Merge branch 'develop' into patch/JAL-3088_finalbracenotinrightplace

[jalview.git] / src / jalview / ext / htsjdk / HtsContigDb.java

diff --git a/src/jalview/ext/htsjdk/HtsContigDb.java b/src/jalview/ext/htsjdk/HtsContigDb.java
index 73d1674..8cce87a 100644 (file)
--- a/src/jalview/ext/htsjdk/HtsContigDb.java
+++ b/src/jalview/ext/htsjdk/HtsContigDb.java
@@ -251,8 +251,8 @@ public class HtsContigDb
   // ///// end of hts bits.
 
   /**
-   * Reads the contig with the given id and returns as a Jalview SequenceI object.
-   * Note the database must be indexed for this operation to succeed.
+   * Reads the contig with the given id and returns as a Jalview SequenceI
+   * object. Note the database must be indexed for this operation to succeed.
    * 
    * @param id
    * @return
@@ -261,7 +261,7 @@ public class HtsContigDb
   {
     if (!isValid() || !refFile.isIndexed())
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Cannot read contig as file is invalid or not indexed");
       return null;
     }