[med-svn] [fastqc] 01/01: fix htsjdk import

[Olivier Sallou]

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osallou pushed a commit to branch master
in repository fastqc.

commit cdad8991b089385cb574ddb5c6b929c78e5a5ac6
Author: Olivier Sallou <olivier.sallou at debian.org>
Date:   Mon Jan 18 10:10:51 2016 +0100

    fix htsjdk import
---
 debian/patches/adapt_to_htslib.patch | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/debian/patches/adapt_to_htslib.patch b/debian/patches/adapt_to_htslib.patch
index c97c5ea..be269ac 100644
--- a/debian/patches/adapt_to_htslib.patch
+++ b/debian/patches/adapt_to_htslib.patch
@@ -6,7 +6,7 @@ Description: Path to samtools changed when switching from libsam-java
 
 --- a/uk/ac/babraham/FastQC/Sequence/BAMFile.java
 +++ b/uk/ac/babraham/FastQC/Sequence/BAMFile.java
-@@ -25,11 +25,11 @@ import java.io.IOException;
+@@ -25,11 +25,12 @@
  import java.util.Iterator;
  import java.util.List;
  
@@ -20,6 +20,16 @@ Description: Path to samtools changed when switching from libsam-java
 +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 @@
+ 		name = file.getName();
+ 		this.onlyMapped = onlyMapped;
+ 
+-		SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.SILENT);
++		SAMFileReader.setDefaultValidationStringency(ValidationStringency.SILENT);
+ 
+ 		fis = new FileInputStream(file);
+ 		

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