[med-svn] [fastqc] 01/05: fix API change

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository fastqc.

commit 59233c0e3f15fa0bc5f1d90d4278b12113041f97
Author: Sascha Steinbiss <satta at debian.org>
Date:   Thu Dec 8 19:03:52 2016 +0000

    fix API change
---
 debian/patches/htsjdk-api.patch | 19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

diff --git a/debian/patches/htsjdk-api.patch b/debian/patches/htsjdk-api.patch
index 8d12b18..ec49398 100644
--- a/debian/patches/htsjdk-api.patch
+++ b/debian/patches/htsjdk-api.patch
@@ -2,17 +2,18 @@ Description: use correct SamReader API
 Author: Sascha Steinbiss <satta at debian.org>
 --- a/uk/ac/babraham/FastQC/Sequence/BAMFile.java
 +++ b/uk/ac/babraham/FastQC/Sequence/BAMFile.java
-@@ -27,7 +27,8 @@
+@@ -27,7 +27,9 @@
  
  import htsjdk.samtools.CigarElement;
  import htsjdk.samtools.CigarOperator;
 -import htsjdk.samtools.SAMFileReader;
++import htsjdk.samtools.SamInputResource;
 +import htsjdk.samtools.SamReader;
 +import htsjdk.samtools.SamReaderFactory;
  import htsjdk.samtools.SAMFormatException;
  import htsjdk.samtools.SAMRecord;
  import htsjdk.samtools.ValidationStringency;
-@@ -44,7 +45,7 @@
+@@ -44,7 +46,7 @@
  	// only way to access the file pointer.
  	private FileInputStream fis;
  
@@ -21,23 +22,23 @@ Author: Sascha Steinbiss <satta at debian.org>
  	private String name;
  	private Sequence nextSequence = null;
  	Iterator<SAMRecord> it;
-@@ -55,12 +56,10 @@
- 		fileSize = file.length();
+@@ -56,11 +58,11 @@
  		name = file.getName();
  		this.onlyMapped = onlyMapped;
--
+ 
 -		SAMFileReader.setDefaultValidationStringency(ValidationStringency.SILENT);
 -
--		fis = new FileInputStream(file);
- 		
+ 		fis = new FileInputStream(file);
+-		
 -		br = new SAMFileReader(fis);
++		SamInputResource sir = SamInputResource.of(fis);
 +		SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);
 +
-+		br = srf.open(file);
++		br = srf.open(sir);
  		
  		it = br.iterator();
  		readNext();
-@@ -135,7 +134,7 @@
+@@ -135,7 +137,7 @@
  		// through the file.
  		if (recordSize == 0) {
  			recordSize = (record.getReadLength()*2)+150;

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