Merge discvr-25.3 to discvr-25.7

Author: bbimber

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/AbstractGatk4Wrapper.java

@@ -91,6 +91,7 @@ public List<String> getBaseArgs(@Nullable String toolName)
         args.add(SequencePipelineService.get().getJavaFilepath());
         args.addAll(SequencePipelineService.get().getJavaOpts(_maxRamOverride));
         args.add("-DGATK_STACKTRACE_ON_USER_EXCEPTION=true");
+        args.add("-Dsamjdk.optimistic_vcf_4_4=true");
         args.add("-jar");
         args.add(getJAR().getPath());
 

SequenceAnalysis/build.gradle

@@ -135,7 +135,7 @@ 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

@@ -366,7 +366,7 @@ 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());
@@ -401,6 +401,27 @@ 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;

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/KingInferenceStep.java

@@ -115,6 +115,10 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno
         plinkArgs.add("--max-alleles");
         plinkArgs.add("2");
 
+        // NOTE: tools like sawfish can report half-called genotypes, like 0/.. For now, be most conservative in PCA:
+        plinkArgs.add("--vcf-half-call");
+        plinkArgs.add("missing");
+
         Integer threads = SequencePipelineService.get().getMaxThreads(getPipelineCtx().getLogger());
         if (threads != null)
         {

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/PlinkPcaStep.java

@@ -227,6 +227,10 @@ private void runBatch(File inputVCF, File outputDirectory, VariantProcessingStep
             args.add(String.valueOf(maxRam));
         }
 
+        // NOTE: tools like sawfish can report half-called genotypes, like 0/.. For now, be most conservative in PCA:
+        args.add("--vcf-half-call");
+        args.add("missing");
+
         args.addAll(getClientCommandArgs());
 
         getWrapper().execute(args);