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debian/changelog
View file @ bfda1c90
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@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@debian.org> Tue, 21 May 2019 22:16:30 +0200
fastqc (0.11.8+dfsg-1) unstable; urgency=medium
......
debian/patches/htsjdk-api.patch
View file @ bfda1c90
......@@ -2,7 +2,7 @@ Description: use correct SamReader API
Author: Sascha Steinbiss <satta@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@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@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;
......