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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);
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