From c37c6a2e2e84b0f3c353de19200934fe85269ff2 Mon Sep 17 00:00:00 2001 From: chapmanb Date: Sun, 6 Apr 2014 13:57:32 -0400 Subject: [PATCH] Include evaluation calls instead of reference calls in concordant output. Thanks to Severine Catreux --- HISTORY.md | 2 ++ src/bcbio/variation/compare.clj | 2 +- test/bcbio/variation/test/compare.clj | 2 +- test/bcbio/variation/test/multiple.clj | 2 +- 4 files changed, 5 insertions(+), 3 deletions(-) diff --git a/HISTORY.md b/HISTORY.md index 09cdc7f..f373e58 100644 --- 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 index 941f4f2..a87e46a 100644 --- 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 index 7990d4d..3b1ffd8 100644 --- 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 index 6a1f904..33f6587 100644 --- 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]))