Fixed calcP and minor typos

dieterich-lab · Jan 31, 2021 · 151bf70 · 151bf70
1 parent 9a9baec
commit 151bf70
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Showing 6 changed files with 10 additions and 11 deletions.
diff --git a/src/jacusa/VersionInfo.java b/src/jacusa/VersionInfo.java
@@ -8,15 +8,15 @@
 public final class VersionInfo {
 
 	public static final String BRANCH 	= "master";
-	public static final String TAG 	= "2.0.0-RC20";
+	public static final String TAG 	= "2.0.0-RC21";
 
-	// changes this manually
+	// change this manually
 	public static final String[] LIBS	= new String[] {
 			"htsjdk 2.12.0",
 			"Apache commons-cli 1.4",
 			"Apache commpon-math3 3.6.1"
 	};
-	
+
 	private final String branch;
 	private final String tag;
 	private final String[] libs;

diff --git a/src/jacusa/cli/parameters/RTarrestParameter.java b/src/jacusa/cli/parameters/RTarrestParameter.java
@@ -35,7 +35,7 @@ public ConditionParameter createConditionParameter(final int condI) {
 		// Pos.:		1234
 		// Read Seq.:	ACGT
 		// Read Basq:	HHHL H=High Quality BC, L=Quality BC
-		// Where does the Read end position 3 or 4?
+		// Where does the Read end? Position 3 or 4?
 		// p.setMinBASQ((byte)0); 
 		return p;
 	}

diff --git a/src/jacusa/io/format/call/VCFcallWriter.java b/src/jacusa/io/format/call/VCFcallWriter.java
@@ -156,7 +156,7 @@ public void writeResult(final Result result) {
 		for (int condI = 0; condI < conditions; condI++) {
 			final int replicates = parallelData.getReplicates(condI);
 			for (int replicateI = 0; replicateI < replicates; replicateI++) {	
-				final String sampleName = "TODO " +  condI + replicateI;
+				final String sampleName = "sample " +  condI + replicateI;
 				final BaseCallCount tmpBCC = 
 						parallelData.getDataContainer(condI, replicateI)
 							.getPileupCount().getBCC();

diff --git a/src/lib/cli/CLI.java b/src/lib/cli/CLI.java
@@ -104,7 +104,6 @@ private AbstractMethod.AbstractFactory getMethodFactory(final String name) {
 		}
 		return null;
 	}
-	// TODO
 	private void generateLatex() {
 		final Map<String, Map<String, List<AbstractACOption>>> opt2method2acOption = 
 				new HashMap<>();

diff --git a/src/lib/stat/dirmult/CallStat.java b/src/lib/stat/dirmult/CallStat.java
@@ -44,7 +44,7 @@ public Result calculate(ParallelData parallelData) {
 		if (dirMultPrm.isCalcPValue()) {
 			stat = dirMult.getLRT(estContainers);
 			// TODO degrees of freedom
-			final ChiSquaredDistribution dist = new ChiSquaredDistribution(1); 
+			final ChiSquaredDistribution dist = new ChiSquaredDistribution(3); 
 			stat = 1 - dist.cumulativeProbability(stat);
 		} else {
 			stat = dirMult.getScore(estContainers);

diff --git a/src/lib/stat/estimation/provider/pileup/AbstractEstimationContainerProvider.java b/src/lib/stat/estimation/provider/pileup/AbstractEstimationContainerProvider.java
@@ -35,10 +35,10 @@ abstract class AbstractEstimationContainerProvider
 	protected abstract List<List<PileupCount>> process(ParallelData parallelData);
 
 	private Base[] getBases(final ParallelData parallelData) {
-		if (calcPValue) {
-			return parallelData.getCombPooledData().getPileupCount().getBCC()
-					.getAlleles().toArray(new Base[0]);
-		}
+		//if (calcPValue) {
+		//	return parallelData.getCombPooledData().getPileupCount().getBCC()
+		//			.getAlleles().toArray(new Base[0]);
+		//}
 
 		return Base.validValues();
 	}