v0.1.8: fix tabix index error for variants at position 1 of contigs.

Fixes bcbio/bcbio-nextgen#2383
bcbio · May 18, 2018 · a22b08a · a22b08a
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diff --git a/HISTORY.md b/HISTORY.md
@@ -1,3 +1,7 @@
+## 0.1.8 (18 May 2018)
+
+- Fix tabix index error for variants present at position 1 of contigs.
+
 ## 0.1.7 (15 August 2016)
 
 - Avoid FreeBayes error when running `--variant-input` without an empty VCF.

diff --git a/project.clj b/project.clj
@@ -1,4 +1,4 @@
-(defproject bcbio.variation.recall "0.1.7"
+(defproject bcbio.variation.recall "0.1.8"
   :description "Parallel merging, squaring off and ensemble calling for genomic variants."
   :url "https://github.com/chapmanb/bcbio.variation.recall"
   :license {:name "MIT" :url "http://www.opensource.org/licenses/mit-license.html"}

diff --git a/src/bcbio/variation/variantcontext.clj b/src/bcbio/variation/variantcontext.clj
@@ -107,7 +107,7 @@
      (variants-in-region retriever (:chr vc) (:start vc) (:end vc)))
   ([retriever space start end]
      (letfn [(get-vcs-in-source [[source fname]]
-               (with-open [vcf-iter (.query source space start end)]
+               (with-open [vcf-iter (.query source space (max 1 start) end)]
                  (doall (map #(assoc (from-vc %) :fname fname) (iterator-seq vcf-iter)))))]
        (mapcat get-vcs-in-source (map vector (:sources retriever) (:fnames retriever))))))