fixes due to bdg-formats 0.14.0

bigdatagenomics · Sep 23, 2019 · 1c20d01 · 1c20d01
1 parent f750a9c
commit 1c20d01
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Showing 2 changed files with 6 additions and 6 deletions.
diff --git a/convert-htsjdk/src/main/java/org/bdgenomics/convert/htsjdk/AlignmentRecordToSamRecord.java b/convert-htsjdk/src/main/java/org/bdgenomics/convert/htsjdk/AlignmentRecordToSamRecord.java
@@ -80,11 +80,11 @@ public SAMRecord convert(final AlignmentRecord alignmentRecord,
         builder.setReadName(alignmentRecord.getReadName());
         builder.setReadString(alignmentRecord.getSequence());
 
-        if (alignmentRecord.getQuality() == null) {
+        if (alignmentRecord.getQualityScores() == null) {
             builder.setBaseQualityString("*");
         }
         else {
-            builder.setBaseQualityString(alignmentRecord.getQuality());
+            builder.setBaseQualityString(alignmentRecord.getQualityScores());
         }
 
         String readGroupId = alignmentRecord.getReadGroupId();
@@ -178,8 +178,8 @@ public SAMRecord convert(final AlignmentRecord alignmentRecord,
         if (alignmentRecord.getMismatchingPositions() != null) {
             builder.setAttribute("MD", alignmentRecord.getMismatchingPositions());
         }
-        if (alignmentRecord.getOriginalQuality() != null) {
-            builder.setOriginalBaseQualities(SAMUtils.fastqToPhred(alignmentRecord.getOriginalQuality()));
+        if (alignmentRecord.getOriginalQualityScores() != null) {
+            builder.setOriginalBaseQualities(SAMUtils.fastqToPhred(alignmentRecord.getOriginalQualityScores()));
         }
         if (alignmentRecord.getOriginalCigar() != null) {
             builder.setAttribute("OC", alignmentRecord.getOriginalCigar());

diff --git a/convert-htsjdk/src/main/java/org/bdgenomics/convert/htsjdk/SamRecordToAlignmentRecord.java b/convert-htsjdk/src/main/java/org/bdgenomics/convert/htsjdk/SamRecordToAlignmentRecord.java
@@ -81,10 +81,10 @@ public AlignmentRecord convert(final SAMRecord samRecord,
         }
 
         if (samRecord.getBaseQualityString() != "*") {
-            builder.setQuality(samRecord.getBaseQualityString());
+            builder.setQualityScores(samRecord.getBaseQualityString());
         }
         if (samRecord.getOriginalBaseQualities() != null) {
-            builder.setOriginalQuality(SAMUtils.phredToFastq(samRecord.getOriginalBaseQualities()));
+            builder.setOriginalQualityScores(SAMUtils.phredToFastq(samRecord.getOriginalBaseQualities()));
         }
 
         int readReference = samRecord.getReferenceIndex();