Merge branch 'hotfix/v1.7.4'

CHANGELOG

@@ -1,4 +1,14 @@
 
+MiXCR 1.7.4 (20 Jun 2016)
+========================
+
+-- Better compatibility with highly-paralelized execution of MiXCR on clusters: "more random" 
+   generation of random temp file names
+-- Human-readable messages for two wrong input cases
+-- NPE fixed in case of align with `VGene`, assemble `VTranscript`
+-- Minor fix for documentation
+
+
 MiXCR 1.7.3 (17 May 2016)
 ========================
 

doc/export.rst

@@ -635,7 +635,7 @@ One can also export all read IDs that were aggregated by eah clone. For this one
 
 ::
 
-    mixcr exportAlignments -p min -readIds index_file clones.clns clones.txt
+    mixcr exportClones -p min -readIds index_file clones.clns clones.txt
 
 This will add a column with full enumeration of all reads that were absorbed by particular clone:
 

pom.xml

@@ -32,7 +32,7 @@
 
     <groupId>com.milaboratory</groupId>
     <artifactId>mixcr</artifactId>
-    <version>1.7.3</version>
+    <version>1.7.4</version>
     <packaging>jar</packaging>
     <name>MiXCR</name>
 

src/main/java/com/milaboratory/mixcr/cli/ActionExportCloneReads.java

@@ -23,6 +23,7 @@
 import org.mapdb.DBMaker;
 
 import java.io.File;
+import java.io.IOException;
 import java.util.Iterator;
 import java.util.List;
 import java.util.NavigableSet;
@@ -46,9 +47,20 @@ public ActionParameters params() {
 
     @Override
     public void go(ActionHelper helper) throws Exception {
-        DB db = DBMaker.newFileDB(new File(parameters.getMapDBFile()))
-                .transactionDisable()
-                .make();
+        if (!originalReadsPresent()) {
+            final String msg = "Error: original reads was not saved in the .vdjca file: re-run align with '-g' option.";
+            throw new IllegalArgumentException(msg);
+        }
+
+        DB db;
+        try {
+            db = DBMaker.newFileDB(new File(parameters.getMapDBFile()))
+                    .transactionDisable()
+                    .make();
+        } catch (Exception | Error e) {
+            final String msg = "Error: corrupted or malformed index file.";
+            throw new IllegalArgumentException(msg, e);
+        }
 
         int[] cloneIds = parameters.getCloneIds();
         if (cloneIds.length == 1) {//byClones
@@ -62,6 +74,14 @@ public void go(ActionHelper helper) throws Exception {
         db.close();
     }
 
+    private boolean originalReadsPresent() throws IOException {
+        try (VDJCAlignmentsReader reader
+                     = new VDJCAlignmentsReader(parameters.getVDJCAFile(), LociLibraryManager.getDefault())) {
+            VDJCAlignments test = reader.take();
+            return test == null || test.getOriginalSequences() != null;
+        }
+    }
+
     public void writeMany(NavigableSet<ReadToCloneMapping> byAlignments, int[] clonIds)
             throws Exception {
         TIntObjectHashMap<SequenceWriter> writers = new TIntObjectHashMap<>(clonIds.length);
@@ -93,7 +113,6 @@ public void writeMany(NavigableSet<ReadToCloneMapping> byAlignments, int[] clonI
                 writer.write(createRead(vdjca.getOriginalSequences(), vdjca.getDescriptions()));
             }
 
-            //todo create empty file!!!!!!!!!!!!!!!!!!!!
             for (SequenceWriter writer : writers.valueCollection())
                 if (writer != null)
                     writer.close();
@@ -108,7 +127,7 @@ public void writeSingle(NavigableSet<ReadToCloneMapping> byClones, int cloneId)
                 new ReadToCloneMapping(Long.MAX_VALUE, 0, cloneId, false, false), true);
 
         if (selected.isEmpty())
-            return;//todo create empty file!!!!!!!!!!!!!!!!!!!!
+            return;
         try (VDJCAlignmentsReader reader = new VDJCAlignmentsReader(parameters.getVDJCAFile(),
                 LociLibraryManager.getDefault())) {
 
@@ -147,9 +166,21 @@ private static String createFileName(String fileName, int id) {
     private static SequenceRead createRead(NSequenceWithQuality[] nseqs, String[] descr) {
         if (nseqs.length == 1)
             return new SingleReadImpl(-1, nseqs[0], descr[0]);
-        else return new PairedRead(
-                new SingleReadImpl(-1, nseqs[0], descr[0]),
-                new SingleReadImpl(-1, nseqs[1], descr[1]));
+        else {
+            String descr1, descr2;
+            if (descr == null)
+                descr1 = descr2 = "";
+            else if (descr.length == 1)
+                descr1 = descr2 = descr[0];
+            else {
+                descr1 = descr[0];
+                descr2 = descr[1];
+            }
+
+            return new PairedRead(
+                    new SingleReadImpl(-1, nseqs[0], descr1),
+                    new SingleReadImpl(-1, nseqs[1], descr2));
+        }
     }
 
     private static SequenceWriter createWriter(boolean paired, String fileName)

src/main/java/com/milaboratory/mixcr/cli/Main.java

@@ -29,10 +29,15 @@
 package com.milaboratory.mixcr.cli;
 
 import com.milaboratory.mitools.cli.JCommanderBasedMain;
+import com.milaboratory.mixcr.util.TempFileManager;
 import com.milaboratory.mixcr.util.VersionInfoProvider;
 
+import java.security.SecureRandom;
+import java.util.Arrays;
+
 public class Main {
     public static void main(String... args) throws Exception {
+        TempFileManager.seed(Arrays.hashCode(args) + 17 * (new SecureRandom()).nextLong());
         // Getting command string if executed from script
         String command = System.getProperty("mixcr.command", "java -jar mixcr.jar");
 

src/main/java/com/milaboratory/mixcr/reference/GeneFeature.java

@@ -378,21 +378,22 @@ public static GeneFeature intersection(GeneFeature gf1, GeneFeature gf2) {
                 if (c > 0) {
                     result.add(new ReferenceRange(maxBegin,
                             gf2.regions[rangePointer2].end));
-                    if (rangePointer2 != gf2.regions.length - 1)
-                        throw new IllegalArgumentException();
-                    break;
+                    if (rangePointer2 == gf2.regions.length - 1)
+                        break;
+                    ++rangePointer2;
                 } else {
                     result.add(new ReferenceRange(maxBegin,
                             gf1.regions[rangePointer1].end));
-                    if (rangePointer1 != gf1.regions.length - 1)
-                        throw new IllegalArgumentException();
-                    break;
+                    if (rangePointer1 == gf1.regions.length - 1)
+                        break;
+                    ++rangePointer1;
                 }
-            } else
+            } else {
                 result.add(new ReferenceRange(maxBegin, gf1.regions[rangePointer1].end));
 
-            ++rangePointer1;
-            ++rangePointer2;
+                ++rangePointer1;
+                ++rangePointer2;
+            }
         }
 
         return new GeneFeature(result.toArray(new ReferenceRange[result.size()]), true);

src/main/java/com/milaboratory/mixcr/util/TempFileManager.java

@@ -28,7 +28,8 @@
  */
 package com.milaboratory.mixcr.util;
 
-import com.milaboratory.util.RandomUtil;
+import org.apache.commons.math3.random.RandomDataGenerator;
+import org.apache.commons.math3.random.Well44497b;
 
 import java.io.File;
 import java.io.IOException;
@@ -38,6 +39,14 @@
 public class TempFileManager {
     private static final AtomicBoolean initialized = new AtomicBoolean(false);
     static final ConcurrentHashMap<String, File> createdFiles = new ConcurrentHashMap<>();
+    static final RandomDataGenerator randomGenerator = new RandomDataGenerator(new Well44497b());
+
+    public static void seed(long seed) {
+        synchronized (randomGenerator) {
+            randomGenerator.reSeed(seed);
+        }
+    }
+
     //static final String tmpdir = getTmpDir();
     //private static String getTmpDir() {
     //    String tmpdir = AccessController.doPrivileged(new GetPropertyAction("java.io.tmpdir"));
@@ -56,7 +65,9 @@ public static File getTempFile() {
             String name;
 
             do {
-                name = "mixcr_" + RandomUtil.getThreadLocalRandomData().nextHexString(40);
+                synchronized (randomGenerator) {
+                    name = "mixcr_" + randomGenerator.nextHexString(40);
+                }
                 file = File.createTempFile(name, null);
             } while (createdFiles.putIfAbsent(name, file) != null);
             if (file.length() != 0)

src/test/java/com/milaboratory/mixcr/reference/GeneFeatureTest.java

@@ -36,6 +36,7 @@
 
 import java.util.*;
 
+import static com.milaboratory.mixcr.reference.ReferencePoint.*;
 import static com.milaboratory.mixcr.reference.GeneFeature.*;
 import static org.junit.Assert.*;
 
@@ -285,7 +286,7 @@ public void testRandom1() {
 
     @Test
     public void testStatic() throws Exception {
-        assertEquals(JRegion, parse("JRegion"));
+        assertEquals(JRegion, GeneFeature.parse("JRegion"));
     }
 
     static final GeneFeature create(int... indexes) {
@@ -359,11 +360,11 @@ public void testContains1() throws Exception {
     public void testEncode1() throws Exception {
         Collection<GeneFeature> features = GeneFeature.getFeaturesByName().values();
         for (GeneFeature feature : features)
-            assertEquals(feature, parse(encode(feature)));
+            assertEquals(feature, GeneFeature.parse(encode(feature)));
     }
 
     private static void assertEncode(String str) {
-        Assert.assertEquals(str.replace(" ", ""), encode(parse(str)).replace(" ", ""));
+        Assert.assertEquals(str.replace(" ", ""), encode(GeneFeature.parse(str)).replace(" ", ""));
     }
 
     @Ignore
@@ -414,4 +415,23 @@ public int compareTo(GFT o) {
             return feature.getFirstPoint().compareTo(o.feature.getFirstPoint());
         }
     }
+
+    @Test
+    public void testIntersection15() throws Exception {
+        assertEquals(intersection(VTranscript, VGene), VTranscript);
+    }
+
+    @Test
+    public void testIntersection16() throws Exception {
+        assertEquals(
+                intersection(VTranscript, new GeneFeature(UTR5Begin.move(1), VEnd)),
+                new GeneFeature(new GeneFeature(UTR5Begin.move(1), L1End), new GeneFeature(L2Begin, VEnd)));
+    }
+
+    @Test
+    public void testIntersection17() throws Exception {
+        assertEquals(
+                intersection(new GeneFeature(new GeneFeature(UTR5Begin, L1End.move(-1)), new GeneFeature(L2Begin.move(-5), VEnd.move(1))), new GeneFeature(UTR5Begin.move(1), VEnd)),
+                new GeneFeature(new GeneFeature(UTR5Begin.move(1), L1End.move(-1)), new GeneFeature(L2Begin.move(-5), VEnd)));
+    }
 }