Bug in ReferencePoints class fixed.

milaboratory · Sep 26, 2015 · 73a71e5 · 73a71e5
1 parent 7143bfb
commit 73a71e5
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Showing 5 changed files with 21 additions and 11 deletions.
diff --git a/doc/export.rst b/doc/export.rst
@@ -211,7 +211,7 @@ each target sequence. In this case arrays are sepparated by comma:
 
     2:61:107:107:118:::::::::::::,:::::::::103:112:120:147:181:208:238:239:
 
-Even if there are no anchor points in either of parts:
+Even if there are no anchor points in one of the parts:
 
 ::
 

diff --git a/src/main/java/com/milaboratory/mixcr/cli/ActionExportParameters.java b/src/main/java/com/milaboratory/mixcr/cli/ActionExportParameters.java
@@ -227,7 +227,7 @@ static ArrayList<FieldExtractor> parsePresetString(OutputMode outputMode, Class
                 "-nFeature FR3 -minFeatureQuality FR3 -nFeature CDR3 -minFeatureQuality CDR3 " +
                 "-nFeature FR4 -minFeatureQuality FR4 " +
                 "-aaFeature FR1 -aaFeature CDR1 -aaFeature FR2 -aaFeature CDR2 " +
-                "-aaFeature FR3 -aaFeature CDR3 -aaFeature FR4 -defaultReferencePoints");
+                "-aaFeature FR3 -aaFeature CDR3 -aaFeature FR4 -defaultAnchorPoints");
         preset.put(Clone.class, clones);
 
         Map<String, String> alignments = new HashMap<>();
@@ -240,7 +240,7 @@ static ArrayList<FieldExtractor> parsePresetString(OutputMode outputMode, Class
                 "-nFeature FR3 -minFeatureQuality FR3 -nFeature CDR3 -minFeatureQuality CDR3 " +
                 "-nFeature FR4 -minFeatureQuality FR4 " +
                 "-aaFeature FR1 -aaFeature CDR1 -aaFeature FR2 -aaFeature CDR2 " +
-                "-aaFeature FR3 -aaFeature CDR3 -aaFeature FR4 -defaultReferencePoints")
+                "-aaFeature FR3 -aaFeature CDR3 -aaFeature FR4 -defaultAnchorPoints")
         ;
         preset.put(VDJCAlignments.class, alignments);
     }

diff --git a/src/main/java/com/milaboratory/mixcr/export/InfoWriter.java b/src/main/java/com/milaboratory/mixcr/export/InfoWriter.java
@@ -29,6 +29,7 @@
 package com.milaboratory.mixcr.export;
 
 import cc.redberry.pipe.InputPort;
+import org.apache.commons.io.output.CloseShieldOutputStream;
 
 import java.io.*;
 import java.util.ArrayList;
@@ -40,7 +41,8 @@ public final class InfoWriter<T> implements InputPort<T>, AutoCloseable {
     boolean initialized;
 
     public InfoWriter(String file) throws FileNotFoundException {
-        this(new BufferedOutputStream(new FileOutputStream(new File(file)), 65536));
+        this(".".equals(file) ? new CloseShieldOutputStream(System.out) :
+                new BufferedOutputStream(new FileOutputStream(new File(file)), 65536));
     }
 
     public void attachInfoProvider(AbstractFieldExtractor<? super T> provider) {

diff --git a/src/main/java/com/milaboratory/mixcr/reference/ReferencePoints.java b/src/main/java/com/milaboratory/mixcr/reference/ReferencePoints.java
@@ -41,20 +41,23 @@
  */
 public final class ReferencePoints extends SequencePartitioning implements java.io.Serializable {
     final int[] points;
+    final boolean reversed;
 
     public ReferencePoints(int[] points) {
         if (points.length != BasicReferencePoint.TOTAL_NUMBER_OF_REFERENCE_POINTS)
             throw new IllegalArgumentException("Illegal length of array.");
-        checkReferencePoints(points);
+        Boolean rev = checkReferencePoints(points);
+        this.reversed = rev == null ? false : rev;
         this.points = points;
     }
 
     public ReferencePoints(int start, int[] points) {
-        checkReferencePoints(points);
+        Boolean rev = checkReferencePoints(points);
         int[] array = new int[BasicReferencePoint.TOTAL_NUMBER_OF_REFERENCE_POINTS];
         Arrays.fill(array, -1);
         System.arraycopy(points, 0, array, start, points.length);
         this.points = array;
+        this.reversed = rev == null ? false : rev;
     }
 
     public int numberOfDefinedPoints() {
@@ -66,7 +69,7 @@ public int numberOfDefinedPoints() {
         return ret;
     }
 
-    private static void checkReferencePoints(int[] points) {
+    private static Boolean checkReferencePoints(int[] points) {
         Boolean reversed = null;
 
         int first = -1;
@@ -83,7 +86,7 @@ else if (first != ref) {
                 }
 
         if (reversed == null)
-            return;
+            return null;
 
         int previousPoint = -1;
         for (int point : points) {
@@ -101,6 +104,8 @@ else if (first != ref) {
 
             previousPoint = point;
         }
+
+        return reversed;
     }
 
     private int getPosition(int referencePointIndex) {
@@ -129,7 +134,7 @@ public int getPosition(ReferencePoint referencePoint) {
         int point = getPosition(referencePoint.getIndex());
         if (point < 0)
             return -1;
-        return point + referencePoint.getOffset();
+        return point + (reversed ? -referencePoint.getOffset() : referencePoint.getOffset());
     }
 
     ReferencePoints getRelativeReferencePoints(GeneFeature geneFeature) {

diff --git a/src/test/java/com/milaboratory/mixcr/reference/LociLibraryIOTest.java b/src/test/java/com/milaboratory/mixcr/reference/LociLibraryIOTest.java
@@ -28,6 +28,7 @@
  */
 package com.milaboratory.mixcr.reference;
 
+import com.milaboratory.core.sequence.AminoAcidSequence;
 import com.milaboratory.core.sequence.NucleotideSequence;
 import org.junit.Assert;
 import org.junit.Ignore;
@@ -112,9 +113,11 @@ public void test3ReadLL() throws Exception {
     public void test3ReadLL1() throws Exception {
         InputStream sample = LociLibraryReader.class.getClassLoader().getResourceAsStream("reference/mi.ll");
         LociLibrary library = LociLibraryReader.read(sample);
-        for (Allele allele : library.getAllAlleles(Species.HomoSapiens)) {
-            if (allele.getName().contains("3-11")) {
+        for (Allele allele : library.getAllAlleles(Species.MusMusculus)) {
+            if (allele.getName().contains("1-33")) {
                 System.out.println(allele.getName());
+                System.out.println(AminoAcidSequence.translate(allele.getFeature(FR3), 0));
+                System.out.println(allele.getFeature(FR3));
                 System.out.println(allele.isFunctional());
                 System.out.println(Arrays.toString(allele.getPartitioning().points));
             }