* Fixed cache problem, when calculating test-statistic for INDELs.

* Added new Option "-i" Count only the start position of an insertion

src/jacusa/VersionInfo.java

@@ -8,7 +8,7 @@
 public final class VersionInfo {
 
 	public static final String BRANCH 	= "master";
-	public static final String TAG 	= "2.0.2-RC";
+	public static final String TAG 	= "2.0.4";
 
 	// change this manually
 	public static final String[] LIBS	= new String[] {

src/jacusa/method/call/CallMethod.java

@@ -38,6 +38,7 @@
 import lib.cli.options.ShowAllSitesOption;
 import lib.cli.options.ShowDeletionCountOption;
 import lib.cli.options.ShowInsertionCountOption;
+import lib.cli.options.ShowInsertionStartCountOption;
 import lib.cli.options.HelpOption;
 import lib.cli.options.MaxThreadOption;
 import lib.cli.options.ResultFileOption;
@@ -121,6 +122,7 @@ protected void initGlobalACOptions() {
 		addACOption(new StratifyByReadTagOption(getParameter()));
 		addACOption(new ShowDeletionCountOption(getParameter()));
 		addACOption(new ShowInsertionCountOption(getParameter()));
+		addACOption(new ShowInsertionStartCountOption(getParameter()));
 
 		addACOption(new BedCoordinatesOption(getParameter()));
 		addACOption(new ResultFileOption(getParameter()));
@@ -276,7 +278,7 @@ protected void addRequired(final AbstractBuilder builder) {
 					addBaseSub2int(builder, DataType.BASE_SUBST2DELETION_COUNT);
 					addBaseSub2int(builder, DataType.BASE_SUBST2COVERAGE);
 				}
-				if (parameter.showInsertionCount()) {
+				if (parameter.showInsertionCount() || parameter.showInsertionStartCount()) {
 					addBaseSub2int(builder, DataType.BASE_SUBST2INSERTION_COUNT);
 					addBaseSub2int(builder, DataType.BASE_SUBST2COVERAGE);
 				}
@@ -285,7 +287,7 @@ protected void addRequired(final AbstractBuilder builder) {
 				add(builder, DataType.DELETION_COUNT);
 				guardedAdd(builder, DataType.COVERAGE);
 			}
-			if (parameter.showInsertionCount()) {
+			if (parameter.showInsertionCount() || parameter.showInsertionStartCount()) {
 				add(builder, DataType.INSERTION_COUNT);
 				guardedAdd(builder, DataType.COVERAGE);
 			}

src/jacusa/method/pileup/PileupMethod.java

@@ -36,6 +36,7 @@
 import lib.cli.options.ResultFormatOption;
 import lib.cli.options.ShowDeletionCountOption;
 import lib.cli.options.ShowInsertionCountOption;
+import lib.cli.options.ShowInsertionStartCountOption;
 import lib.cli.options.ThreadWindowSizeOption;
 import lib.cli.options.WindowSizeOption;
 import lib.cli.options.condition.MaxDepthConditionOption;
@@ -99,6 +100,7 @@ protected void initGlobalACOptions() {
 		addACOption(new StratifyByReadTagOption(getParameter()));
 		addACOption(new ShowDeletionCountOption(getParameter()));
 		addACOption(new ShowInsertionCountOption(getParameter()));
+		addACOption(new ShowInsertionStartCountOption(getParameter()));
 
 		addACOption(new BedCoordinatesOption(getParameter()));
 		addACOption(new ResultFileOption(getParameter()));
@@ -239,7 +241,7 @@ protected void addRequired(final AbstractBuilder builder) {
 					addBaseSub2int(builder, DataType.BASE_SUBST2DELETION_COUNT);
 					addBaseSub2int(builder, DataType.BASE_SUBST2COVERAGE);
 				}
-				if (parameter.showInsertionCount()) {
+				if (parameter.showInsertionCount() || parameter.showInsertionStartCount()) {
 					addBaseSub2int(builder, DataType.BASE_SUBST2INSERTION_COUNT);
 					addBaseSub2int(builder, DataType.BASE_SUBST2COVERAGE);
 				}
@@ -248,7 +250,7 @@ protected void addRequired(final AbstractBuilder builder) {
 				add(builder, DataType.DELETION_COUNT);
 				guardedAdd(builder, DataType.COVERAGE);
 			}
-			if (parameter.showInsertionCount()) {
+			if (parameter.showInsertionCount() || parameter.showInsertionStartCount()) {
 				add(builder, DataType.INSERTION_COUNT);
 				guardedAdd(builder, DataType.COVERAGE);
 			}

src/jacusa/method/rtarrest/RTarrestMethod.java

@@ -35,6 +35,7 @@
 import lib.cli.options.ResultFormatOption;
 import lib.cli.options.ShowDeletionCountOption;
 import lib.cli.options.ShowInsertionCountOption;
+import lib.cli.options.ShowInsertionStartCountOption;
 import lib.cli.options.HelpOption;
 import lib.cli.options.MaxThreadOption;
 import lib.cli.options.ResultFileOption;
@@ -114,6 +115,7 @@ protected void initGlobalACOptions() {
 		addACOption(new StratifyByReadTagOption(getParameter()));
 		addACOption(new ShowDeletionCountOption(getParameter()));
 		addACOption(new ShowInsertionCountOption(getParameter()));
+		addACOption(new ShowInsertionStartCountOption(getParameter()));
 
 		addACOption(new BedCoordinatesOption(getParameter()));
 		addACOption(new ResultFileOption(getParameter()));
@@ -293,7 +295,7 @@ protected void addRequired(final AbstractBuilder builder) {
 					addBaseSub2int(builder, DataType.BASE_SUBST2DELETION_COUNT);
 					addBaseSub2int(builder, DataType.BASE_SUBST2COVERAGE);
 				}
-				if (parameter.showInsertionCount()) {
+				if (parameter.showInsertionCount() || parameter.showInsertionStartCount()) {
 					addBaseSub2int(builder, DataType.BASE_SUBST2INSERTION_COUNT);
 					addBaseSub2int(builder, DataType.BASE_SUBST2COVERAGE);
 				}
@@ -302,7 +304,7 @@ protected void addRequired(final AbstractBuilder builder) {
 				add(builder, DataType.DELETION_COUNT);
 				guardedAdd(builder, DataType.COVERAGE);
 			}
-			if (parameter.showInsertionCount()) {
+			if (parameter.showInsertionCount() || parameter.showInsertionStartCount()) {
 				add(builder, DataType.INSERTION_COUNT);
 				guardedAdd(builder, DataType.COVERAGE);
 			}

src/jacusa/worker/CallWorker.java

@@ -67,7 +67,7 @@ protected Result process(final ParallelData parallelData) {
 			result = new DeletionCountResult(baseSubs, result, minkaPrm, delCountProv);
 		}
 
-		if (getParameter().showInsertionCount()) {
+		if (getParameter().showInsertionCount() || getParameter().showInsertionStartCount()) {
 			final MinkaParameter minkaPrm = new MinkaParameter();
 			final InsertionEstCountProvider insCountProv = 
 					new InsertionEstCountProvider(minkaPrm.getMaxIterations());

src/jacusa/worker/PileupWorker.java

@@ -62,7 +62,7 @@ protected Result process(final ParallelData parallelData) {
 			result = new DeletionCountResult(baseSubs, result, minkaPrm, delCountProv);
 		}
 
-		if (getParameter().showInsertionCount()) {
+		if (getParameter().showInsertionCount() || getParameter().showInsertionStartCount()) {
 			final MinkaParameter minkaPrm = new MinkaParameter();
 			final InsertionEstCountProvider insCountProv = 
 					new InsertionEstCountProvider(minkaPrm.getMaxIterations());

src/jacusa/worker/RTArrestWorker.java

@@ -76,7 +76,7 @@ protected Result process(final ParallelData parallelData) {
 			result = new DeletionCountResult(baseSubs, result, minkaPrm, delCountProv);
 		}
 
-		if (getParameter().showInsertionCount()) {
+		if (getParameter().showInsertionCount() || getParameter().showInsertionStartCount()) {
 			final MinkaParameter minkaPrm = new MinkaParameter();
 			final InsertionEstCountProvider insCountProv = 
 					new InsertionEstCountProvider(minkaPrm.getMaxIterations());

src/lib/cli/options/ShowInsertionStartCountOption.java

@@ -0,0 +1,34 @@
+package lib.cli.options;
+
+import lib.cli.parameter.GeneralParameter;
+
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Option;
+
+public class ShowInsertionStartCountOption extends AbstractACOption {
+
+	private final GeneralParameter parameter;
+
+	public ShowInsertionStartCountOption(final GeneralParameter parameter) {
+		super("i", "show-start-insertions");
+		this.parameter = parameter;
+	}
+
+	@Override
+	public Option getOption(final boolean printExtendedHelp) {
+		return Option.builder(getOpt())
+				.hasArg(false)
+		        .desc("Show start insertion score")
+		        .build();
+	}
+
+	/**
+	 * Tested in @see test.lib.cli.options.FilterModusOptionTest
+	 */
+
+	@Override
+	public void process(final CommandLine line) throws Exception {
+		parameter.showInsertionStartsCount(true);
+	}
+
+}

src/lib/cli/parameter/GeneralParameter.java

@@ -48,6 +48,7 @@ public class GeneralParameter
 	private final SortedSet<BaseSub> baseSubs;
 	private boolean showDeletionCount;
 	private boolean showInsertionCount;
+	private boolean showInsertionStartCount;
 	private boolean showAllSites;
 
 	// debug flag
@@ -227,21 +228,35 @@ public boolean showDeletionCount() {
 	public boolean showInsertionCount() {
 		return showInsertionCount;
 	}
+
+	public boolean showInsertionStartCount() {
+		return showInsertionStartCount;
+	}
 
 	/**
 	 * @param showDeletionCount the showDeletionCount to set
 	 */
 	public void showDeletionCount(boolean showDeletionCount) {
 		this.showDeletionCount = showDeletionCount;
 	}
-
+	
 	/**
 	 * @param showInsertionCount the showInsertionCount to set
 	 */
-	public void showInsertionCount(boolean showInsertionCount) {
+	public void showInsertionCount(boolean showInsertionCount) throws Exception {
+		if (showInsertionStartCount && showInsertionCount) {
+			throw new Exception("Cannot set both to true");
+		}
 		this.showInsertionCount = showInsertionCount;
 	}
-
+
+	public void showInsertionStartsCount(boolean showInsertionStartCount) throws Exception {
+		if (this.showInsertionCount && showInsertionStartCount) {
+			throw new Exception("Cannot set both to true");
+		}
+		this.showInsertionStartCount = showInsertionStartCount;
+	}
+
 	/**
 	 * @return the showDeletionCount
 	 */

src/lib/data/assembler/factory/AbstractSiteDataAssemblerFactory.java

@@ -79,10 +79,12 @@ protected void addInsertionCache(
 			final SharedStorage sharedStorage,
 			final Cache cache) {
 
-		if (parameter.showInsertionCount()) {
-				cache.addCache(createInsertionCache(
-								sharedStorage, 
-								DataType.INSERTION_COUNT.getFetcher()));
+		if (parameter.showInsertionCount() || parameter.showInsertionStartCount()) {
+			final boolean onlyStart = parameter.showInsertionStartCount();
+			cache.addCache(createInsertionCache(
+							sharedStorage, 
+							DataType.INSERTION_COUNT.getFetcher(),
+							onlyStart));
 		}
 	}
 
@@ -115,7 +117,7 @@ Cache createDeletionCache(
 	}
 
 	Cache createInsertionCache(
-			final SharedStorage sharedStorage, final Fetcher<IntegerData> insFetcher) {
+			final SharedStorage sharedStorage, final Fetcher<IntegerData> insFetcher, final boolean onlyStart) {
 
 		final Cache cache = new Cache();
 
@@ -125,7 +127,7 @@ Cache createInsertionCache(
 		final CoordinateTranslator translator = sharedStorage.getCoordinateController()
 				.getCoordinateTranslator();
 
-		cache.addRecordProcessor(new InsertionRecordProcessor(translator, insStorage));
+		cache.addRecordProcessor(new InsertionRecordProcessor(translator, insStorage, onlyStart));
 
 		return cache;
 	}
@@ -174,7 +176,7 @@ protected void stratifyByBaseSub(
 			algnPosProc.addStorage(bccStorage);
 			baseSub2algnPosProc.put(baseSub, algnPosProc);
 
-			if (prm.showInsertionCount() || prm.showDeletionCount()) {
+			if (prm.showInsertionCount() || prm.showInsertionStartCount() || prm.showDeletionCount()) {
 				final PositionProcessor covPosProc = new PositionProcessor();
 				final Fetcher<IntegerData> covFetcher = new IntegerDataExtractor(
 						baseSub, 
@@ -186,7 +188,7 @@ protected void stratifyByBaseSub(
 				covPosProc.addStorage(covStorage);
 				baseSub2covPosProc.put(baseSub, covPosProc);
 			}
-			if (prm.showInsertionCount()) {
+			if (prm.showInsertionCount() || prm.showInsertionStartCount()) {
 				final PositionProcessor insPosProc = new PositionProcessor();
 				final Fetcher<IntegerData> insFetcher = new IntegerDataExtractor(
 						baseSub, 
@@ -221,7 +223,8 @@ protected void stratifyByBaseSub(
 				baseSub2algnPosProc,
 				baseSub2covPosProc,
 				baseSub2insPosProc,
-				baseSub2delPosProc));
+				baseSub2delPosProc,
+				prm.showInsertionStartCount()));
 	}
 
 }

src/lib/data/assembler/factory/CallDataAssemblerFactory.java

@@ -57,7 +57,7 @@ protected Cache createCache(
 		final PositionProcessor positionProcessor = new PositionProcessor(validators, bcqcStorage);
 		cache.addRecordProcessor(new AlignmentBlockProcessor(translator, positionProcessor));
 
-		if (parameter.showInsertionCount() || parameter.showDeletionCount()) {
+		if (parameter.showInsertionCount() || parameter.showInsertionStartCount() || parameter.showDeletionCount()) {
 			cache.addCache(createCoverageCache(sharedStorage, DataType.COVERAGE.getFetcher()));
 		}
 		addDeletionCache(parameter, sharedStorage, cache);

src/lib/data/assembler/factory/PileupDataAssemblerFactory.java

@@ -54,7 +54,7 @@ protected Cache createCache(
 				positionProcessor));
 		cache.addStorage(bcqcStorage);
 
-		if (parameter.showInsertionCount() || parameter.showDeletionCount()) {
+		if (parameter.showInsertionCount() || parameter.showInsertionStartCount() || parameter.showDeletionCount()) {
 			cache.addCache(createCoverageCache(sharedStorage, DataType.COVERAGE.getFetcher()));
 		}
 		addInsertionCache(parameter, sharedStorage, cache);

src/lib/data/assembler/factory/RTarrestDataAssemblerFactory.java

@@ -66,7 +66,7 @@ public Cache createCache(
 				locInterpreter, 
 				validators));
 
-		if (parameter.showInsertionCount() || parameter.showDeletionCount()) {
+		if (parameter.showInsertionCount() || parameter.showInsertionStartCount() || parameter.showDeletionCount()) {
 			cache.addCache(createCoverageCache(sharedStorage, DataType.COVERAGE.getFetcher()));
 		}
 		addInsertionCache(parameter, sharedStorage, cache);
@@ -161,7 +161,7 @@ private Cache createStratifyByBaseSub(
 			alignedPosProcessor.addStorage(rtArrestCountStorage);
 			baseSub2alignedPosProcessor.put(baseSub, alignedPosProcessor);
 
-			if (parameter.showInsertionCount() || parameter.showDeletionCount()) {
+			if (parameter.showInsertionCount() || parameter.showInsertionStartCount() || parameter.showDeletionCount()) {
 				final PositionProcessor covPosProcessor = new PositionProcessor();
 				final Fetcher<IntegerData> covFetcher = new IntegerDataExtractor(
 						baseSub, 
@@ -173,7 +173,7 @@ private Cache createStratifyByBaseSub(
 				covPosProcessor.addStorage(covStorage);
 				baseSub2covPosProcessor.put(baseSub, covPosProcessor);
 			}
-			if (parameter.showInsertionCount()) {
+			if (parameter.showInsertionCount() || parameter.showInsertionStartCount()) {
 				final PositionProcessor insPosProcessor = new PositionProcessor();
 				final Fetcher<IntegerData> insFetcher = new IntegerDataExtractor(
 						baseSub, 
@@ -211,7 +211,8 @@ private Cache createStratifyByBaseSub(
 				baseSub2alignedPosProcessor,
 				baseSub2covPosProcessor,
 				baseSub2insPosProcessor,
-				baseSub2delPosProcessor) );
+				baseSub2delPosProcessor,
+				parameter.showInsertionStartCount()));
 		return cache;
 	}
 

src/lib/data/storage/processor/DeletionRecordProcessor.java

@@ -29,7 +29,7 @@ public void preProcess() {
 		// nothing to be done
 	}
 
-	@Override
+	@Override // TODO adjust deletion at every position
 	public void process(final Record record) {
 		// store deletions
 		final PositionProvider delPosProvider = 

src/lib/data/storage/processor/InsertionRecordProcessor.java

@@ -15,13 +15,16 @@ public class InsertionRecordProcessor implements GeneralRecordProcessor {
 	private final CoordinateTranslator translator;
 
 	private final Storage insStorage;
+	private final boolean onlyStart;
 
 	public InsertionRecordProcessor(
 			final CoordinateTranslator translator,
-			final Storage insStorage) {
+			final Storage insStorage,
+			final boolean onlyStart) {
 
 		this.translator	= translator;
 		this.insStorage	= insStorage;
+		this.onlyStart	= onlyStart;
 	}
 
 	@Override
@@ -33,7 +36,7 @@ public void preProcess() {
 	public void process(final Record record) {
 		// store insertions
 		final PositionProvider insPosProvider = 
-				new AllInsertionsPosProvider(record, translator);
+				new AllInsertionsPosProvider(record, translator, onlyStart);
 		while (insPosProvider.hasNext()) {
 			final Position pos = insPosProvider.next();
 			insStorage.increment(pos);