Update htsjdk to 2.14.3.

Update some code to avoid deprecated methods.
RealTimeGenomics · Mar 12, 2018 · 04c37b2 · 04c37b2
1 parent 488f8c1
commit 04c37b2
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Showing 7 changed files with 5 additions and 5 deletions.
diff --git a/build.xml b/build.xml
@@ -32,7 +32,7 @@
 
   <property name="regression.update" value=""/> <!-- Empty means don't update nano-regression results -->
 
-  <property name="htsjdk.jar" value="sam-2.12.0.jar"/> <!-- This must currently be built from the RTG fork of htsjdk -->
+  <property name="htsjdk.jar" value="sam-2.14.3.jar"/> <!-- This must currently be built from the RTG fork of htsjdk -->
 
 
   <!-- Define resource collections for compilation, running, etc -->

diff --git a/lib/sam-2.12.0-src.jar → lib/sam-2.14.3-src.jar b/lib/sam-2.12.0-src.jar → lib/sam-2.14.3-src.jar
diff --git a/lib/sam-2.12.0.jar → lib/sam-2.14.3.jar b/lib/sam-2.12.0.jar → lib/sam-2.14.3.jar
diff --git a/src/com/rtg/reader/SamSequence.java b/src/com/rtg/reader/SamSequence.java
@@ -101,7 +101,7 @@ static byte getFlags(SAMRecord record) {
     if (record.getReadNegativeStrandFlag()) {
       flags ^= READ_STRAND_FLAG;
     }
-    if (record.getNotPrimaryAlignmentFlag()) {
+    if (record.isSecondaryAlignment()) {
       flags ^= NOT_PRIMARY_ALIGNMENT_FLAG;
     }
     return flags;

diff --git a/src/com/rtg/sam/DuplicateSamFilter.java b/src/com/rtg/sam/DuplicateSamFilter.java
@@ -49,7 +49,7 @@ public boolean acceptRecord(SAMRecord rec) {
     if (rec == null || rec.getReadName() == null) {
       return false;
     }
-    if (!rec.getNotPrimaryAlignmentFlag()) {
+    if (!rec.isSecondaryAlignment()) {
       return true;
     }
     final long hash = internalHash(rec.getReadName(), !rec.getReadPairedFlag() || rec.getFirstOfPairFlag());

diff --git a/src/com/rtg/sam/SamUtils.java b/src/com/rtg/sam/SamUtils.java
@@ -631,7 +631,7 @@ public static Integer getNHOrIH(SAMRecord sam) {
    */
   public static boolean uniquelyMapped(SAMRecord record) {
     assert !record.getReadUnmappedFlag();
-    if (record.getMappingQuality() == 0 || record.getNotPrimaryAlignmentFlag()) {
+    if (record.getMappingQuality() == 0 || record.isSecondaryAlignment()) {
       return false;
     }
     final Integer nh = SamUtils.getNHOrIH(record);

diff --git a/test/com/rtg/sam/SkipInvalidRecordsIteratorTest.java b/test/com/rtg/sam/SkipInvalidRecordsIteratorTest.java
@@ -343,7 +343,7 @@ public void testBad2First4() throws IOException {
   public void testBad2First5() throws IOException {
     checkWarning(SAM_HEAD10 + SAM_REC_BAD4, 0, "SAM record is invalid in file ",
       "badread4" + TAB + "2308" + TAB + "gi0" + TAB + "3" + TAB + "255" + TAB + "10M" + TAB + "*" + TAB + "0" + TAB + "0" + TAB + "AAAAAAAAAA" + TAB + "GC@=I3IIII" + TAB /*+ "AS:i:0" + TAB + "IH:i:0"*/,
-      "ERROR: Read name badread4, Not primary alignment flag should not be set for unmapped read.",
+      "ERROR: Read name badread4, Secondary alignment flag should not be set for unmapped read.",
       "ERROR: Read name badread4, Supplementary alignment flag should not be set for unmapped read.",
       "ERROR: Read name badread4, MAPQ should be 0 for unmapped read.]",
       "At data line 1"); //"Line: badread4", "MRNM not specified but flags indicate mate mapped;");