Merge pull request #86 from wtsi-npg/devel

Release 1.19

Author: jenniferliddle

Changes

@@ -1,3 +1,6 @@
+release 1.19
+- cope with unknown sort order in header
+
 release 1.18
 - new command line option CHANGE_RG_NAME default false
 - NB this is a change to previous behaviour, where it was always true

nbproject/project.properties

@@ -33,7 +33,7 @@ file.reference.jackson-core-2.0.0.jar=lib/jackson/jackson-core-2.0.0.jar
 file.reference.jackson-databind-2.0.0.jar=lib/jackson/jackson-databind-2.0.0.jar
 file.reference.picard.jar=lib/picard/picard-1.96.jar
 file.reference.sam.jar=lib/picard/sam-1.96.jar
-illumina2bam.version=1.18
+illumina2bam.version=1.19
 includes=**
 jar.compress=false
 javac.classpath=\

src/uk/ac/sanger/npg/picard/BamIndexDecoder.java

@@ -354,6 +354,11 @@ public void generateOutputFile(SAMFileHeader header) {
                         + OUTPUT_FORMAT;
                 final SAMFileHeader perBarcodeOutputHeader = outputHeader.clone();
                 perBarcodeOutputHeader.setReadGroups(readGroupList);
+                try {
+                    perBarcodeOutputHeader.getSortOrder();
+                } catch(IllegalArgumentException e) {
+                    perBarcodeOutputHeader.setSortOrder(SAMFileHeader.SortOrder.unsorted);
+                }
                 final SAMFileWriter outPerBarcode = new SAMFileWriterFactory().makeSAMOrBAMWriter(perBarcodeOutputHeader, true, new File(barcodeBamOutputName));
                 outputList.put(barcode, outPerBarcode);
             }
@@ -363,6 +368,12 @@ public void generateOutputFile(SAMFileHeader header) {
         if (OUTPUT != null) {
             log.info("Open output file with header: " + OUTPUT.getName());
             outputHeader.setReadGroups(fullReadGroupList);
+            try {
+                outputHeader.getSortOrder();
+            } catch(IllegalArgumentException e) {
+                outputHeader.setSortOrder(SAMFileHeader.SortOrder.unsorted);
+            }
+
             this.out = new SAMFileWriterFactory().makeSAMOrBAMWriter(outputHeader, true, OUTPUT);
         }
 

src/uk/ac/sanger/npg/picard/PicardCommandLine.java

@@ -32,7 +32,7 @@
  */
 public abstract class PicardCommandLine extends CommandLineProgram {
 
-    public static final String version = "1.17";
+    public static final String version = "1.19";
 
     /**
      * Generate Program Record for this program itself