closes #3

CHANGES.md

@@ -1,3 +1,7 @@
+v0.0.5
+======
++ fix bug that occurred with SVs near either end of chromosome (brentp/duphold#2). thanks Brad for reporting and providing a test-case.
+
 v0.0.4
 ======
 + small bug-fixes

duphold.nimble

@@ -1,6 +1,6 @@
 # Package
 
-version       = "0.0.5-dev"
+version       = "0.0.5"
 author        = "Brent Pedersen"
 description   = "find depth support for DUP/DEL/CNV calls that use PE/SR"
 license       = "MIT"

src/duphold.nim

@@ -101,7 +101,7 @@ proc get_or_empty[T](variant:Variant, field:string, input:var seq[T]) =
     else:
         quit "unknown type in get_or_empty"
 
-proc check_rapid_depth_change[T](start:int, stop:int, values: var seq[T], w:int=7): int32 =
+proc check_rapid_depth_change*[T](start:int, stop:int, values: var seq[T], w:int=7): int32 =
     ## if start and end indicate the bounds of a deletion, we can often expect to see a rapid change in
     ## depth at or near the break-point.
     var
@@ -115,7 +115,7 @@ proc check_rapid_depth_change[T](start:int, stop:int, values: var seq[T], w:int=
     for bi, bp in @[start, stop]:
       var
         close_changes = 0
-        cs = bp - dist
+        cs = max(w, bp - dist - w)
         left = Stats()
         right = Stats()
 
@@ -124,7 +124,7 @@ proc check_rapid_depth_change[T](start:int, stop:int, values: var seq[T], w:int=
       for i in cs..<(cs + w):
           right.addm(values[i])
 
-      for k in cs..(bp + dist + w):
+      for k in cs..min(bp + dist + w, values.len - w - 1):
         if (k - last_change) > w:
             var
                 lm = left.mean

tests/all.nim

@@ -0,0 +1 @@
+import ./duphold_tests

tests/duphold_tests.nim

@@ -0,0 +1,18 @@
+import unittest
+import duphold
+
+suite "test duphold":
+  test "test start near 0":
+      var values = newSeq[int32](2000)
+      for i, v in values:
+          values[i] = i.int32
+      var r = check_rapid_depth_change[int32](0, 2, values, w=7)
+      check r >= 0
+
+  test "test end near chrom length":
+      var values = newSeq[int32](2000)
+      for i, v in values:
+          values[i] = i.int32
+      for w in 1..70:
+          var r = check_rapid_depth_change[int32](values.len - 3, values.len - 1, values, w=w)
+          check r >= 0

tests/nim.cfg

@@ -0,0 +1 @@
+path = "$projectPath/../src"