Author: Andreas Tille <tille@debian.org>
Last-Update: Thu, 14 Jan 2016 13:50:56 +0100
Bug-Debian: https://bugs.debian.org/810843
Description: Path to samtools changed when switching from libsam-java
 to libhtsjdk-java

--- a/uk/ac/babraham/FastQC/Sequence/BAMFile.java
+++ b/uk/ac/babraham/FastQC/Sequence/BAMFile.java
@@ -25,11 +25,12 @@ import java.io.IOException;
 import java.util.Iterator;
 import java.util.List;
 
-import net.sf.samtools.CigarElement;
-import net.sf.samtools.CigarOperator;
-import net.sf.samtools.SAMFileReader;
-import net.sf.samtools.SAMFormatException;
-import net.sf.samtools.SAMRecord;
+import htsjdk.samtools.CigarElement;
+import htsjdk.samtools.CigarOperator;
+import htsjdk.samtools.SAMFileReader;
+import htsjdk.samtools.SAMFormatException;
+import htsjdk.samtools.SAMRecord;
+import htsjdk.samtools.ValidationStringency;
 
 public class BAMFile implements SequenceFile {
 
@@ -55,7 +56,7 @@ public class BAMFile implements Sequence
 		name = file.getName();
 		this.onlyMapped = onlyMapped;
 
-		SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.SILENT);
+		SAMFileReader.setDefaultValidationStringency(ValidationStringency.SILENT);
 
 		fis = new FileInputStream(file);