Your message dated Tue, 22 Nov 2016 15:03:55 +0000
with message-id <[email protected]>
and subject line Bug#844760: fixed in fastqc 0.11.5+dfsg-5
has caused the Debian Bug report #844760,
regarding fastqc: Please temporarily drop support for fast5 files
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
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misconfiguration somewhere. Please contact [email protected]
immediately.)
--
844760: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=844760
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: fastqc
Version: 0.11.5+dfsg-4
Severity: important
Tags: patch
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Hi,
HDF5 1.10 is about to transition into unstable [1], and unfortunately a
FastQC build-dependency, libsis-jhdf5-java, doesn't support this new
release yet [2], and we have no information about its upstream schedule
wrt HDF5 1.10.
I've had a look at the FastQC code, and AFAIUI, libsis-jhdf5-java is
required only to support fast5 files from nanopore sequences.
Since these files can easily be converted to FastQ format using
poretools [3], I propose to temporarily drop fast5 support from FastQC
to avoid a removal from testing.
Please find attached a patch proposal to this end.
Thanks in advance,
_g.
[1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=842177#40
[2] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=842815
{3] https://bioinfoexpert.com/2016/06/15/minion-fast5-to-fastq/
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diff --git a/debian/changelog b/debian/changelog
index aeba166..20d6f39 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,13 @@
+fastqc (0.11.5+dfsg-4.1) unstable; urgency=medium
+
+ * Non-maintainer upload.
+ * New patch drop-fast5.patch to temporarily drop support for fast5
+ file format. This way we can drop the build-dependency on
+ libsis-jhdf5-java which doesn't support HDF5 1.10 yet (#842815).
+ fast5 files can easily be converted to fastq using poretools.
+
+ -- Gilles Filippini <[email protected]> Fri, 18 Nov 2016 19:03:15 +0100
+
fastqc (0.11.5+dfsg-4) unstable; urgency=low
* Team upload.
diff --git a/debian/control b/debian/control
index 7fa5f02..9cd7223 100644
--- a/debian/control
+++ b/debian/control
@@ -11,8 +11,7 @@ Build-Depends: debhelper (>= 9),
ant,
libhtsjdk-java,
libjbzip2-java,
- libcommons-math3-java,
- libsis-jhdf5-java
+ libcommons-math3-java
Standards-Version: 3.9.8
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/fastqc.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/fastqc.git
diff --git a/debian/patches/drop-fast5.patch b/debian/patches/drop-fast5.patch
new file mode 100644
index 0000000..f9a0cf6
--- /dev/null
+++ b/debian/patches/drop-fast5.patch
@@ -0,0 +1,151 @@
+Index: fastqc/fastqc
+===================================================================
+--- fastqc.orig/fastqc
++++ fastqc/fastqc
+@@ -74,7 +74,6 @@ my $quiet;
+ my $nogroup;
+ my $expgroup;
+ my $casava;
+-my $nano;
+ my $nofilter;
+ my $kmer_size;
+ my $temp_directory;
+@@ -91,7 +90,6 @@ my $result = GetOptions('version' => \$v
+ 'threads=i' => \$threads,
+ 'kmers=i' => \$kmer_size,
+ 'casava' => \$casava,
+- 'nano' => \$nano,
+ 'nofilter' => \$nofilter,
+ 'contaminants=s' => \$contaminant,
+ 'adapters=s' => \$adapter,
+@@ -183,10 +181,6 @@ if ($casava) {
+ push @java_args ,"-Dfastqc.casava=true";
+ }
+
+-if ($nano) {
+- push @java_args ,"-Dfastqc.nano=true";
+-}
+-
+
+ if ($nofilter) {
+ push @java_args ,"-Dfastqc.nofilter=true";
+@@ -320,11 +314,6 @@ DESCRIPTION
+ (including being gzipped and ending with .gz) otherwise they
+ won't be grouped together correctly.
+
+- --nano Files come from naopore sequences and are in fast5 format. In
+- this mode you can pass in directories to process and the program
+- will take in all fast5 files within those directories and produce
+- a single output file from the sequences found in all files.
+-
+ --nofilter If running with --casava then don't remove read flagged by
+ casava as poor quality when performing the QC analysis.
+
+Index: fastqc/uk/ac/babraham/FastQC/Sequence/SequenceFactory.java
+===================================================================
+--- fastqc.orig/uk/ac/babraham/FastQC/Sequence/SequenceFactory.java
++++ fastqc/uk/ac/babraham/FastQC/Sequence/SequenceFactory.java
+@@ -99,9 +99,6 @@ public class SequenceFactory {
+ // We default to using all reads
+ return new BAMFile(file,false);
+ }
+- else if (file.getName().toLowerCase().endsWith(".fast5")) {
+- return new Fast5File(file);
+- }
+ else {
+ return new FastQFile(config,file);
+ }
+Index: fastqc/uk/ac/babraham/FastQC/Sequence/Fast5File.java
+===================================================================
+--- fastqc.orig/uk/ac/babraham/FastQC/Sequence/Fast5File.java
++++ /dev/null
+@@ -1,89 +0,0 @@
+-/**
+- * Copyright Copyright 2010-15 Simon Andrews
+- *
+- * This file is part of FastQC.
+- *
+- * FastQC is free software; you can redistribute it and/or modify
+- * it under the terms of the GNU General Public License as published by
+- * the Free Software Foundation; either version 3 of the License, or
+- * (at your option) any later version.
+- *
+- * FastQC is distributed in the hope that it will be useful,
+- * but WITHOUT ANY WARRANTY; without even the implied warranty of
+- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+- * GNU General Public License for more details.
+- *
+- * You should have received a copy of the GNU General Public License
+- * along with FastQC; if not, write to the Free Software
+- * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+- */
+-package uk.ac.babraham.FastQC.Sequence;
+-
+-import java.io.File;
+-import java.io.IOException;
+-
+-import ch.systemsx.cisd.hdf5.HDF5Factory;
+-import ch.systemsx.cisd.hdf5.IHDF5SimpleReader;
+-
+-public class Fast5File implements SequenceFile {
+-
+- private Sequence nextSequence = null;
+- private File file;
+-
+- private String name;
+-
+- protected Fast5File(File file) throws SequenceFormatException, IOException {
+- this.file = file;
+- name = file.getName();
+-
+- IHDF5SimpleReader reader = HDF5Factory.openForReading(file);
+-
+- if (reader.exists("Analyses/Basecall_2D_000/BaseCalled_template/Fastq")) {
+-
+- String fastq = reader.readString("Analyses/Basecall_2D_000/BaseCalled_template/Fastq");
+-
+- String [] sections = fastq.split("\\n");
+-
+- if (sections.length != 4) {
+- throw new SequenceFormatException("Didn't get 4 sections from "+fastq);
+- }
+-
+- nextSequence = new Sequence(this, sections[1].toUpperCase(),sections[3], sections[0]);
+- }
+- reader.close();
+-
+- }
+-
+- public String name() {
+- return name;
+- }
+-
+- public int getPercentComplete() {
+- if (! hasNext()) return 100;
+-
+- return 0;
+- }
+-
+- public boolean isColorspace() {
+- return false;
+- }
+-
+- public boolean hasNext() {
+- return nextSequence != null;
+- }
+-
+- public Sequence next() throws SequenceFormatException {
+- Sequence seq = nextSequence;
+- nextSequence = null;
+- return seq;
+- }
+-
+- public void remove() {
+- // No action here
+- }
+-
+- public File getFile() {
+- return file;
+- }
+-
+-}
diff --git a/debian/patches/series b/debian/patches/series
index 0801e7d..6f96f87 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -3,3 +3,4 @@ fastqc.patch
fix-help-call.patch
set_configuration_path.patch
adapt_to_htslib.patch
+drop-fast5.patch
--- End Message ---
--- Begin Message ---
Source: fastqc
Source-Version: 0.11.5+dfsg-5
We believe that the bug you reported is fixed in the latest version of
fastqc, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated fastqc package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Tue, 22 Nov 2016 14:43:31 +0100
Source: fastqc
Binary: fastqc
Architecture: source all
Version: 0.11.5+dfsg-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
fastqc - quality control for high throughput sequence data
Closes: 844760
Changes:
fastqc (0.11.5+dfsg-5) unstable; urgency=medium
.
[ Gilles Filippini ]
* New patch drop-fast5.patch to temporarily drop support for fast5
file format. This way we can drop the build-dependency on
libsis-jhdf5-java which doesn't support HDF5 1.10 yet (#842815).
fast5 files can easily be converted to fastq using poretools.
Closes: #844760
.
[ Andreas Tille ]
* debhelper 10
* d/watch: version=4
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