v0.1.8: Prevent swapped headers/samples during prep in cases where multi-sample input files have not previously been through GATK. The GATK LeftAlign steps re-sort the samples and this header was not being correctly passed to the next step. Fixes #19

Author: chapmanb

HISTORY.md

@@ -1,5 +1,9 @@
-## 0.1.8 (in progress)
+## 0.1.8 (29 October 2014)
 
+- Fix variant-prep problem for multiple sample input where headers would get out
+  of sync with samples. Does not effect files previously run through GATK but
+  would cause problems with multiple sample inputs not sorted in standard GATK
+  sample manner.
 - Move to latest MIT licensed GATK release: 3.2
 - Library updates and fixes to work with java 1.8
 - Improve debugging output for failed lines during pre-clean step.

README.md

@@ -33,7 +33,7 @@ associated with different variant representations.
 
 ### Download
 
-The latest release is 0.1.7 (23 July 2014): [bcbio.variation-0.1.7-standalone.jar][dl].
+The latest release is 0.1.8 (29 October 2014): [bcbio.variation-0.1.8-standalone.jar][dl].
 Run from the command line:
 
     $ java -jar bcbio.variation-VERSION-standalone.jar [arguments]
@@ -44,7 +44,7 @@ the library for variant comparison, normalization and ensemble calling.  Note
 that bcbio.variation requires Java 1.7 since the underlying GATK libraries are
 not compatible with earlier versions.
 
-[dl]: https://github.com/chapmanb/bcbio.variation/releases/download/v0.1.7/bcbio.variation-0.1.7-standalone.jar
+[dl]: https://github.com/chapmanb/bcbio.variation/releases/download/v0.1.8/bcbio.variation-0.1.8-standalone.jar
 
 ### As a library
 

project.clj

@@ -1,4 +1,4 @@
-(defproject bcbio.variation "0.1.8-SNAPSHOT"
+(defproject bcbio.variation "0.1.8"
   :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"]

src/bcbio/variation/complex.clj

@@ -414,7 +414,7 @@
            (fs/delete out-pre-file))
          (let [la-file (left-align-variants in-file ref :out-dir out-dir :rerun? true)]
            (with-open [vcf-iter (get-vcf-iterator la-file ref)]
-             (write-vcf-w-template in-file {:out out-pre-file}
+             (write-vcf-w-template la-file {:out out-pre-file}
                                    (get-normalized-vcs (parse-vcf vcf-iter) ref)
                                    ref))
            (fs/rename (left-align-variants out-pre-file ref :out-dir out-dir :rerun? true)