[med-svn] [Git][med-team/fastqc][master] 2 commits: Fix debian/patches/htsjdk-api.patch

[Dylan Aïssi]

Dylan Aïssi pushed to branch master at Debian Med / fastqc


Commits:
82509227 by Dylan Aïssi at 2019-05-21T20:00:58Z
Fix debian/patches/htsjdk-api.patch

- - - - -
bfda1c90 by Dylan Aïssi at 2019-05-21T20:19:32Z
Update d/changelog

- - - - -


2 changed files:

- debian/changelog
- debian/patches/htsjdk-api.patch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,5 +1,7 @@
 fastqc (0.11.8+dfsg-2) UNRELEASED; urgency=medium
 
+  * Team upload.
+
   [ Jelmer Vernooij ]
   * Trim trailing whitespace.
   * Use secure copyright file specification URI.
@@ -7,7 +9,11 @@ fastqc (0.11.8+dfsg-2) UNRELEASED; urgency=medium
   [ Michael R. Crusoe ]
   * debian/fastqc.desktop: Update path to the icon.
 
- -- Jelmer Vernooij <jelmer at debian.org>  Sat, 20 Oct 2018 20:48:12 +0000
+  [ Dylan Aïssi ]
+  * Update d/patches/htsjdk-api.patch to fix processing
+      of SAM/BAM files (Closes: #897109). Thanks to Chris Norman.
+
+ -- Dylan Aïssi <daissi at debian.org>  Tue, 21 May 2019 22:16:30 +0200
 
 fastqc (0.11.8+dfsg-1) unstable; urgency=medium
 


=====================================
debian/patches/htsjdk-api.patch
=====================================
@@ -2,7 +2,7 @@ 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 +27,9 @@ import java.util.List;
+@@ -27,7 +27,9 @@
  
  import htsjdk.samtools.CigarElement;
  import htsjdk.samtools.CigarOperator;
@@ -13,7 +13,7 @@ Author: Sascha Steinbiss <satta at debian.org>
  import htsjdk.samtools.SAMFormatException;
  import htsjdk.samtools.SAMRecord;
  import htsjdk.samtools.ValidationStringency;
-@@ -44,7 +46,7 @@ public class BAMFile implements Sequence
+@@ -44,7 +46,7 @@
  	// only way to access the file pointer.
  	private FileInputStream fis;
  
@@ -22,22 +22,24 @@ Author: Sascha Steinbiss <satta at debian.org>
  	private String name;
  	private Sequence nextSequence = null;
  	Iterator<SAMRecord> it;
-@@ -56,11 +58,10 @@ public class BAMFile implements Sequence
+@@ -56,11 +58,12 @@
  		name = file.getName();
  		this.onlyMapped = onlyMapped;
  
 -		SAMFileReader.setDefaultValidationStringency(ValidationStringency.SILENT);
-+		SamInputResource sir = SamInputResource.of(fis);
-+		SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(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(sir);
  		
  		it = br.iterator();
  		readNext();
-@@ -135,7 +136,7 @@ public class BAMFile implements Sequence
+@@ -135,7 +138,7 @@
  		// through the file.
  		if (recordSize == 0) {
  			recordSize = (record.getReadLength()*2)+150;



View it on GitLab: https://salsa.debian.org/med-team/fastqc/compare/46b4ba0665b3aca2d53cad704e8f0db4900bff1c...bfda1c90add9818e96ed1d0686d3c64060fa09dc

-- 
View it on GitLab: https://salsa.debian.org/med-team/fastqc/compare/46b4ba0665b3aca2d53cad704e8f0db4900bff1c...bfda1c90add9818e96ed1d0686d3c64060fa09dc
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