Cuppa: updated version to use latest SV factory

hartwigmedical · Sep 11, 2024 · 33ee63e · 33ee63e
1 parent e4c22c3
commit 33ee63e
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Showing 3 changed files with 19 additions and 23 deletions.
diff --git a/cuppa/src/main/java/com/hartwig/hmftools/cup/prep/CuppaDataPrep.java b/cuppa/src/main/java/com/hartwig/hmftools/cup/prep/CuppaDataPrep.java
@@ -98,9 +98,9 @@ public void extractSingleSample(boolean keepDataItems)
         for(CategoryType categoryType : mConfig.Categories)
         {
             CategoryPrep categoryPrep = createCategoryPrep(categoryType);
-            SampleOneCategoryTask sampleTask = new SampleOneCategoryTask(0, mConfig, categoryPrep, null);
+            SamplePrepTask sampleTask = new SamplePrepTask(0, mConfig, categoryPrep, null);
             sampleTask.run();
-            dataItems.addAll(sampleTask.mDataItems);
+            dataItems.addAll(sampleTask.dataItems());
         }
 
         if(keepDataItems)
@@ -116,11 +116,11 @@ public DataItemMatrix extractMultiSampleOneCategory(CategoryType categoryType)
 
         ConcurrentHashMap<DataItem.Index, String[]> featureBySampleMatrix = new ConcurrentHashMap<>();
 
-        List<SampleOneCategoryTask> sampleTasks = new ArrayList<>();
+        List<SamplePrepTask> sampleTasks = new ArrayList<>();
         for(int sampleIndex = 0; sampleIndex < mConfig.SampleIds.size(); ++sampleIndex)
         {
             CategoryPrep categoryPrep = createCategoryPrep(categoryType);
-            sampleTasks.add(new SampleOneCategoryTask(sampleIndex, mConfig, categoryPrep, featureBySampleMatrix));
+            sampleTasks.add(new SamplePrepTask(sampleIndex, mConfig, categoryPrep, featureBySampleMatrix));
         }
 
         List<Callable> callableTasks = sampleTasks.stream().collect(Collectors.toList());

diff --git a/...tools/cup/prep/SampleOneCategoryTask.java → ...wig/hmftools/cup/prep/SamplePrepTask.java b/...tools/cup/prep/SampleOneCategoryTask.java → ...wig/hmftools/cup/prep/SamplePrepTask.java
@@ -8,22 +8,22 @@
 
 import org.jetbrains.annotations.Nullable;
 
-public class SampleOneCategoryTask implements Callable
+public class SamplePrepTask implements Callable
 {
-    public final PrepConfig mConfig;
-    public final int mSampleIndex;
-    public final String mSampleName;
+    private final PrepConfig mConfig;
+    private final int mSampleIndex;
+    private final String mSampleName;
 
-    @Nullable public CategoryPrep mCategoryPrep;
+    @Nullable private CategoryPrep mCategoryPrep;
 
-    @Nullable public List<DataItem> mDataItems;
-    @Nullable public ConcurrentHashMap<DataItem.Index, String[]> FeatureBySampleMatrix;
+    @Nullable private List<DataItem> mDataItems;
+    @Nullable private ConcurrentHashMap<DataItem.Index, String[]> FeatureBySampleMatrix;
 
-    public SampleOneCategoryTask(
+    public SamplePrepTask(
             final int sampleIndex,
             final PrepConfig prepConfig,
-            CategoryPrep categoryPrep,
-            @Nullable ConcurrentHashMap<DataItem.Index, String[]> featureBySampleMatrix)
+            final CategoryPrep categoryPrep,
+            @Nullable final ConcurrentHashMap<DataItem.Index,String[]> featureBySampleMatrix)
     {
         mConfig = prepConfig;
         mCategoryPrep = categoryPrep;
@@ -63,15 +63,11 @@ public synchronized void addDataItemsToMatrix()
         }
     }
 
-    public void clearDataItems()
-    {
-        mDataItems = null;
-    }
+    public List<DataItem> dataItems() { return mDataItems; }
 
-    public void clearCategoryPrep()
-    {
-        mCategoryPrep = null;
-    }
+    public void clearDataItems() { mDataItems = null; }
+
+    public void clearCategoryPrep() { mCategoryPrep = null; }
 
     public void run()
     {

diff --git a/pom.xml b/pom.xml
@@ -70,7 +70,7 @@
         <cobalt.version>2.0</cobalt.version>
         <compar.version>1.3</compar.version>
         <crest.version>1.0.0</crest.version>
-        <cuppa.version>2.2.1</cuppa.version>
+        <cuppa.version>2.3</cuppa.version>
         <esvee.version>1.0</esvee.version>
         <fastq-tools.version>1.0</fastq-tools.version>
         <gene-utils.version>1.2</gene-utils.version>