fix for #22

brentp · May 1, 2019 · 89327be · 89327be
1 parent 0f931a6
commit 89327be
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diff --git 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
@@ -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
@@ -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):
-Original file line number
+Diff line change
@@ Expand Up @@
     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
     ```
@@ Expand Down @@