Bug#929348: unblock: fastqc/0.11.8+dfsg-2
Package: release.debian.org
Severity: normal
User: release.debian.org@packages.debian.org
Usertags: unblock
Please unblock package fastqc
I admit this upload contains a bit more than just a simple fix. In git
we kept some trimming of trailing whitespace done by Jelmer Vernoo as
well as his fix for the secure URI in d/copyright.
Fixing the icon path in copyright as well as fixes for the syntax in
debian/upstream/metadata should be sensible changes as well we did not
want to remove from HEAD before the actual fix of bug #897109.
So please excuse these extra but non-critical changes besides the
bug fix.
Thanks for working on the Buster release
Andreas.
unblock fastqc/0.11.8+dfsg-2
-- System Information:
Debian Release: 9.9
APT prefers stable-updates
APT policy: (500, 'stable-updates'), (500, 'stable')
Architecture: amd64 (x86_64)
Kernel: Linux 4.9.0-6-amd64 (SMP w/1 CPU core)
Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8), LANGUAGE=de_DE.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
diff -Nru fastqc-0.11.8+dfsg/debian/changelog fastqc-0.11.8+dfsg/debian/changelog
--- fastqc-0.11.8+dfsg/debian/changelog 2018-10-17 19:25:09.000000000 +0200
+++ fastqc-0.11.8+dfsg/debian/changelog 2019-05-21 22:20:32.000000000 +0200
@@ -1,3 +1,20 @@
+fastqc (0.11.8+dfsg-2) unstable; urgency=medium
+
+ * Team upload.
+
+ [ Jelmer Vernooij ]
+ * Trim trailing whitespace.
+ * Use secure copyright file specification URI.
+
+ [ Michael R. Crusoe ]
+ * debian/fastqc.desktop: Update path to the icon.
+
+ [ 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 22:20:32 +0200
+
fastqc (0.11.8+dfsg-1) unstable; urgency=medium
* New upstream release.
@@ -9,7 +26,7 @@
fastqc (0.11.7+dfsg-1) unstable; urgency=medium
[ Steffen Moeller ]
- * debian/upstream/metadata: Added references to
+ * debian/upstream/metadata: Added references to
OMICtools, SciCrunch, bio.tools registries
[ Andreas Tille ]
@@ -63,8 +80,8 @@
fastqc (0.11.5+dfsg-3) unstable; urgency=medium
* Team upload.
-
- [ Canberk Koç ]
+
+ [ Canberk Koç ]
* Autopkgtest added
[ Andreas Tille ]
@@ -138,14 +155,14 @@
fastqc (0.11.2+dfsg-1) unstable; urgency=medium
- * New upstream release
+ * New upstream release
-- Olivier Sallou <osallou@debian.org> Mon, 09 Jun 2014 10:41:06 +0200
fastqc (0.10.1+dfsg-2) unstable; urgency=low
* Add patch to fix Templates and Contaminants loading
- in non interactive mode (Closes: #697604)
+ in non interactive mode (Closes: #697604)
-- Olivier Sallou <osallou@debian.org> Wed, 05 Jun 2013 17:08:44 +0200
diff -Nru fastqc-0.11.8+dfsg/debian/copyright fastqc-0.11.8+dfsg/debian/copyright
--- fastqc-0.11.8+dfsg/debian/copyright 2018-10-17 19:25:09.000000000 +0200
+++ fastqc-0.11.8+dfsg/debian/copyright 2019-05-21 22:20:32.000000000 +0200
@@ -1,4 +1,4 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: FastQC
Source: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Files-Excluded:
diff -Nru fastqc-0.11.8+dfsg/debian/fastqc.desktop fastqc-0.11.8+dfsg/debian/fastqc.desktop
--- fastqc-0.11.8+dfsg/debian/fastqc.desktop 2018-10-17 19:25:09.000000000 +0200
+++ fastqc-0.11.8+dfsg/debian/fastqc.desktop 2019-05-21 22:20:32.000000000 +0200
@@ -3,7 +3,7 @@
Exec=fastqc
GenericName[en_US]=FastQC quality control
GenericName=FastQC quality control
-Icon=fastqc_icon
+Icon=/usr/share/icons/hicolor/32x32/apps/fastqc_icon.png
Name[en_US]=FastQC quality control
Name=FastQC quality control
Categories=Science;Biology;
diff -Nru fastqc-0.11.8+dfsg/debian/patches/htsjdk-api.patch fastqc-0.11.8+dfsg/debian/patches/htsjdk-api.patch
--- fastqc-0.11.8+dfsg/debian/patches/htsjdk-api.patch 2018-10-17 19:25:09.000000000 +0200
+++ fastqc-0.11.8+dfsg/debian/patches/htsjdk-api.patch 2019-05-21 22:20:32.000000000 +0200
@@ -2,7 +2,7 @@
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 @@
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 @@
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;
diff -Nru fastqc-0.11.8+dfsg/debian/tests/run-unit-test fastqc-0.11.8+dfsg/debian/tests/run-unit-test
--- fastqc-0.11.8+dfsg/debian/tests/run-unit-test 2018-10-17 19:25:09.000000000 +0200
+++ fastqc-0.11.8+dfsg/debian/tests/run-unit-test 2019-05-21 22:20:32.000000000 +0200
@@ -11,6 +11,7 @@
cd $AUTOPKGTEST_TMP
+set -x
gunzip *.gz
/usr/bin/fastqc example.fastq
diff -Nru fastqc-0.11.8+dfsg/debian/upstream/edam fastqc-0.11.8+dfsg/debian/upstream/edam
--- fastqc-0.11.8+dfsg/debian/upstream/edam 2018-10-17 19:25:09.000000000 +0200
+++ fastqc-0.11.8+dfsg/debian/upstream/edam 2019-05-21 22:20:32.000000000 +0200
@@ -6,9 +6,9 @@
- name: summary
function:
- Sequencing quality control
- inputs:
+ input:
- data: Sequence
formats: [FASTQ, BAM, SAM]
- outputs:
+ output:
- data: Report
formats: [Text, HTML]
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