Include evaluation calls instead of reference calls in concordant out…

…put. Thanks to Severine Catreux
chapmanb · Apr 6, 2014 · c37c6a2 · c37c6a2
1 parent ae632b0
commit c37c6a2
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diff --git a/HISTORY.md b/HISTORY.md
@@ -4,6 +4,8 @@
   variant calling. Thanks to Shalabh Suman.
 - Prioritize depth attribute when choosing representative callset from multiple
   choices during Ensemble calling. Thanks to Shalabh Suman.
+- Use evaluation calls instead of reference calls in concordance output. Thanks
+  to Severine Catreux.
 - Avoid identifying mitochondrial-only test datasets as haploid reference genomes.
 
 ## 0.1.5 (15 March 2014)

diff --git a/src/bcbio/variation/compare.clj b/src/bcbio/variation/compare.clj
@@ -52,7 +52,7 @@
     (if-not (fs/exists? base-dir)
       (fs/mkdirs base-dir))
     (doall
-     (for [[c1 c2 cmp-type] [[call1 call2 "concordance"]
+     (for [[c1 c2 cmp-type] [[call2 call1 "concordance"]
                              [call1 call2 "discordance"]
                              [call2 call1 "discordance"]]]
        (let [file-info {:out-vcf (str (fs/file base-dir

diff --git a/test/bcbio/variation/test/compare.clj b/test/bcbio/variation/test/compare.clj
@@ -63,7 +63,7 @@
                match-out {:concordant (fsp/add-file-part combo-out "concordant")
                           :discordant (fsp/add-file-part combo-out "discordant")}
                select-out (doall (map #(str (fs/file data-dir (format "%s-%s.vcf" sample %)))
-                                      ["gatk-freebayes-concordance"
+                                      ["freebayes-gatk-concordance"
                                        "gatk-freebayes-discordance"
                                        "freebayes-gatk-discordance"]))
                out-callable (map #(format "%s-%s.bed" (fsp/file-root align-bam) %)

diff --git a/test/bcbio/variation/test/multiple.clj b/test/bcbio/variation/test/multiple.clj
@@ -86,4 +86,4 @@
 
 (facts "Identify variants with less call support"
   (with-open [vcf-iter (get-vcf-iterator union-file (-> config :experiments first :ref))]
-    (take 5 (map #(poor-call-support? % :thresh {:dp 250 :ad -0.1}) (parse-vcf vcf-iter))) => [false true false false false]))
+    (take 5 (map #(poor-call-support? % :thresh {:dp 250 :ad -0.1}) (parse-vcf vcf-iter))) => [false false false false false]))