Merge branch 'release/v3.0.2'

milaboratory · Oct 30, 2018 · 485533c · 485533c
2 parents f826d72 + 49a614d
commit 485533c
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Showing 8 changed files with 185 additions and 86 deletions.
diff --git a/CHANGELOG b/CHANGELOG
@@ -1,4 +1,12 @@
 
+MiXCR 3.0.2 (30 Oct 2018)
+========================
+
+-- Additional fix for error in `exportAlignments` / `exportClones` with repeated non-parametrized 
+   options
+-- Added support for affine alignments in `assembleContigs`
+
+
 MiXCR 3.0.1 (25 Oct 2018)
 ========================
 

diff --git a/itests.sh b/itests.sh
@@ -104,9 +104,11 @@ fi
 
 if [[ $run_tests == true ]]; then
   echo "Running test case 1"
-  mixcr align -s hs -OvParameters.geneFeatureToAlign=VGeneWithP test_R1.fastq test_R2.fastq case1.vdjca
+  mixcr align -s hs -OvParameters.geneFeatureToAlign=VGeneWithP -OsaveOriginalReads=true test_R1.fastq test_R2.fastq case1.vdjca
   mixcr assemble case1.vdjca case1.clns
 
+  mixcr exportAlignments -nFeatureImputed VDJRegion -descrsR1 -descrsR2 case1.vdjca case1.alignments.txt
+
   echo "Running test case 2"
   mixcr analyze shotgun -f --species hs --contig-assembly --impute-germline-on-export --starting-material rna test_R1.fastq test_R2.fastq case2
 

diff --git a/pom.xml b/pom.xml
@@ -33,7 +33,7 @@
 
     <groupId>com.milaboratory</groupId>
     <artifactId>mixcr</artifactId>
-    <version>3.0.1</version>
+    <version>3.0.2</version>
     <packaging>jar</packaging>
     <name>MiXCR</name>
 

diff --git a/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java b/src/main/java/com/milaboratory/mixcr/assembler/fullseq/FullSeqAssembler.java
diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java
@@ -32,7 +32,6 @@
 import cc.redberry.pipe.OutputPort;
 import cc.redberry.pipe.OutputPortCloseable;
 import cc.redberry.pipe.util.CountingOutputPort;
-import cc.redberry.pipe.util.StatusReporter;
 import com.milaboratory.mixcr.util.MiXCRVersionInfo;
 import com.milaboratory.primitivio.PipeDataInputReader;
 import com.milaboratory.primitivio.PrimitivI;
@@ -258,34 +257,34 @@ public synchronized void writeAlignmentsAndIndex() {
         // Writer
         try ( // TODO parametrise
               BasicVDJCAlignmentWriterFactory writerFactory = new BasicVDJCAlignmentWriterFactory(
-                      Math.min(16, Runtime.getRuntime().availableProcessors()),
+                      Math.min(4, Runtime.getRuntime().availableProcessors()),
                       true);
               // Writer
               BasicVDJCAlignmentWriterFactory.Writer writer =
                       writerFactory.createWriter(outputState, outputStream, false)) {
 
-            StatusReporter reporter = new StatusReporter();
-            reporter.addCustomProvider(new StatusReporter.StatusProvider() {
-                volatile String status;
-                volatile boolean isClosed = false;
-
-                @Override
-                public void updateStatus() {
-                    status = "Busy encoders: " + writerFactory.getBusyEncoders() + " / " + writerFactory.getEncodersCount();
-                    isClosed = writerFactory.isClosed();
-                }
-
-                @Override
-                public boolean isFinished() {
-                    return isClosed;
-                }
-
-                @Override
-                public String getStatus() {
-                    return status;
-                }
-            });
-            reporter.start();
+            // StatusReporter reporter = new StatusReporter();
+            // reporter.addCustomProvider(new StatusReporter.StatusProvider() {
+            //     volatile String status;
+            //     volatile boolean isClosed = false;
+            //
+            //     @Override
+            //     public void updateStatus() {
+            //         status = "Busy encoders: " + writerFactory.getBusyEncoders() + " / " + writerFactory.getEncodersCount();
+            //         isClosed = writerFactory.isClosed();
+            //     }
+            //
+            //     @Override
+            //     public boolean isFinished() {
+            //         return isClosed;
+            //     }
+            //
+            //     @Override
+            //     public String getStatus() {
+            //         return status;
+            //     }
+            // });
+            // reporter.start();
 
             List<VDJCAlignments> block = new ArrayList<>();
             // Writing alignments and writing indices

diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/PipelineConfigurationReader.java b/src/main/java/com/milaboratory/mixcr/basictypes/PipelineConfigurationReader.java
@@ -12,6 +12,8 @@ public interface PipelineConfigurationReader {
      * Read pipeline configuration from file or return null
      */
     static PipelineConfiguration fromFileOrNull(String fileName, IOUtil.MiXCRFileInfo fileInfo) {
+        if (fileInfo == null)
+            return null;
         if (!fileInfo.valid)
             return null;
         try {

diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java b/src/main/java/com/milaboratory/mixcr/cli/CommandAnalyze.java
@@ -56,21 +56,23 @@ public String description() {
 
 
     enum _Chains implements WithNameWithDescription {
-        tcr("All T-cell receptor types (TRA/TRB/TRG/TRD)"),
-        bcr("All B-cell receptor types (IGH/IGK/IGL/TRD)"),
-        xcr("All T- and B-cell receptor types"),
-        tra("TRA chain"),
-        trb("TRB chain"),
-        trd("TRD chain"),
-        trg("TRG chain"),
-        igh("IGH chain"),
-        igk("IGK chain"),
-        igl("IGL chain");
+        tcr("All T-cell receptor types (TRA/TRB/TRG/TRD)", Chains.TCR),
+        bcr("All B-cell receptor types (IGH/IGK/IGL/TRD)", Chains.IG),
+        xcr("All T- and B-cell receptor types", Chains.ALL),
+        tra("TRA chain", Chains.TRA),
+        trb("TRB chain", Chains.TRB),
+        trd("TRD chain", Chains.TRD),
+        trg("TRG chain", Chains.TRG),
+        igh("IGH chain", Chains.IGH),
+        igk("IGK chain", Chains.IGK),
+        igl("IGL chain", Chains.IGL);
         final String key, description;
+        final Chains chains;
 
-        _Chains(String description) {
+        _Chains(String description, Chains chains) {
             this.key = this.toString();
             this.description = description;
+            this.chains = chains;
         }
 
         @Override
@@ -215,14 +217,10 @@ static class _AdaptersCandidates extends EnumCandidates {
             description = "Receptor type. Possible values: ${COMPLETION-CANDIDATES}",
             required = false /* This will be overridden for amplicon */)
     public void setChains(String chains) {
-        if (chains.equalsIgnoreCase("xcr"))
-            this.chains = Chains.ALL;
-        else {
-            Chains c = Chains.parse(chains.toUpperCase());
-            if (c == null)
-                throwValidationException("Illegal value " + chains + " for --receptor-type option.");
-            this.chains = c;
-        }
+        _Chains c = parse0(_Chains.class, chains);
+        if (c == null)
+            throwValidationException("Illegal value " + chains + " for --receptor-type option.");
+        this.chains = c.chains;
     }
 
     @Option(names = "--starting-material",

diff --git a/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java b/src/main/java/com/milaboratory/mixcr/cli/CommandExport.java
@@ -351,7 +351,8 @@ <E> List<FieldExtractor<E>> extractor(FieldData fd, Class<E> clazz, OutputMode m
         for (Field f : FieldExtractors.getFields()) {
             if (fd.field.equalsIgnoreCase(f.getCommand()) && f.canExtractFrom(clazz)) {
                 if (f.nArguments() == 0) {
-                    if (fd.args.length != 0)
+                    if (!(fd.args.length == 0 || (
+                            fd.args.length == 1 && (fd.args[0].equalsIgnoreCase("true") || fd.args[0].equalsIgnoreCase("false")))))
                         throw new RuntimeException();
                     return Collections.singletonList(f.create(m, new String[0]));
                 } else {