Release 1.2

.gitignore

@@ -1,3 +1,2 @@
-*.iml
+mixcr.iml
 target
-.idea

CHANGELOG

@@ -0,0 +1,29 @@
+
+MiXCR v1.2 (16 Jun 2015)
+========================
+
+-- new feature: added ability to export keep read descrptions in .vdjca file
+   (option '--save-description' for align command and options '-descrR1' and
+   '-descrR2' for exportAlignments command)
+-- fixed crash caused by '-OcloneClusteringParameters=null'
+-- bug with clonatype ordering in exportClones fixed 
+   (occurred with '-OcloneClusteringParameters=null')
+
+
+
+MiXCR v1.1 (29 Apr 2015)
+========================
+
+-- new feature: `exportAlignmentsPretty` action for exporting BLAST-style
+   alignments
+-- adjust D-gene aligner parameters
+-- various performance improvements
+-- bash script support for OS X and Linux
+-- migration to MiLib 1.0
+
+
+
+MiXCR v1.0 (1 Jan 2015)
+=======================
+
+-- first release

mixcr

@@ -52,7 +52,7 @@ fi
 
 jar=""
 
-for j in "$DIR/../jar/mixcr.jar" "$DIR/mixcr.jar" "$DIR/target/mixcr-1.1-distribution.jar"
+for j in "$DIR/../jar/mixcr.jar" "$DIR/mixcr.jar" "$DIR/target/mixcr-1.2-distribution.jar"
 do
     if [[ -e "$j" ]];
     then

pom.xml

@@ -32,7 +32,7 @@
 
     <groupId>com.milaboratory</groupId>
     <artifactId>mixcr</artifactId>
-    <version>1.1</version>
+    <version>1.2</version>
     <packaging>jar</packaging>
     <name>MiXCR</name>
 
@@ -46,19 +46,19 @@
         <dependency>
             <groupId>com.milaboratory</groupId>
             <artifactId>milib</artifactId>
-            <version>1.0</version>
+            <version>1.0.1</version>
         </dependency>
 
         <dependency>
             <groupId>com.milaboratory</groupId>
             <artifactId>mitools</artifactId>
-            <version>1.0</version>
+            <version>1.0.1</version>
         </dependency>
 
         <dependency>
             <groupId>com.milaboratory</groupId>
             <artifactId>milib</artifactId>
-            <version>1.0</version>
+            <version>1.0.1</version>
             <type>test-jar</type>
             <scope>test</scope>
         </dependency>
@@ -131,6 +131,15 @@
                 </configuration>
             </plugin>
 
+            <plugin>
+                <artifactId>maven-assembly-plugin</artifactId>
+                <configuration>
+                    <descriptorRefs>
+                        <descriptorRef>jar-with-dependencies</descriptorRef>
+                    </descriptorRefs>
+                </configuration>
+            </plugin>
+
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-shade-plugin</artifactId>

src/main/java/com/milaboratory/mixcr/assembler/AbstractClonalAlignerParameters.java

@@ -30,7 +30,8 @@
 
 import com.milaboratory.mixcr.reference.GeneFeature;
 
-public abstract class AbstractClonalAlignerParameters<T extends AbstractClonalAlignerParameters<T>> {
+public abstract class AbstractClonalAlignerParameters<T extends AbstractClonalAlignerParameters<T>>
+        implements java.io.Serializable {
     protected float relativeMinScore;
     protected GeneFeature featureToAlign;
 

src/main/java/com/milaboratory/mixcr/assembler/AlignmentsProvider.java

@@ -49,7 +49,7 @@ public interface AlignmentsProvider {
      */
     long getTotalNumberOfReads();
 
-    public final static class Util {
+    final class Util {
         static AlignmentsProvider createProvider(final byte[] rawData, final AlleleResolver alleleResolver) {
             return new VDJCAlignmentsReaderWrapper(new Factory<VDJCAlignmentsReader>() {
                 @Override

src/main/java/com/milaboratory/mixcr/assembler/CloneAssembler.java

@@ -495,8 +495,19 @@ void buildClones() {
             Collection<CloneAccumulator> source;
             if (clusteredClonesAccumulators != null)
                 source = clusteredClonesAccumulators;
-            else
-                source = clones.values();
+            else {
+                //sort clones by count (if not yet sorted by clustering)
+                CloneAccumulator[] sourceArray = clones.values().toArray(new CloneAccumulator[clones.size()]);
+                Arrays.sort(sourceArray, new Comparator<CloneAccumulator>() {
+                    @Override
+                    public int compare(CloneAccumulator o1, CloneAccumulator o2) {
+                        return Long.compare(o2.count, o1.count);
+                    }
+                });
+                for (int i = 0; i < sourceArray.length; i++)
+                    sourceArray[i].setCloneIndex(i);
+                source = Arrays.asList(sourceArray);
+            }
             realClones = new Clone[source.size()];
             int i = 0;
             Iterator<CloneAccumulator> iterator = source.iterator();
@@ -509,4 +520,4 @@ void buildClones() {
             }
         }
     }
-}
+}

src/main/java/com/milaboratory/mixcr/assembler/CloneAssemblerParameters.java

@@ -40,7 +40,7 @@
 
 @JsonAutoDetect(fieldVisibility = JsonAutoDetect.Visibility.ANY, isGetterVisibility = JsonAutoDetect.Visibility.NONE,
         getterVisibility = JsonAutoDetect.Visibility.NONE)
-public final class CloneAssemblerParameters {
+public final class CloneAssemblerParameters implements java.io.Serializable {
     private static final int MAX_MAPPING_REGION = 1000;
     GeneFeature[] assemblingFeatures;
     CloneClusteringParameters cloneClusteringParameters;

src/main/java/com/milaboratory/mixcr/assembler/CloneClusteringParameters.java

@@ -35,7 +35,7 @@
 
 @JsonAutoDetect(fieldVisibility = JsonAutoDetect.Visibility.ANY, isGetterVisibility = JsonAutoDetect.Visibility.NONE,
         getterVisibility = JsonAutoDetect.Visibility.NONE)
-public final class CloneClusteringParameters {
+public final class CloneClusteringParameters implements java.io.Serializable {
     private int searchDepth;
     private int allowedMutationsInNRegions;
     private TreeSearchParameters searchParameters;

src/main/java/com/milaboratory/mixcr/assembler/CloneFactoryParameters.java

@@ -39,7 +39,7 @@
 import java.util.EnumMap;
 import java.util.Map;
 
-public final class CloneFactoryParameters {
+public final class CloneFactoryParameters implements java.io.Serializable {
     EnumMap<GeneType, VJCClonalAlignerParameters> vdcParameters = new EnumMap<>(GeneType.class);
     DAlignerParameters dParameters;
 

src/main/java/com/milaboratory/mixcr/assembler/ClusteringFilter.java

@@ -39,7 +39,7 @@
         getterVisibility = JsonAutoDetect.Visibility.NONE)
 @JsonTypeInfo(use = JsonTypeInfo.Id.NAME, include = JsonTypeInfo.As.PROPERTY, property = "type")
 @JsonSubTypes({@JsonSubTypes.Type(value = RelativeConcentrationFilter.class, name = "relativeConcentration")})
-public interface ClusteringFilter {
+public interface ClusteringFilter extends java.io.Serializable {
     boolean allow(Mutations<NucleotideSequence> mutations,
                   long majorClusterCount, long minorClusterCount,
                   ClonalSequence majorSequence);

src/main/java/com/milaboratory/mixcr/assembler/DClonalAlignerParameters.java

@@ -37,7 +37,8 @@
 
 @JsonAutoDetect(fieldVisibility = JsonAutoDetect.Visibility.ANY, isGetterVisibility = JsonAutoDetect.Visibility.NONE,
         getterVisibility = JsonAutoDetect.Visibility.NONE)
-public final class DClonalAlignerParameters extends AbstractClonalAlignerParameters<DClonalAlignerParameters> {
+public final class DClonalAlignerParameters extends AbstractClonalAlignerParameters<DClonalAlignerParameters>
+        implements java.io.Serializable {
     AlignmentScoring<NucleotideSequence> scoring;
 
     @JsonCreator

src/main/java/com/milaboratory/mixcr/assembler/VJCClonalAlignerParameters.java

@@ -36,7 +36,8 @@
 
 @JsonAutoDetect(fieldVisibility = JsonAutoDetect.Visibility.ANY, isGetterVisibility = JsonAutoDetect.Visibility.NONE,
         getterVisibility = JsonAutoDetect.Visibility.NONE)
-public final class VJCClonalAlignerParameters extends AbstractClonalAlignerParameters<VJCClonalAlignerParameters> {
+public final class VJCClonalAlignerParameters extends AbstractClonalAlignerParameters<VJCClonalAlignerParameters>
+        implements java.io.Serializable {
     BandedAlignerParameters alignmentParameters;
 
     @JsonCreator

src/main/java/com/milaboratory/mixcr/basictypes/IO.java

@@ -80,6 +80,7 @@ public static class VDJCAlignmentsSerializer implements Serializer<VDJCAlignment
         @Override
         public void write(PrimitivO output, VDJCAlignments object) {
             output.writeObject(object.targets);
+            output.writeObject(object.descriptions);
             output.writeByte(object.hits.size());
             for (Map.Entry<GeneType, VDJCHit[]> entry : object.hits.entrySet()) {
                 output.writeObject(entry.getKey());
@@ -91,13 +92,16 @@ public void write(PrimitivO output, VDJCAlignments object) {
         @Override
         public VDJCAlignments read(PrimitivI input) {
             NSequenceWithQuality[] targets = input.readObject(NSequenceWithQuality[].class);
+            String[] descriptions = input.readObject(String[].class);
             int size = input.readByte();
             EnumMap<GeneType, VDJCHit[]> hits = new EnumMap<>(GeneType.class);
             for (int i = 0; i < size; i++) {
                 GeneType key = input.readObject(GeneType.class);
                 hits.put(key, input.readObject(VDJCHit[].class));
             }
-            return new VDJCAlignments(input.readLong(), hits, targets);
+            VDJCAlignments vdjcAlignments = new VDJCAlignments(input.readLong(), hits, targets);
+            vdjcAlignments.setDescriptions(descriptions);
+            return vdjcAlignments;
         }
 
         @Override

src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignments.java

@@ -36,6 +36,7 @@
 
 @Serializable(by = IO.VDJCAlignmentsSerializer.class)
 public final class VDJCAlignments extends VDJCObject {
+    String[] descriptions;
     final long readId;
     private volatile long alignmentsIndex = -1;
 
@@ -67,6 +68,14 @@ public void setAlignmentsIndex(long alignmentsIndex) {
         this.alignmentsIndex = alignmentsIndex;
     }
 
+    public void setDescriptions(String[] description) {
+        this.descriptions = description;
+    }
+
+    public String[] getDescriptions() {
+        return descriptions;
+    }
+
     @Override
     public boolean equals(Object o) {
         if (this == o) return true;

src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java

@@ -40,8 +40,7 @@
 import java.util.Arrays;
 import java.util.List;
 
-import static com.milaboratory.mixcr.basictypes.VDJCAlignmentsWriter.MAGIC_BYTES;
-import static com.milaboratory.mixcr.basictypes.VDJCAlignmentsWriter.MAGIC_LENGTH;
+import static com.milaboratory.mixcr.basictypes.VDJCAlignmentsWriter.*;
 
 public class VDJCAlignmentsReader implements OutputPortCloseable<VDJCAlignments>, CanReportProgress {
     VDJCAlignerParameters parameters;
@@ -80,7 +79,7 @@ public void init() {
         byte[] magic = new byte[MAGIC_LENGTH];
         input.readFully(magic);
         if (!Arrays.equals(magic, MAGIC_BYTES))
-            throw new RuntimeException("Wrong file format.");
+            throw new RuntimeException("Conflicting file format; .vdjca file of version " + new String(magic) + " while you are running MiXCR " + MAGIC);
 
         parameters = input.readObject(VDJCAlignerParameters.class);
 

src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriter.java

@@ -38,7 +38,7 @@
 import java.util.List;
 
 public final class VDJCAlignmentsWriter implements AutoCloseable {
-    static final String MAGIC = "MiXCR.VDJC.V02";
+    static final String MAGIC = "MiXCR.VDJC.V03";
     static final int MAGIC_LENGTH = 14;
     static final byte[] MAGIC_BYTES = MAGIC.getBytes(StandardCharsets.US_ASCII);
     final PrimitivO output;

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

@@ -111,8 +111,11 @@ public long getIndex(VDJCAlignmentResult o) {
                             }))) {
                 if (result.alignment == null)
                     continue;
-                if (writer != null)
+                if (writer != null) {
+                    if (actionParameters.saveReadDescription)
+                        result.alignment.setDescriptions(extractDescription(result.read));
                     writer.write(result.alignment);
+                }
             }
             if (writer != null)
                 writer.setNumberOfProcessedReads(reader.getNumberOfReads());
@@ -123,6 +126,13 @@ public long getIndex(VDJCAlignmentResult o) {
                     helper.getCommandLineArguments(), actionParameters.report, report);
     }
 
+    private static String[] extractDescription(SequenceRead r) {
+        String[] descrs = new String[r.numberOfReads()];
+        for (int i = 0; i < r.numberOfReads(); i++)
+            descrs[i] = r.getRead(i).getDescription();
+        return descrs;
+    }
+
     @Override
     public String command() {
         return "align";
@@ -174,6 +184,11 @@ public static class AlignParameters extends ActionParametersWithOutput {
                 names = {"-d", "--noMerge"})
         public Boolean noMerge = false;
 
+        @Parameter(description = "Copy read(s) description line from .fastq or .fasta to .vdjca file (can be then " +
+                "exported with -descrR1 and -descrR2 options in exportAlignments action).",
+                names = {"-a", "--save-description"})
+        public Boolean saveReadDescription = false;
+
         public int getTaxonID() {
             return Species.fromStringStrict(species);
         }

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

@@ -59,7 +59,7 @@ public void parseParameters(String[] args) {
         params().parseParameters(args);
     }
 
-    abstract void go0() throws Exception;
+    protected abstract void go0() throws Exception;
 
     @Override
     public ActionExportParameters params() {

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

@@ -45,12 +45,18 @@
 
 @Parameters(commandDescription = "Export binary data",
         optionPrefixes = "^")
-public final class ActionExportParameters extends ActionParameters {
+public class ActionExportParameters extends ActionParameters {
     final Class clazz;
     final String helpString;
     final String fieldsHelpString;
+    final String defaultPreset;
 
-    protected ActionExportParameters(Class clazz) {
+    public ActionExportParameters(Class clazz) {
+        this(clazz, "full");
+    }
+
+    public ActionExportParameters(Class clazz, String defaultPreset) {
+        this.defaultPreset = defaultPreset;
         this.clazz = clazz;
         ArrayList<String>[] description = new ArrayList[]{new ArrayList(), new ArrayList()};
         description[0].add("-h, --help");
@@ -103,7 +109,7 @@ public final void parseParameters(String[] args) throws ParameterException {
             throw new ParameterException("No output file specified.");
 
         if (args.length == 2)
-            exporters = getPresetParameters(clazz, "full");
+            exporters = getPresetParameters(clazz, defaultPreset);
         else
             exporters = parseParametersString(clazz, args, 0, args.length - 2);
 

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

@@ -81,10 +81,12 @@ private static boolean override1(JsonNode node, String path, String value, boole
         boolean b = false;
         if (override0(node, path, value))
             b = true;
-        Iterator<JsonNode> iterator = node.iterator();
-        while (iterator.hasNext())
-            if (override1(iterator.next(), path, value, b || v))
-                b = true;
+        else {
+            Iterator<JsonNode> iterator = node.iterator();
+            while (iterator.hasNext())
+                if (override1(iterator.next(), path, value, b || v))
+                    b = true;
+        }
         if (v && b)
             throw new IllegalArgumentException("Multiple matches of parameter " + path);
         return b;