Merge branch 'release/v3.0.5'

milaboratory · Feb 24, 2019 · 02da502 · 02da502
2 parents 131c95e + 71dbda1
commit 02da502
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diff --git a/CHANGELOG b/CHANGELOG
@@ -1,4 +1,11 @@
 
+MiXCR 3.0.5 (25 Feb 2019)
+========================
+
+-- Fixed `writing empty block` exception arising with empty input files and in several other 
+   situations
+
+
 MiXCR 3.0.4 (15 Feb 2019)
 ========================
 

diff --git a/doc/install.rst b/doc/install.rst
@@ -17,13 +17,13 @@ To install MiXCR using Homebrew just type the following commands:
 ::
 
     brew tap milaboratory/all
-    brew install mixcr3
+    brew install mixcr
 
 To install the old MiXCR 2.x series you can use
 
 ::
 
-    brew install mixcr
+    brew install mixcr2
 
 
 Installation on Mac OS X / Linux / FreeBSD from zip distribution

diff --git a/itests.sh b/itests.sh
@@ -48,7 +48,7 @@ case $os in
     ;;
 esac
 
-tests=("case1" "case2" "case3" "case4" "case5")
+tests=("case1" "case2" "case3" "case4" "case5" "case6")
 
 create_standard_results=false
 run_tests=false

diff --git a/itests/case6.sh b/itests/case6.sh
@@ -0,0 +1,7 @@
+#!/usr/bin/env bash
+
+set -euxo pipefail
+
+touch empty_R1.fastq
+touch empty_R2.fastq
+mixcr analyze amplicon --receptor-type tra --impute-germline-on-export -s hs --starting-material rna --contig-assembly --5-end v-primers --3-end j-primers --adapters no-adapters empty_R1.fastq empty_R2.fastq case6
diff --git a/pom.xml b/pom.xml
@@ -33,7 +33,7 @@
 
     <groupId>com.milaboratory</groupId>
     <artifactId>mixcr</artifactId>
-    <version>3.0.4</version>
+    <version>3.0.5</version>
     <packaging>jar</packaging>
     <name>MiXCR</name>
 

diff --git a/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java b/src/main/java/com/milaboratory/mixcr/basictypes/ClnAWriter.java
@@ -60,8 +60,8 @@
  * writeAlignmentsAndIndex() 5. close()
  */
 public final class ClnAWriter implements PipelineConfigurationWriter,
-        AutoCloseable,
-        CanReportProgressAndStage {
+                                         AutoCloseable,
+                                         CanReportProgressAndStage {
     static final String MAGIC_V3 = "MiXCR.CLNA.V03";
     static final String MAGIC_V4 = "MiXCR.CLNA.V04";
     static final String MAGIC = MAGIC_V4;
@@ -328,7 +328,10 @@ public synchronized void writeAlignmentsAndIndex() {
             }
 
             // Writing last block, and waiting for all the data to be flushed
-            writer.writeSync(block);
+            if (!block.isEmpty())
+                writer.writeSync(block);
+            else
+                writer.waitPreviousBlock();
         }
         // Closing sorted output port, this will delete presorted file
         sortedAlignments.close();