From 76f77af36fabab8709493d2db3dffac33fca31e9 Mon Sep 17 00:00:00 2001
From: Brent Pedersen <bpederse@gmail.com>
Date: Tue, 10 Sep 2019 12:40:40 -0600
Subject: [PATCH] support for more ALT types (e.g DUP:TANDEM, DEL:ME, etc)
closes #26
---
CHANGES.md | 5 +++++
duphold.nimble | 2 +-
src/duphold.nim | 33 ++++++++++++++++++---------------
src/dupholdpkg/version.nim | 2 +-
4 files changed, 25 insertions(+), 17 deletions(-)
diff --git a/CHANGES.md b/CHANGES.md
index a656a03..a9d111a 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -1,3 +1,8 @@
+v0.1.5
+======
++ support for more ALT types (e.g DUP:TANDEM, DEL:ME, etc)
++ flush stdout properly (#25)
+
v0.1.4
======
+ output DHSP for BND elements on same chrom
diff --git a/duphold.nimble b/duphold.nimble
index b4dd5c6..f997528 100644
--- a/duphold.nimble
+++ b/duphold.nimble
@@ -18,7 +18,7 @@ license = "MIT"
# Dependencies
-requires "hts >= 0.2.7", "genoiser >= 0.2.2", "docopt >= 0.6.8"
+requires "hts >= 0.2.21", "genoiser >= 0.2.2", "docopt >= 0.6.8"
srcDir = "src"
installExt = @["nim"]
diff --git a/src/duphold.nim b/src/duphold.nim
index e8b0893..c95895a 100644
--- a/src/duphold.nim
+++ b/src/duphold.nim
@@ -204,21 +204,24 @@ proc duphold*[T](variant:Variant, values:var seq[T], sample_i: int, stats:var Me
var
s = variant.start
e = variant.stop
+ isBnd = false
- var bnd = get_bnd_mate_pos(variant)
- var isBnd = false
- if bnd != -1:
- if bnd < s and s - bnd < 20000000:
- e = s
- s = bnd
- elif bnd > e and bnd - e < 20000000:
- s = e
- e = bnd - 1
- isBnd = true
-
- if bnd == -1:
- # skip distant BND's as this is not informative
- if ':' in variant.ALT[0]: return -1
+
+ if variant.ALT[0][0] != '<':
+ var bnd = get_bnd_mate_pos(variant)
+ var isBnd = false
+ if bnd != -1:
+ if bnd < s and s - bnd < 20000000:
+ e = s
+ s = bnd
+ elif bnd > e and bnd - e < 20000000:
+ s = e
+ e = bnd - 1
+ isBnd = true
+
+ if bnd == -1:
+ # skip distant BND's as this is not informative
+ if ':' in variant.ALT[0]: return -1
if e - s < 10:
s = max(0, s - 50)
@@ -276,7 +279,7 @@ proc duphold*[T](variant:Variant, values:var seq[T], sample_i: int, stats:var Me
if discordants.len == 0: return
- if isBnd or variant.ALT[0] == "<DEL>" or (variant.ALT[0] != "<" and len(variant.REF) > len(variant.ALT[0])):
+ if isBnd or variant.ALT[0].startswith("<DEL") or (variant.ALT[0] != "<" and len(variant.REF) > len(variant.ALT[0])):
var ints = newSeq[int32](variant.vcf.n_samples)
get_or_empty(variant, "DHSP", ints)
ints[sample_i] = discordants.count(s, e, i99).int32
diff --git a/src/dupholdpkg/version.nim b/src/dupholdpkg/version.nim
index 3c5c552..6c4e9d4 100644
--- a/src/dupholdpkg/version.nim
+++ b/src/dupholdpkg/version.nim
@@ -1 +1 @@
-const dupholdVersion* = "0.1.4"
+const dupholdVersion* = "0.1.5"