From 9934a6f4fb9533fb436c93e4e9489db07d81d77d Mon Sep 17 00:00:00 2001 From: jenniferliddle Date: Tue, 23 Feb 2016 12:15:04 +0000 Subject: [PATCH 1/2] handle unknown sort order in header --- Changes | 3 +++ src/uk/ac/sanger/npg/picard/BamIndexDecoder.java | 11 +++++++++++ 2 files changed, 14 insertions(+) diff --git a/Changes b/Changes index bfb3a77..86b8ef5 100644 --- a/Changes +++ b/Changes @@ -1,3 +1,6 @@ + +- 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 diff --git a/src/uk/ac/sanger/npg/picard/BamIndexDecoder.java b/src/uk/ac/sanger/npg/picard/BamIndexDecoder.java index 93143d2..35cdc7a 100644 --- a/src/uk/ac/sanger/npg/picard/BamIndexDecoder.java +++ b/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); } From 04cd70b5222878bd36f17b24477583b35a4e1e36 Mon Sep 17 00:00:00 2001 From: jenniferliddle Date: Thu, 25 Feb 2016 14:31:52 +0000 Subject: [PATCH 2/2] Updated version number for release --- Changes | 2 +- nbproject/project.properties | 2 +- src/uk/ac/sanger/npg/picard/PicardCommandLine.java | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/Changes b/Changes index 86b8ef5..8e99693 100644 --- a/Changes +++ b/Changes @@ -1,4 +1,4 @@ - +release 1.19 - cope with unknown sort order in header release 1.18 diff --git a/nbproject/project.properties b/nbproject/project.properties index 51e97b0..73adf25 100644 --- a/nbproject/project.properties +++ b/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=\ diff --git a/src/uk/ac/sanger/npg/picard/PicardCommandLine.java b/src/uk/ac/sanger/npg/picard/PicardCommandLine.java index 980c7af..6de69f2 100644 --- a/src/uk/ac/sanger/npg/picard/PicardCommandLine.java +++ b/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