From a1872278477448e3b3aeb6edc9e471d39c97b7fb Mon Sep 17 00:00:00 2001
From: Brent Pedersen <bpederse@gmail.com>
Date: Tue, 7 Mar 2017 15:30:06 -0700
Subject: [PATCH] add conf file for gnomad

---
 api/api.go          |  4 ++
 example/gnomad.conf | 92 +++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 96 insertions(+)
 create mode 100644 example/gnomad.conf

diff --git a/api/api.go b/api/api.go
index 52dc03b..65fab36 100644
--- a/api/api.go
+++ b/api/api.go
@@ -539,12 +539,16 @@ func (a *Annotator) PostAnnotate(chrom string, start int, end int, info interfac
 					vals = append(vals, val)
 				} else {
 					if e != nil {
+						//log.Println(field, e, vals, chrom, start, end)
 						err = e
 					}
 				}
 			}
 			// run this as long as we found any of the values.
 			if len(vals) != 0 {
+				if post.Op == "div2" && len(vals) < 2 {
+					continue
+				}
 				fn := Reducers[post.Op]
 				if post.Name == "ID" && prefix == "" {
 					newid = fmt.Sprintf("%s", fn(vals))
diff --git a/example/gnomad.conf b/example/gnomad.conf
new file mode 100644
index 0000000..bb1f011
--- /dev/null
+++ b/example/gnomad.conf
@@ -0,0 +1,92 @@
+[[annotation]]
+file="gnomad.exomes.r2.0.1.sites.no-VEP.nohist.tidy.vcf.gz"
+fields = ["AC", "AN", "AC_AFR", "AN_AFR", "AC_AMR", "AN_AMR", "AC_ASJ", "AN_ASJ", "AC_EAS", "AN_EAS", "AC_FIN", "AN_FIN", "AC_NFE", "AN_NFE", "AC_OTH", "AN_OTH", "AC_SAS", "AN_SAS"]
+
+names = ["ac_gnomad_all", "an_gnomad_all", "ac_gnomad_afr", "an_gnomad_afr", "ac_gnomad_amr", "an_gnomad_amr", "ac_gnomad_asj", "an_gnomad_asj", "ac_gnomad_eas", "an_gnomad_eas", "ac_gnomad_fin", "an_gnomad_fin", "ac_gnomad_nfe", "an_gnomad_nfe", "ac_gnomad_oth", "an_gnomad_oth", "ac_gnomad_sas", "an_gnomad_sas"]
+ops=["max", "self", "max", "self", "max", "self", "max", "self", "max", "self", "max", "self", "max", "self", "max", "self", "max", "self"] 
+
+[[annotation]]
+file="clinvar_20160203.tidy.vcf.gz"
+fields=["CLNSIG", "CLNDBN"]
+names=["clinvar_pathogenic", "clinvar_disease_name"]
+ops=["self", "self"]
+
+# convert 5 to 'pathogenic', 255 to 'unknown', etc.
+[[postannotation]]
+fields=["clinvar_pathogenic"]
+op="lua:clinvar_sig(clinvar_pathogenic)"
+name="clinvar_sig"
+type="String"
+
+# calculate allele frequencies for all populations.
+[[postannotation]]
+fields=["ac_gnomad_all", "an_gnomad_all"]
+name="af_gnomad_all"
+op="div2"
+type="Float"
+
+[[postannotation]]
+fields=["ac_gnomad_afr", "an_gnomad_afr"]
+name="af_gnomad_afr"
+op="div2"
+type="Float"
+
+[[postannotation]]
+fields=["ac_gnomad_amr", "an_gnomad_amr"]
+name="af_gnomad_amr"
+op="div2"
+type="Float"
+
+[[postannotation]]
+fields=["ac_gnomad_eas", "an_gnomad_eas"]
+name="af_gnomad_eas"
+op="div2"
+type="Float"
+
+[[postannotation]]
+fields=["ac_gnomad_fin", "an_gnomad_fin"]
+name="af_gnomad_fin"
+op="div2"
+type="Float"
+
+[[postannotation]]
+fields=["ac_gnomad_nfe", "an_gnomad_nfe"]
+name="af_gnomad_nfe"
+op="div2"
+type="Float"
+
+[[postannotation]]
+fields=["ac_gnomad_oth", "an_gnomad_oth"]
+name="af_gnomad_oth"
+op="div2"
+type="Float"
+
+[[postannotation]]
+fields=["ac_gnomad_sas", "an_gnomad_sas"]
+name="af_gnomad_sas"
+op="div2"
+type="Float"
+
+[[postannotation]]
+fields=["ac_gnomad_sas", "an_gnomad_sas"]
+name="af_gnomad_sas"
+op="div2"
+type="Float"
+
+[[postannotation]]
+fields=["ac_gnomad_asj", "an_gnomad_asj"]
+name="af_gnomad_asj"
+op="div2"
+type="Float"
+
+[[postannotation]]
+fields=['af_gnomad_afr', 'af_gnomad_amr', 'af_gnomad_eas', 'af_gnomad_fin', 'af_gnomad_nfe', 'af_gnomad_oth', 'af_gnomad_sas']
+op="max"
+name="max_aaf_all"
+type="Float"
+
+[[postannotation]]
+fields=["clinvar_sig", "max_aaf_all"]
+op="lua:check_clinvar_aaf(clinvar_sig, max_aaf_all, 0.005)"
+name="common_pathogenic"
+type="Flag"