Trim off stray whitespace in BED file input to handle problematic lin…

…e breaks. #24
chapmanb · Jan 15, 2015 · e977673 · e977673
1 parent bd7af84
commit e977673
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Showing 2 changed files with 4 additions and 3 deletions.
diff --git a/project.clj b/project.clj
@@ -1,4 +1,4 @@
-(defproject bcbio.variation "0.2.2"
+(defproject bcbio.variation "0.2.3-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"]

diff --git a/src/bcbio/align/ref.clj b/src/bcbio/align/ref.clj
@@ -76,9 +76,10 @@
   (let [ref-map (get-seq-name-map ref-file)
         is-tab? (with-open [rdr (reader bed-file)]
                   (.contains (first (drop-while #(.startsWith % "track") (line-seq rdr))) "\t"))]
-    (fn [line]
+    (fn [raw-line]
       (when-not (.startsWith line "track")
-        (let [parts (if is-tab?
+        (let [line (string/trimr raw-line)
+              parts (if is-tab?
                       (string/split line #"\t")
                       (string/split line #" "))]
           (let [[chr start end] (take 3 parts)]