Merge pull request #343 from BimberLab/25.3_fb_htsjdk

Update HTSJDK and picard versions

Author: bbimber

SequenceAnalysis/build.gradle

@@ -124,7 +124,7 @@ dependencies {
     BuildUtils.addExternalDependency(
             project,
             new ExternalDependency(
-                    "com.github.broadinstitute:picard:3.1.0",
+                    "com.github.broadinstitute:picard:3.4.0",
                     "Picard Tools Lib",
                     "PicardTools",
                     "https://github.com/broadinstitute/picard",

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/FastqcRunner.java

@@ -368,7 +368,7 @@ private List<String> getBaseParams() throws FileNotFoundException
             throw new RuntimeException("Not found: " + jbzip2.getPath());
         }
 
-        File htsjdkJar = new File(libDir, "htsjdk-4.0.0.jar");
+        File htsjdkJar = findJar(libDir, "htsjdk-");
         if (!htsjdkJar.exists())
         {
             throw new RuntimeException("Not found: " + htsjdkJar.getPath());
@@ -403,6 +403,27 @@ private List<String> getBaseParams() throws FileNotFoundException
         return params;
     }
 
+    private File findJar(final File libDir, final String prefix)
+    {
+        if (!libDir.exists())
+        {
+            throw new RuntimeException("Missing directory: " + libDir);
+        }
+
+        List<String> jarNames = Arrays.stream(libDir.list()).filter(fn -> fn.startsWith(prefix)).sorted().toList();
+        if (jarNames.isEmpty())
+        {
+            throw new RuntimeException("Unable to find JAR with prefix: " + prefix);
+        }
+
+        if (jarNames.size() > 1)
+        {
+            _logger.info("More than one JAR found with prefix: " + prefix);
+        }
+
+        return new File(libDir, jarNames.get(jarNames.size() - 1));
+    }
+
     private int getThreads()
     {
         return _threads;