Include genotype quality in output Ensemble called VCFs. Thanks to Sh…

…alabh Suman

project.clj

@@ -1,4 +1,4 @@
-(defproject bcbio.variation "0.1.3"
+(defproject bcbio.variation "0.1.4-SNAPSHOT"
   :description "Toolkit to analyze genomic variation data, built on the GATK with Clojure"
   :license {:name "MIT" :url "http://www.opensource.org/licenses/mit-license.html"}
   :dependencies [[org.clojure/clojure "1.5.1"]

src/bcbio/variation/recall.clj

@@ -58,7 +58,7 @@
        :call-type (:type g)
        :ref-allele (:ref-allele vc)
        :alleles (sort-by allele-order (:alleles g))
-       :attributes (select-keys (:attributes g) ["PL" "DP" "AD" "PVAL"])
+       :attributes (select-keys (:attributes g) ["PL" "DP" "AD" "PVAL" "GQ"])
        :has-likelihood (if (seq (get-in g [:attributes "PL"])) 1 0)
        :attr-count (+ (if (seq (get-in g [:attributes "PL"])) 1 0)
                       (if (seq (get-in g [:attributes "PVAL"])) 1 0)
@@ -128,7 +128,7 @@
           (.attributes (-> (map :attributes (reverse other-vcs))
                            (#(apply merge %))
                            (assoc "set" (update-set-info (get-in vc [:attributes "set"]) calls))))
-          (.genotypes (gvc/create-genotypes most-likely-gs :attrs #{"PL" "PVAL" "DP" "AD" "AO"}))
+          (.genotypes (gvc/create-genotypes most-likely-gs :attrs #{"PL" "PVAL" "DP" "AD" "AO" "GQ"}))
           .make))))
 
 (defn- recall-w-consensus

src/bcbio/variation/variantcontext.clj

@@ -230,6 +230,7 @@
   [gs & {:keys [attrs]}]
   (let [all-attrs [["PL" seq (fn [x _ v] (.PL x (int-array v)))]
                    ["PVAL" identity (fn [x k v] (.attribute x k v))]
+                   ["GQ" identity (fn [x _ v] (.GQ x v))]
                    ["DP" identity (fn [x _ v] (.DP x v))]
                    ["AD" seq (fn [x _ v] (.AD x (int-array v)))]
                    ["AO" identity (fn [x a v] (.attribute x a v))]]]