Source: fastqc
Version: 0.11.5+dfsg-4
Severity: important
Tags: patch
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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 <p...@debian.org> 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
