Fixed simultaneous insertion and deletion calling.

dieterich-lab · Apr 12, 2021 · 968bdca · 968bdca
1 parent 151bf70
commit 968bdca
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Showing 8 changed files with 83 additions and 46 deletions.
diff --git a/src/jacusa/VersionInfo.java b/src/jacusa/VersionInfo.java
@@ -8,7 +8,7 @@
 public final class VersionInfo {
 
 	public static final String BRANCH 	= "master";
-	public static final String TAG 	= "2.0.0-RC21";
+	public static final String TAG 	= "2.0.0-RC22";
 
 	// change this manually
 	public static final String[] LIBS	= new String[] {

diff --git a/src/lib/data/assembler/factory/AbstractSiteDataAssemblerFactory.java b/src/lib/data/assembler/factory/AbstractSiteDataAssemblerFactory.java
@@ -27,6 +27,7 @@
 import lib.data.storage.container.SharedStorage;
 import lib.data.storage.integer.ArrayIntegerStorage;
 import lib.data.storage.integer.MapIntegerStorage;
+import lib.data.storage.processor.CoverageRecordProcessor;
 import lib.data.storage.processor.DeletionRecordProcessor;
 import lib.data.storage.processor.InsertionRecordProcessor;
 import lib.data.storage.readsubstitution.BaseCallInterpreter;
@@ -69,7 +70,6 @@ protected void addDeletionCache(
 		if (parameter.showDeletionCount()) {
 				cache.addCache(createDeletionCache(
 								sharedStorage, 
-								DataType.COVERAGE.getFetcher(), 
 								DataType.DELETION_COUNT.getFetcher()));
 		}
 	}
@@ -82,49 +82,50 @@ protected void addInsertionCache(
 		if (parameter.showInsertionCount()) {
 				cache.addCache(createInsertionCache(
 								sharedStorage, 
-								DataType.COVERAGE.getFetcher(), 
 								DataType.INSERTION_COUNT.getFetcher()));
 		}
 	}
 
-	Cache createDeletionCache(
-			final SharedStorage sharedStorage, 
-			final Fetcher<IntegerData> covFetcher, final Fetcher<IntegerData> delFetcher) {
-
+	Cache createCoverageCache(final SharedStorage sharedStorage, final Fetcher<IntegerData> covFetcher) {
 		final Cache cache = new Cache();
 		final Storage covStorage = new ArrayIntegerStorage(sharedStorage, covFetcher);
 		cache.addStorage(covStorage);
-
+
+		final CoordinateTranslator translator = sharedStorage.getCoordinateController()
+				.getCoordinateTranslator();
+
+		cache.addRecordProcessor(new CoverageRecordProcessor(translator, covStorage));
+		return cache;
+	}
+
+	Cache createDeletionCache(
+			final SharedStorage sharedStorage, final Fetcher<IntegerData> delFetcher) {
+
+		final Cache cache = new Cache();
+
 		final Storage delStorage = new MapIntegerStorage(sharedStorage, delFetcher);
 		cache.addStorage(delStorage);
 
 		final CoordinateTranslator translator = sharedStorage.getCoordinateController()
 				.getCoordinateTranslator();
 
-		cache.addRecordProcessor(new DeletionRecordProcessor(
-				translator,
-				covStorage, delStorage));
-
+		cache.addRecordProcessor(new DeletionRecordProcessor(translator, delStorage));
+
 		return cache;
 	}
 
 	Cache createInsertionCache(
-			final SharedStorage sharedStorage, 
-			final Fetcher<IntegerData> covFetcher, final Fetcher<IntegerData> insFetcher) {
+			final SharedStorage sharedStorage, final Fetcher<IntegerData> insFetcher) {
 
 		final Cache cache = new Cache();
-		final Storage covStorage = new ArrayIntegerStorage(sharedStorage, covFetcher);
-		cache.addStorage(covStorage);
 
 		final Storage insStorage = new MapIntegerStorage(sharedStorage, insFetcher);
 		cache.addStorage(insStorage);
 
 		final CoordinateTranslator translator = sharedStorage.getCoordinateController()
 				.getCoordinateTranslator();
 
-		cache.addRecordProcessor(new InsertionRecordProcessor(
-				translator,
-				covStorage, insStorage));
+		cache.addRecordProcessor(new InsertionRecordProcessor(translator, insStorage));
 
 		return cache;
 	}

diff --git a/src/lib/data/assembler/factory/CallDataAssemblerFactory.java b/src/lib/data/assembler/factory/CallDataAssemblerFactory.java
@@ -56,11 +56,15 @@ protected Cache createCache(
 
 		final PositionProcessor positionProcessor = new PositionProcessor(validators, bcqcStorage);
 		cache.addRecordProcessor(new AlignmentBlockProcessor(translator, positionProcessor));
-
+
+		if (parameter.showInsertionCount() || parameter.showDeletionCount()) {
+			cache.addCache(createCoverageCache(sharedStorage, DataType.COVERAGE.getFetcher()));
+		}
 		addDeletionCache(parameter, sharedStorage, cache);
 		addInsertionCache(parameter, sharedStorage, cache);
+
 		stratifyByBaseSub(parameter, sharedStorage,  conditionParameter, cache);
-		
+
 		return cache;
 	}
 

diff --git a/src/lib/data/assembler/factory/PileupDataAssemblerFactory.java b/src/lib/data/assembler/factory/PileupDataAssemblerFactory.java
@@ -54,6 +54,10 @@ protected Cache createCache(
 				positionProcessor));
 		cache.addStorage(bcqcStorage);
 
+		if (parameter.showInsertionCount() || parameter.showDeletionCount()) {
+			cache.addCache(createCoverageCache(sharedStorage, DataType.COVERAGE.getFetcher()));
+		}
+		addInsertionCache(parameter, sharedStorage, cache);
 		addDeletionCache(parameter, sharedStorage, cache);
 		stratifyByBaseSub(parameter, sharedStorage,  conditionParameter, cache);
 

diff --git a/src/lib/data/assembler/factory/RTarrestDataAssemblerFactory.java b/src/lib/data/assembler/factory/RTarrestDataAssemblerFactory.java
@@ -66,6 +66,10 @@ public Cache createCache(
 				locInterpreter, 
 				validators));
 
+		if (parameter.showInsertionCount() || parameter.showDeletionCount()) {
+			cache.addCache(createCoverageCache(sharedStorage, DataType.COVERAGE.getFetcher()));
+		}
+		addInsertionCache(parameter, sharedStorage, cache);
 		addDeletionCache(parameter, sharedStorage, cache);
 
 		// stratify by base substitutions

diff --git a/src/lib/data/storage/processor/CoverageRecordProcessor.java b/src/lib/data/storage/processor/CoverageRecordProcessor.java
@@ -0,0 +1,48 @@
+package lib.data.storage.processor;
+
+import lib.data.storage.Storage;
+import lib.record.Record;
+import lib.util.coordinate.CoordinateTranslator;
+import lib.util.position.ConsumingRefPosProviderBuilder;
+import lib.util.position.Position;
+import lib.util.position.PositionProvider;
+
+/**
+ * TODO
+ */
+public class CoverageRecordProcessor implements GeneralRecordProcessor {
+
+	private final CoordinateTranslator translator;
+
+	private final Storage covStorage;
+
+	public CoverageRecordProcessor(
+			final CoordinateTranslator translator,
+			final Storage covStorage) {
+
+		this.translator	= translator;
+		this.covStorage	= covStorage;
+	}
+
+	@Override
+	public void preProcess() {
+		// nothing to be done
+	}
+
+	@Override
+	public void process(final Record record) {
+		// store total coverage
+		final PositionProvider covPosProvider = 
+				new ConsumingRefPosProviderBuilder(record, translator).build();
+		while (covPosProvider.hasNext()) {
+			final Position pos = covPosProvider.next();
+			covStorage.increment(pos);
+		}
+	}
+
+	@Override
+	public void postProcess() {
+		// nothing to be done
+	}
+
+}
diff --git a/src/lib/data/storage/processor/DeletionRecordProcessor.java b/src/lib/data/storage/processor/DeletionRecordProcessor.java
@@ -4,7 +4,6 @@
 import lib.record.Record;
 import lib.util.coordinate.CoordinateTranslator;
 import lib.util.position.AllDeletionsPositionProvider;
-import lib.util.position.ConsumingRefPosProviderBuilder;
 import lib.util.position.Position;
 import lib.util.position.PositionProvider;
 
@@ -15,16 +14,13 @@ public class DeletionRecordProcessor implements GeneralRecordProcessor {
 
 	private final CoordinateTranslator translator;
 
-	private final Storage covStorage;
 	private final Storage delStorage;
 
 	public DeletionRecordProcessor(
 			final CoordinateTranslator translator,
-			final Storage covStorage,
 			final Storage delStorage) {
 
 		this.translator	= translator;
-		this.covStorage	= covStorage;
 		this.delStorage	= delStorage;
 	}
 
@@ -35,14 +31,6 @@ public void preProcess() {
 
 	@Override
 	public void process(final Record record) {
-		// store total coverage
-		final PositionProvider covPosProvider = 
-				new ConsumingRefPosProviderBuilder(record, translator).build();
-		while (covPosProvider.hasNext()) {
-			final Position pos = covPosProvider.next();
-			covStorage.increment(pos);
-		}
-
 		// store deletions
 		final PositionProvider delPosProvider = 
 				new AllDeletionsPositionProvider(record, translator);

diff --git a/src/lib/data/storage/processor/InsertionRecordProcessor.java b/src/lib/data/storage/processor/InsertionRecordProcessor.java
@@ -4,7 +4,6 @@
 import lib.record.Record;
 import lib.util.coordinate.CoordinateTranslator;
 import lib.util.position.AllInsertionsPosProvider;
-import lib.util.position.ConsumingRefPosProviderBuilder;
 import lib.util.position.Position;
 import lib.util.position.PositionProvider;
 
@@ -15,16 +14,13 @@ public class InsertionRecordProcessor implements GeneralRecordProcessor {
 
 	private final CoordinateTranslator translator;
 
-	private final Storage covStorage;
 	private final Storage insStorage;
 
 	public InsertionRecordProcessor(
 			final CoordinateTranslator translator,
-			final Storage covStorage,
 			final Storage insStorage) {
 
 		this.translator	= translator;
-		this.covStorage	= covStorage;
 		this.insStorage	= insStorage;
 	}
 
@@ -35,15 +31,7 @@ public void preProcess() {
 
 	@Override
 	public void process(final Record record) {
-		// store total coverage
-		final PositionProvider covPosProvider = 
-				new ConsumingRefPosProviderBuilder(record, translator).build();
-		while (covPosProvider.hasNext()) {
-			final Position pos = covPosProvider.next();
-			covStorage.increment(pos);
-		}
-
-		// store insetions
+		// store insertions
 		final PositionProvider insPosProvider = 
 				new AllInsertionsPosProvider(record, translator);
 		while (insPosProvider.hasNext()) {