[med-svn] [fastqc] 01/01: use new htsjdk API

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository fastqc.

commit 19b42d0cd0d79c8b298e19b160cb7aa0c79ea13d
Author: Sascha Steinbiss <satta at debian.org>
Date:   Thu Dec 8 15:49:39 2016 +0000

    use new htsjdk API
---
 debian/changelog                |  7 ++++++
 debian/patches/htsjdk-api.patch | 48 +++++++++++++++++++++++++++++++++++++++++
 debian/patches/series           |  1 +
 3 files changed, 56 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index f70200d..ee1abe7 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+fastqc (0.11.5+dfsg-6) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * Avoid use of SAMFileReader to fix FTBFS.
+
+ -- Sascha Steinbiss <satta at debian.org>  Thu, 08 Dec 2016 15:40:00 +0000
+
 fastqc (0.11.5+dfsg-5) unstable; urgency=medium
 
   [ Gilles Filippini ]
diff --git a/debian/patches/htsjdk-api.patch b/debian/patches/htsjdk-api.patch
new file mode 100644
index 0000000..8d12b18
--- /dev/null
+++ b/debian/patches/htsjdk-api.patch
@@ -0,0 +1,48 @@
+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 @@
+ 
+ import htsjdk.samtools.CigarElement;
+ import htsjdk.samtools.CigarOperator;
+-import htsjdk.samtools.SAMFileReader;
++import htsjdk.samtools.SamReader;
++import htsjdk.samtools.SamReaderFactory;
+ import htsjdk.samtools.SAMFormatException;
+ import htsjdk.samtools.SAMRecord;
+ import htsjdk.samtools.ValidationStringency;
+@@ -44,7 +45,7 @@
+ 	// only way to access the file pointer.
+ 	private FileInputStream fis;
+ 
+-	private SAMFileReader br;
++	private SamReader br;
+ 	private String name;
+ 	private Sequence nextSequence = null;
+ 	Iterator<SAMRecord> it;
+@@ -55,12 +56,10 @@
+ 		fileSize = file.length();
+ 		name = file.getName();
+ 		this.onlyMapped = onlyMapped;
+-
+-		SAMFileReader.setDefaultValidationStringency(ValidationStringency.SILENT);
+-
+-		fis = new FileInputStream(file);
+ 		
+-		br = new SAMFileReader(fis);
++		SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);
++
++		br = srf.open(file);
+ 		
+ 		it = br.iterator();
+ 		readNext();
+@@ -135,7 +134,7 @@
+ 		// through the file.
+ 		if (recordSize == 0) {
+ 			recordSize = (record.getReadLength()*2)+150;
+-			if (br.isBinary()) {
++			if (br.type() == SamReader.Type.BAM_TYPE || br.type() == SamReader.Type.CRAM_TYPE) {
+ 				recordSize /= 4;
+ 			}
+ 		}
diff --git a/debian/patches/series b/debian/patches/series
index 6f96f87..3cd2634 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -4,3 +4,4 @@ fix-help-call.patch
 set_configuration_path.patch
 adapt_to_htslib.patch
 drop-fast5.patch
+htsjdk-api.patch

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