Changing htsjdk to produce sam version 1.6 (#1211)

* Changing htsjdk to produce sam version 1.6 * Htsjdk has technically been producing Sam version 1.6 since support for long cigars was added. * Updating that list of acceptable versions to include 1.6 and setting the header version of new bams to 1.6. * There is a known issue with writing utf-8 characters in the sam header, this is now allowed for some fields but not handled correctly. See #1202
samtools · Nov 7, 2018 · 393f2c0 · 393f2c0
1 parent 4408649
commit 393f2c0
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Showing 6 changed files with 7 additions and 7 deletions.
diff --git a/src/main/java/htsjdk/samtools/SAMFileHeader.java b/src/main/java/htsjdk/samtools/SAMFileHeader.java
@@ -40,8 +40,8 @@ public class SAMFileHeader extends AbstractSAMHeaderRecord
     public static final String VERSION_TAG = "VN";
     public static final String SORT_ORDER_TAG = "SO";
     public static final String GROUP_ORDER_TAG = "GO";
-    public static final String CURRENT_VERSION = "1.5";
-    public static final Set<String> ACCEPTABLE_VERSIONS = CollectionUtil.makeSet("1.0", "1.3", "1.4", "1.5");
+    public static final String CURRENT_VERSION = "1.6";
+    public static final Set<String> ACCEPTABLE_VERSIONS = CollectionUtil.makeSet("1.0", "1.3", "1.4", "1.5", CURRENT_VERSION );
 
     private SortOrder sortOrder = null;
     private GroupOrder groupOrder = null;

diff --git a/src/test/java/htsjdk/samtools/ValidateSamFileTest.java b/src/test/java/htsjdk/samtools/ValidateSamFileTest.java
@@ -528,7 +528,7 @@ public void testHeaderVersions() throws Exception {
         }
 
         // Test an unacceptable version
-        testHeaderVersion("1.6", false);
+        testHeaderVersion("1.1", false);
     }
 
     @Test(enabled = false)

diff --git a/src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/case1/expected_output.sam b/src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/case1/expected_output.sam
@@ -1,4 +1,4 @@
-@HD	VN:1.5	GO:none	SO:coordinate
+@HD	VN:1.6	GO:none	SO:coordinate
 @SQ	SN:chrM	LN:16571	AS:HG18	UR:/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta	M5:d2ed829b8a1628d16cbeee88e88e39eb	SP:Homo sapiens
 @RG	ID:1	PL:ILLUMINA	SM:sample1
 @PG	ID:1	PN:something

diff --git a/src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/case2/chr11sub_file1.sam b/src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/case2/chr11sub_file1.sam
@@ -1,4 +1,4 @@
-@HD	VN:1.0	GO:none	SO:coordinate
+@HD	VN:1.6	GO:none	SO:coordinate
 @SQ	SN:chrM	LN:16571	AS:HG18	UR:/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta	M5:d2ed829b8a1628d16cbeee88e88e39eb	SP:Homo sapiens
 @RG	ID:1	SM:sample1	PL:ILLUMINA
 @PG	ID:1	PN:A

diff --git a/src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/case2/expected_output.sam b/src/test/resources/htsjdk/samtools/SamFileHeaderMergerTest/case2/expected_output.sam
@@ -1,4 +1,4 @@
-@HD	VN:1.5	GO:none	SO:coordinate
+@HD	VN:1.6	GO:none	SO:coordinate
 @SQ	SN:chrM	LN:16571	AS:HG18	UR:/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta	M5:d2ed829b8a1628d16cbeee88e88e39eb	SP:Homo sapiens
 @RG	ID:1	PL:ILLUMINA	SM:sample1
 @RG	ID:1.1	PL:ILLUMINA	SM:sample2

diff --git a/src/test/resources/htsjdk/samtools/roundtrip.sam b/src/test/resources/htsjdk/samtools/roundtrip.sam
@@ -1,4 +1,4 @@
-@HD	VN:1.5	SO:unsorted
+@HD	VN:1.6	SO:unsorted
 @SQ	SN:chr1	LN:101
 @SQ	SN:chr2	LN:101
 @SQ	SN:chr3	LN:101