add sv+gff example

api/api.go

@@ -1,6 +1,7 @@
 package api
 
 import (
+	"bytes"
 	"fmt"
 	"log"
 	"os"
@@ -359,6 +360,10 @@ func collect(v interfaces.IVariant, rels []interfaces.Relatable, src *Source, st
 			if !ok {
 				continue
 			}
+			if src.Column-1 >= len(o.Fields) {
+				log.Println(src)
+				log.Println(string(bytes.Join(o.Fields, []byte{'\t'})))
+			}
 			sval := string(o.Fields[src.Column-1])
 			if src.IsNumber() {
 

docs/examples/gff_sv/gff_gene_name.lua

@@ -0,0 +1,27 @@
+function gff_to_gene_name(infos, name_field)
+    if infos == nil or #infos == 0 then
+        return nil
+    end
+    local result = {}
+
+    for i=1,#infos do
+        info = infos[i]
+        local s, e = string.find(info, name_field .. "=")
+        if s ~= nil then
+            name = info:sub(e + 1)
+            s, e = string.find(name, ";")
+            if e == nil then
+                e = name:len()
+            else
+                e = e - 1
+            end
+
+            result[name:sub(0, e)] = 1
+        end
+    end
+    local keys = {}
+    for k, v in pairs(result) do
+        keys[#keys+1] = k
+    end
+    return table.concat(keys,",")
+end

docs/examples/gff_sv/gff_sv.conf

@@ -0,0 +1,5 @@
+[[annotation]]
+file="sample.gff3.gz"
+columns=[9]
+names=["xgene"]
+ops=["lua:gff_to_gene_name(vals, 'gene_name')"]

docs/examples/gff_sv/gff_sv.md

@@ -0,0 +1,49 @@
+Annotating with GFF
+===================
+
+GFF often contains the location of genes and features.
+It has a column that contains key=value pairs like the INFO
+field in a VCF. `vcfanno` does not support these natively,
+but one can access particular fields using lua. This is an example of
+how to do this.
+
+Given a variant in `sample.vcf` like:
+```
+22	1000	DEL000SUR	N	<DEL>	.	PASS	END=1051060
+```
+
+And genomic features annotated in `genes.gff3.gz`:
+
+```
+22	ensembl_havana	gene	69091	70008	.	+	.	ID=ENST00000335137;geneID=ENSG00000186092;gene_name=OR4F5
+22	ensembl	mRNA	182393	184158	.	+	.	ID=ENST00000624431;geneID=ENSG00000279928;gene_name=FO538757.3
+22	ensembl	mRNA	184923	195411	.	-	.	ID=ENST00000623834;geneID=ENSG00000279457;gene_name=FO538757.2
+22	ensembl	mRNA	184925	195411	.	-	.	ID=ENST00000623083;geneID=ENSG00000279457;gene_name=FO538757.2
+22	ensembl	mRNA	184927	200322	.	-	.	ID=ENST00000624735;geneID=ENSG00000279457;gene_name=FO538757.2
+22	ensembl_havana	mRNA	450740	451678	.	-	.	ID=ENST00000426406;geneID=ENSG00000278566;gene_name=OR4F29
+22	ensembl_havana	mRNA	685716	686654	.	-	.	ID=ENST00000332831;geneID=ENSG00000273547;gene_name=OR4F16
+22	havana	mRNA	924880	939291	.	+	.	ID=ENST00000420190;geneID=ENSG00000187634;gene_name=SAMD11
+22	havana	mRNA	925150	935793	.	+	.	ID=ENST00000437963;geneID=ENSG00000187634;gene_name=SAMD11
+...
+```
+
+We can write a conf file [gff_sv.conf](https://github.com/brentp/vcfanno/blob/master/docs/examples/gff_sv/gff_sv.conf)
+```
+[[annotation]]
+file="genes.gff3.gz"
+columns=[9]
+names=["gene"]
+ops=["lua:gff_to_gene_name(vals, 'gene_name')"]
+```
+
+This will extract the full text of the 9th column. Then we can use some lua to get just the `gene_name` field.
+The lua uses a table so each observed gene is reported only once.
+This is in [gff_sv.lua](https://github.com/brentp/vcfanno/blob/master/docs/examples/gff_sv/gff_sv.lua)
+
+
+Then we can run `vcfanno` as:
+```
+vcfanno -lua gff_sv.lua gff_sv.conf sample.vcf
+```
+
+and `gene=FO538757.3,OR4F29,FO538757.2,OR4F16,OR4F5` is added to the INFO. The lua allows the user to do more complex things like only reporting genes, or taking uniq values.