amber: Bug Fix: fix NullPointerException when no -ref_genome argument…

… is provided
hartwigmedical · Feb 15, 2022 · b990584 · b990584
1 parent bc0a83a
commit b990584
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diff --git a/amber/README.md b/amber/README.md
@@ -23,7 +23,7 @@ After installing [R](https://www.r-project.org/) or [RStudio](https://rstudio.co
     install("copynumber")
 ```
 
-AMBER requires Java 1.8+ to be installed.
+AMBER requires Java 11+ to be installed.
 
 ## Paired Normal/Tumor Mode
 This is the default and recommended mode.
@@ -106,7 +106,6 @@ No change is made to the SNPCheck or contamination output. These will be run on
 
 ```
 java -Xmx32G -cp amber.jar com.hartwig.hmftools.amber.AmberApplication \
-   -tumor_only \
    -tumor COLO829T -tumor_bam /run_dir/COLO829T.bam \ 
    -output_dir /run_dir/amber/ \
    -threads 16 \
@@ -205,6 +204,8 @@ Peak memory is measure in gigabytes.
 
 
 # Version History and Download Links
+- [3.7](https://github.com/hartwigmedical/hmftools/releases/tag/amber-v3.7)
+  - Fixed `NullPointerException` when no `-ref_genome` argument is provided
 - [3.6](https://github.com/hartwigmedical/hmftools/releases/tag/amber-v3.6)
   - Added detection of regions of homozygosity, consanguinity proportion and uniparentaldisomy.
   - Remove `tumor_only` config.

diff --git a/amber/src/main/java/com/hartwig/hmftools/amber/AmberApplication.java b/amber/src/main/java/com/hartwig/hmftools/amber/AmberApplication.java
@@ -296,7 +296,7 @@ private static <T> List<T> getFuture(final List<Future<T>> futures) throws Execu
     private static SamReaderFactory readerFactory(final AmberConfig config)
     {
         final SamReaderFactory readerFactory = SamReaderFactory.make().validationStringency(config.Stringency);
-        if(!config.RefGenomePath.isEmpty())
+        if(config.RefGenomePath != null)
         {
             return readerFactory.referenceSource(new ReferenceSource(new File(config.RefGenomePath)));
         }

diff --git a/pom.xml b/pom.xml
@@ -57,7 +57,7 @@
 
         <hmf-common.version>local-SNAPSHOT</hmf-common.version>
 
-        <amber.version>3.6</amber.version>
+        <amber.version>3.7</amber.version>
         <ckb-importer.version>1.3</ckb-importer.version>
         <cobalt.version>1.12</cobalt.version>
         <compar.version>1.0</compar.version>