From 89327beeee482346fb234270b32f844f4b5dd4dd Mon Sep 17 00:00:00 2001
From: Brent Pedersen <bpederse@gmail.com>
Date: Wed, 1 May 2019 07:28:58 -0600
Subject: [PATCH] fix for #22

---
 CHANGES.md      | 1 +
 README.md       | 2 +-
 src/duphold.nim | 2 +-
 3 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/CHANGES.md b/CHANGES.md
index 96dd183..a656a03 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -1,6 +1,7 @@
 v0.1.4
 ======
 + output DHSP for BND elements on same chrom
++ fix for #22: allow GQ of type Integer or Float
 
 v0.1.3
 ======
diff --git a/README.md b/README.md
index ee7062b..9908476 100644
--- a/README.md
+++ b/README.md
@@ -23,7 +23,7 @@ It also adds **GCF** to the INFO field indicating the fraction of G or C bases i
 After annotating with `duphold`, a sensible way to filter to high-quality variants is:
 
 ```
-bcftools view -i '(SVTYPE = "DEL" & FMT/DHFFC[0] < 0.7) | (SVTYPE = "DUP" & FMT/DHBFC[0] > 1.3)" $svvcf
+bcftools view -i '(SVTYPE = "DEL" & FMT/DHFFC[0] < 0.7) | (SVTYPE = "DUP" & FMT/DHBFC[0] > 1.3)' $svvcf
 
 ```
 
diff --git a/src/duphold.nim b/src/duphold.nim
index e0b247d..a7e0e53 100644
--- a/src/duphold.nim
+++ b/src/duphold.nim
@@ -494,7 +494,7 @@ proc read(snps:VCF, chrom:string): snpset =
       gq.setLen(o.len)
       for i, v in o:
         gq[i] = v.int32
-    else:
+    elif st != Status.OK:
       quit "expected GQ field in snps VCF"
 
     if not hq(0, gq, ad, alts):