum coordinate of right breakends|
-|right_max_pos|Int|Maximum coordinate of right breakends|
+|right_min_pos|Int|Minimum coordinate of right breakends (1-based)|
+|right_max_pos|Int|Maximum coordinate of right breakends (1-based)|
 |right_strand|Char|Strand at right breakends|
 |split_reads|Int|Total number of split reads supporting the breakpoints in the cluster|
 |read_pairs|Int|Total number of read pairs supporting the breakpoints in the cluster|
@@ -82,10 +82,10 @@ the only information comes from read-pairs and the breakpoint information should
 |------|----|-----------|
 |id|String|An ID assigned to the breakpoint that can be used to lookup supporting reads in the BAM.|
 |left_contig|String|The contig of chromosome on which the left hand side of the breakpoint exists.|
-|left_pos|Int|The position (possibly imprecise) of the left-hand breakend.|
+|left_pos|Int|The position (possibly imprecise) of the left-hand breakend (1-based).|
 |left_strand|Char|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.|
 |right_contig|String|The contig of chromosome on which the left hand side of the breakpoint exists.|
-|right_pos|Int|The position (possibly imprecise) of the right-hand breakend.|
+|right_pos|Int|The position (possibly imprecise) of the right-hand breakend (1-based).|
 |right_strand|Char|The strand of the right-hand breakend;. sequence reads would continue reading onto                      this strand after transiting the breakpoint from the left breakend|
 |split_reads|Int|The number of templates/inserts with split-read alignments that identified this breakpoint.|
 |read_pairs|Int|The number of templates/inserts with read-pair alignments (and without split-read alignments)                      that identified this breakpoint.|

docs/tools/AggregateSvPileup.md

@@ -36,7 +36,7 @@ of the overlapping target regions are copied from the `SvPiluep` input (if prese
 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.
 
 ## Arguments
 

docs/tools/SvPileup.md

@@ -15,9 +15,9 @@ Two output files will be created:
 
 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:

docs/tools/index.md

@@ -4,7 +4,7 @@ title: fgsv tools
 
 # fgsv tools
 
-The following tools are available in fgsv version 0.1.1-acc9276.
+The following tools are available in fgsv version 0.2.0-d603e95.
 ## Breakpoint and SV Tools
 
 Primary tools for calling and transforming breakpoints and SVs.

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:

src/test/scala/com/fulcrumgenomics/sv/tools/AggregateSvPileupToBedPETest.scala

@@ -17,18 +17,18 @@ class AggregateSvPileupToBedPETest extends UnitSpec {
     id             = "112",
     category       = "Inter-contig rearrangement",
     left_contig    = "chr1",
-    left_min_pos   = 100,
-    left_max_pos   = 100,
+    left_min_pos   = 101,
+    left_max_pos   = 101,
     left_strand    = '+',
     right_contig   = "chr3",
-    right_min_pos  = 200,
-    right_max_pos  = 200,
+    right_min_pos  = 201,
+    right_max_pos  = 201,
     right_strand   = '-',
     split_reads    = 1,
     read_pairs     = 1,
     total          = 2,
-    left_pileups   = PositionList(100),
-    right_pileups  = PositionList(200),
+    left_pileups   = PositionList(101),
+    right_pileups  = PositionList(201),
   )
 
   /** A companion test BEDPE record. */