Merge branch 'feature/#11' into develop

milaboratory · Sep 1, 2015 · 843bcd6 · 843bcd6
2 parents b3fd046 + 64d6ad9
commit 843bcd6
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Showing 8 changed files with 68 additions and 26 deletions.
diff --git a/CHANGELOG_CURRENT b/CHANGELOG_CURRENT
@@ -1 +1,3 @@
-Added export options -vHitsWithoutScores (same for J and D genes)
+Added export options -vHitsWithoutScores (same for J and D genes)
+
+Added compression for .vdjca and .clns files (when specifying additional ".gz" extension: e.g. "mixcr align inut.fastq output.vdjca.gz" etc.)
diff --git a/src/main/java/com/milaboratory/mixcr/assembler/AlignmentsProvider.java b/src/main/java/com/milaboratory/mixcr/assembler/AlignmentsProvider.java
@@ -34,10 +34,7 @@
 import com.milaboratory.mixcr.reference.AlleleResolver;
 import com.milaboratory.util.Factory;
 
-import java.io.ByteArrayInputStream;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.InputStream;
+import java.io.*;
 
 public interface AlignmentsProvider {
     OutputPortCloseable<VDJCAlignments> create();
@@ -65,7 +62,7 @@ public static AlignmentsProvider createProvider(final String file, final AlleleR
                 public VDJCAlignmentsReader create() {
                     try {
                         return new VDJCAlignmentsReader(file, alleleResolver);
-                    } catch (FileNotFoundException e) {
+                    } catch (IOException e) {
                         throw new RuntimeException(e);
                     }
                 }
@@ -78,7 +75,7 @@ public static AlignmentsProvider createProvider(final File file, final AlleleRes
                 public VDJCAlignmentsReader create() {
                     try {
                         return new VDJCAlignmentsReader(file, alleleResolver);
-                    } catch (FileNotFoundException e) {
+                    } catch (IOException e) {
                         throw new RuntimeException(e);
                     }
                 }

diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetIO.java b/src/main/java/com/milaboratory/mixcr/basictypes/CloneSetIO.java
@@ -48,13 +48,21 @@ public final class CloneSetIO {
     static final int MAGIC_LENGTH = 14;
     static final byte[] MAGIC_BYTES = MAGIC.getBytes(StandardCharsets.US_ASCII);
 
-    public static class CloneSetWriter implements CanReportProgressAndStage {
+    public static class CloneSetWriter implements CanReportProgressAndStage, Closeable {
         final String stage = "Writing clones";
         final PrimitivO output;
         final CloneSet cloneSet;
         final int size;
         volatile int current;
 
+        public CloneSetWriter(CloneSet cloneSet, String fileName) throws IOException {
+            this(cloneSet, new File(fileName));
+        }
+
+        public CloneSetWriter(CloneSet cloneSet, File file) throws IOException {
+            this(cloneSet, IOUtil.createOS(file));
+        }
+
         public CloneSetWriter(CloneSet cloneSet, OutputStream outputStream) {
             this.output = new PrimitivO(outputStream);
             this.cloneSet = cloneSet;
@@ -89,6 +97,11 @@ public void write() {
                 ++current;
             }
         }
+
+        @Override
+        public void close() {
+            output.close();
+        }
     }
 
     public static void read(CloneSet cloneSet, File file) throws IOException {
@@ -119,13 +132,11 @@ public static void write(CloneSet cloneSet, OutputStream outputStream) {
     }
 
     public static CloneSet read(String fileName, AlleleResolver alleleResolver) throws IOException {
-        try (InputStream inputStream = new BufferedInputStream(new FileInputStream(fileName), 32768)) {
-            return read(inputStream, alleleResolver);
-        }
+        return read(new File(fileName), alleleResolver);
     }
 
     public static CloneSet read(File file, AlleleResolver alleleResolver) throws IOException {
-        try (InputStream inputStream = new BufferedInputStream(new FileInputStream(file), 32768)) {
+        try (InputStream inputStream = IOUtil.createIS(file)) {
             return read(inputStream, alleleResolver);
         }
     }

diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/IOUtil.java b/src/main/java/com/milaboratory/mixcr/basictypes/IOUtil.java
@@ -28,6 +28,7 @@
  */
 package com.milaboratory.mixcr.basictypes;
 
+import com.milaboratory.core.io.CompressionType;
 import com.milaboratory.core.sequence.NucleotideSequence;
 import com.milaboratory.mixcr.reference.Allele;
 import com.milaboratory.mixcr.reference.AlleleId;
@@ -36,6 +37,7 @@
 import com.milaboratory.primitivio.PrimitivI;
 import com.milaboratory.primitivio.PrimitivO;
 
+import java.io.*;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -93,4 +95,32 @@ public static List<Allele> readAlleleReferences(PrimitivI input, AlleleResolver
 
         return alleles;
     }
+
+    public static InputStream createIS(String file) throws IOException {
+        return createIS(CompressionType.detectCompressionType(file), new FileInputStream(file));
+    }
+
+    public static InputStream createIS(File file) throws IOException {
+        return createIS(CompressionType.detectCompressionType(file), new FileInputStream(file));
+    }
+
+    public static InputStream createIS(CompressionType ct, InputStream is) throws IOException {
+        if (ct == CompressionType.None)
+            return new BufferedInputStream(is, 65536);
+        else return ct.createInputStream(is, 65536);
+    }
+
+    public static OutputStream createOS(String file) throws IOException {
+        return createOS(CompressionType.detectCompressionType(file), new FileOutputStream(file));
+    }
+
+    public static OutputStream createOS(File file) throws IOException {
+        return createOS(CompressionType.detectCompressionType(file), new FileOutputStream(file));
+    }
+
+    public static OutputStream createOS(CompressionType ct, OutputStream os) throws IOException {
+        if (ct == CompressionType.None)
+            return new BufferedOutputStream(os, 65536);
+        else return ct.createOutputStream(os, 65536);
+    }
 }
diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsReader.java
@@ -29,6 +29,7 @@
 package com.milaboratory.mixcr.basictypes;
 
 import cc.redberry.pipe.OutputPortCloseable;
+import com.milaboratory.core.io.CompressionType;
 import com.milaboratory.mixcr.reference.Allele;
 import com.milaboratory.mixcr.reference.AlleleResolver;
 import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters;
@@ -53,12 +54,12 @@ public class VDJCAlignmentsReader implements OutputPortCloseable<VDJCAlignments>
     final long size;
     final CountingInputStream countingInputStream;
 
-    public VDJCAlignmentsReader(String fileName, AlleleResolver alleleResolver) throws FileNotFoundException {
+    public VDJCAlignmentsReader(String fileName, AlleleResolver alleleResolver) throws IOException {
         this(new File(fileName), alleleResolver);
     }
 
-    public VDJCAlignmentsReader(File file, AlleleResolver alleleResolver) throws FileNotFoundException {
-        this(new BufferedInputStream(new FileInputStream(file), 65536), alleleResolver, file.length());
+    public VDJCAlignmentsReader(File file, AlleleResolver alleleResolver) throws IOException {
+        this(IOUtil.createIS(file), alleleResolver, file.length());
     }
 
     public VDJCAlignmentsReader(InputStream input, AlleleResolver alleleResolver) {

diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriter.java b/src/main/java/com/milaboratory/mixcr/basictypes/VDJCAlignmentsWriter.java
@@ -28,12 +28,16 @@
  */
 package com.milaboratory.mixcr.basictypes;
 
+import com.milaboratory.core.io.CompressionType;
 import com.milaboratory.mixcr.reference.Allele;
 import com.milaboratory.mixcr.vdjaligners.VDJCAligner;
 import com.milaboratory.mixcr.vdjaligners.VDJCAlignerParameters;
 import com.milaboratory.primitivio.PrimitivO;
 
-import java.io.*;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.OutputStream;
 import java.nio.charset.StandardCharsets;
 import java.util.List;
 
@@ -45,12 +49,12 @@ public final class VDJCAlignmentsWriter implements AutoCloseable {
     long numberOfProcessedReads = -1;
     boolean header = false, closed = false;
 
-    public VDJCAlignmentsWriter(String fileName) throws FileNotFoundException {
-        this(new BufferedOutputStream(new FileOutputStream(fileName), 65536));
+    public VDJCAlignmentsWriter(String fileName) throws IOException {
+        this(new File(fileName));
     }
 
-    public VDJCAlignmentsWriter(File file) throws FileNotFoundException {
-        this(new BufferedOutputStream(new FileOutputStream(file), 65536));
+    public VDJCAlignmentsWriter(File file) throws IOException {
+        this(IOUtil.createOS(file));
     }
 
     public VDJCAlignmentsWriter(OutputStream output) {

diff --git a/src/main/java/com/milaboratory/mixcr/cli/ActionAssemble.java b/src/main/java/com/milaboratory/mixcr/cli/ActionAssemble.java
@@ -44,9 +44,6 @@
 import com.milaboratory.primitivio.PipeWriter;
 import com.milaboratory.util.SmartProgressReporter;
 
-import java.io.BufferedOutputStream;
-import java.io.FileOutputStream;
-import java.io.OutputStream;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
@@ -86,8 +83,7 @@ public void go(ActionHelper helper) throws Exception {
                     assembler, actionParameters.threads);
             SmartProgressReporter.startProgressReport(assemblerRunner);
             assemblerRunner.run();
-            try (OutputStream outputStream = new BufferedOutputStream(new FileOutputStream(actionParameters.getOutputFileName()), 65536)) {
-                CloneSetIO.CloneSetWriter writer = new CloneSetIO.CloneSetWriter(assemblerRunner.getCloneSet(), outputStream);
+            try (CloneSetIO.CloneSetWriter writer = new CloneSetIO.CloneSetWriter(assemblerRunner.getCloneSet(), actionParameters.getOutputFileName())) {
                 SmartProgressReporter.startProgressReport(writer);
                 writer.write();
             }

diff --git a/src/main/java/com/milaboratory/mixcr/cli/ActionExportClones.java b/src/main/java/com/milaboratory/mixcr/cli/ActionExportClones.java
@@ -31,6 +31,7 @@
 import com.milaboratory.mixcr.basictypes.Clone;
 import com.milaboratory.mixcr.basictypes.CloneSet;
 import com.milaboratory.mixcr.basictypes.CloneSetIO;
+import com.milaboratory.mixcr.basictypes.IOUtil;
 import com.milaboratory.mixcr.export.InfoWriter;
 import com.milaboratory.mixcr.reference.LociLibraryManager;
 import com.milaboratory.util.CanReportProgressAndStage;
@@ -48,7 +49,7 @@ public ActionExportClones() {
 
     @Override
     public void go0() throws Exception {
-        try (InputStream inputStream = new BufferedInputStream(new FileInputStream(parameters.inputFile), 65536);
+        try (InputStream inputStream = IOUtil.createIS(parameters.inputFile);
              InfoWriter<Clone> writer = new InfoWriter<>(parameters.outputFile)) {
             CloneSet set = CloneSetIO.read(inputStream, LociLibraryManager.getDefault());
             writer.attachInfoProviders((List) parameters.exporters);