v0.2.6: Really avoid removing reference calls when using sort-vcf on …

…structural variant calls. Thanks to @mjafin
chapmanb · Jul 17, 2015 · a2e13ca · a2e13ca
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diff --git a/HISTORY.md b/HISTORY.md
@@ -1,3 +1,9 @@
+## 0.2.6 (17 July 2015)
+
+- Really fix issues with removing reference calls when using `sort-vcf` on
+  structural variant calls.
+- Update clojure and associated libraries.
+
 ## 0.2.5 (16 July 2015)
 
 - Do not remove reference calls or do any chromosome renaming when sorting

diff --git a/README.md b/README.md
@@ -33,7 +33,7 @@ associated with different variant representations.
 
 ### Download
 
-The latest release is 0.2.5 (16 July 2015): [bcbio.variation-0.2.5-standalone.jar][dl].
+The latest release is 0.2.6 (17 July 2015): [bcbio.variation-0.2.6-standalone.jar][dl].
 Run from the command line:
 
     $ java -jar bcbio.variation-VERSION-standalone.jar [arguments]

diff --git a/project.clj b/project.clj
@@ -1,12 +1,12 @@
-(defproject bcbio.variation "0.2.5"
+(defproject bcbio.variation "0.2.6"
   :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"]
+  :dependencies [[org.clojure/clojure "1.7.0"]
                  [org.clojure/math.combinatorics "0.1.1" :exclusions [org.clojure/clojure]]
                  [org.clojure/data.csv "0.1.2" :exclusions [org.clojure/clojure]]
                  [org.clojure/tools.cli "0.2.2"]
                  [clj-stacktrace "0.2.5"]
-                 [bcbio.run "0.0.1"]
+                 [bcbio.run "0.0.5"]
                  ;; GATK requirements
                  [org.clojars.chapmanb/gatk-engine "3.2"]
                  [org.clojars.chapmanb/gatk-tools-public "3.2"]
@@ -48,10 +48,10 @@
                  [enlive "1.0.1" :exclusions [org.clojure/clojure]]]
   :min-lein-version "2.0.0"
   :plugins [[lein-marginalia "0.7.1"]
-            [lein-midje "3.0.1"]]
+            [lein-midje "3.1.3"]]
   :profiles {:dev {:dependencies
                    ;; Testing dependencies
-                   [[midje "1.5.1" :exclusions [org.clojure/clojure ordered]]
+                   [[midje "1.7.0" :exclusions [org.clojure/clojure ordered]]
                     ;; Non-uberjar dependencies we should extract into separate functionality
                     [incanter/incanter-core "1.5.1" :exclusions [org.clojure/clojure junit]]
                     [incanter/incanter-charts "1.5.1" :exclusions [org.clojure/clojure junit]]
@@ -60,8 +60,8 @@
                                                                     junit]]
                     [clj-genomespace "0.1.3"]
                     [clj-blend "0.1.1-SNAPSHOT"]
-                    [clj-aws-s3 "0.3.1" :exclusions [org.codehaus.jackson/jackson-mapper-asl
-                                                     org.codehaus.jackson/jackson-core-asl]]]}}
+                    [clj-aws-s3 "0.3.10" :exclusions [org.codehaus.jackson/jackson-mapper-asl
+                                                      org.codehaus.jackson/jackson-core-asl]]]}}
   :repositories {"sonatype-snapshots" {:url "http://oss.sonatype.org/content/repositories/snapshots"
                                        :snapshots true}}
   :java-source-paths ["src/java"]

diff --git a/src/bcbio/variation/utils/core.clj b/src/bcbio/variation/utils/core.clj
@@ -18,8 +18,9 @@
              ["-s" "--sortpos" "Sort by position" :flag true])]
     (normalize/prep-vcf vcf-file ref-file nil
                         :config {:prep-sort-pos (:sortpos options)
+                                 :prep-sv-genotype true
                                  :remove-refcalls false
-                                 :prep-org nil})))
+                                 :prep-org :default})))
 
 (def ^{:private true} progs
   {:callsummary callsummary/annotate-with-callsummary

diff --git a/test/bcbio/variation/test/multiple.clj b/test/bcbio/variation/test/multiple.clj
@@ -78,8 +78,9 @@
 
 (facts "Identify technology or caller specific variants from combined callsets"
   (with-open [vcf-iter (get-vcf-iterator union-file (-> config :experiments first :ref))]
-    (let [vc (first (parse-vcf vcf-iter))
-          vc2 (first (drop 4 (parse-vcf vcf-iter)))
+    (let [recs (vec (parse-vcf vcf-iter))
+          vc (first recs)
+          vc2 (first (drop 4 recs))
           calls (-> config :experiments first :calls)]
       (get-x-specific-designation vc calls) => {}
       (get-x-specific-designation vc2 calls) => {:technology "illumina"})))