X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fhtsjdk%2FHtsContigDb.java;h=37ce625bbc95119702cfcee32605b92cb562d242;hb=3d0101179759ef157b088ea135423cd909512d9f;hp=4357abd546366b707d23d2dc14661d3f2a8fcfb5;hpb=7c70cb09e9de68ab567e38520d6d09f0c17a3939;p=jalview.git

diff --git a/src/jalview/ext/htsjdk/HtsContigDb.java b/src/jalview/ext/htsjdk/HtsContigDb.java
index 4357abd..37ce625 100644
--- a/src/jalview/ext/htsjdk/HtsContigDb.java
+++ b/src/jalview/ext/htsjdk/HtsContigDb.java
@@ -70,8 +70,8 @@ public class HtsContigDb
       return;
     }
 
-    refFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(
-            dbLocation, true);
+    refFile = ReferenceSequenceFileFactory
+            .getReferenceSequenceFile(dbLocation, true);
     if (refFile == null || refFile.getSequenceDictionary() == null)
     {
       // refFile = initSequenceDictionaryFor(dbLocation);
@@ -144,7 +144,8 @@ public class HtsContigDb
     ReferenceSequence refSeq;
     List<SAMSequenceRecord> ret = new ArrayList<SAMSequenceRecord>();
     Set<String> sequenceNames = new HashSet<String>();
-    for (int numSequences = 0; (refSeq = refSeqFile.nextSequence()) != null; ++numSequences)
+    for (int numSequences = 0; (refSeq = refSeqFile
+            .nextSequence()) != null; ++numSequences)
     {
       if (sequenceNames.contains(refSeq.getName()))
       {