v0.2.3: roll out latest fixes and update to biojava4

HISTORY.md

@@ -1,3 +1,9 @@
+## 0.2.3 (1 February 2015)
+
+- Correctly handle sample names with all numbers -- parse as strings.
+- Handle BED inputs with non-system line breaks.
+- Update to BioJava 4.
+
 ## 0.2.2 (9 January 2015)
 
 - Ensemble calling: correctly handle inputs with same base filename in different

README.md

@@ -33,7 +33,7 @@ associated with different variant representations.
 
 ### Download
 
-The latest release is 0.2.1 (3 January 2015): [bcbio.variation-0.2.1-standalone.jar][dl].
+The latest release is 0.2.3 (1 February 2015): [bcbio.variation-0.2.3-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/v0.2.1/bcbio.variation-0.2.1-standalone.jar
+[dl]: https://github.com/chapmanb/bcbio.variation/releases/download/v0.2.3/bcbio.variation-0.2.3-standalone.jar
 
 ### As a library
 

project.clj

@@ -1,4 +1,4 @@
-(defproject bcbio.variation "0.2.3-SNAPSHOT"
+(defproject bcbio.variation "0.2.3"
   :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"]
@@ -22,8 +22,8 @@
                  [org.simpleframework/simple-xml "2.0.4"]
                  [org.apache.servicemix.bundles/org.apache.servicemix.bundles.jets3t "0.8.1_1"]
                  ;;
-                 [org.biojava/biojava3-core "4.0.0-SNAPSHOT"]
-                 [org.biojava/biojava3-alignment "4.0.0-SNAPSHOT"]
+                 [org.biojava/biojava-core "4.0.0"]
+                 [org.biojava/biojava-alignment "4.0.0"]
                  [org.clojars.chapmanb/circdesigna "0.0.2" :exclusions [net.sf.beaver/beaver-ant]]
                  [nz.ac.waikato.cms.weka/weka-stable "3.6.6"]
                  [org.clojars.chapmanb/fast-random-forest "0.98"]

src/bcbio/variation/complex.clj

@@ -3,8 +3,8 @@
    polymorphisms and indels."
   (:import [htsjdk.variant.variantcontext Allele
             VariantContextBuilder GenotypesContext GenotypeBuilder]
-           [org.biojava3.core.sequence DNASequence]
-           [org.biojava3.alignment Alignments SimpleGapPenalty
+           [org.biojava.nbio.core.sequence DNASequence]
+           [org.biojava.nbio.alignment Alignments SimpleGapPenalty
             Alignments$PairwiseSequenceScorerType])
   (:use [clojure.java.io]
         [clojure.set :only [union]]