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.classpath 0 → 100644
View file @ 30567660
<?xml version="1.0" encoding="UTF-8"?>
<classpath>
<classpathentry kind="src" path=""/>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
<classpathentry kind="lib" path="jbzip2-0.9.jar"/>
<classpathentry kind="lib" path="sam-1.103.jar"/>
<classpathentry kind="lib" path="cisd-jhdf5.jar"/>
<classpathentry kind="output" path="bin"/>
</classpath>
.gitignore 0 → 100644
View file @ 30567660
# Compiled files
/bin/
# Compiled class file
*.class
# Log file
*.log
# BlueJ files
*.ctxt
# Mobile Tools for Java (J2ME)
.mtj.tmp/
# Package Files #
*.jar
*.war
*.ear
*.zip
*.tar.gz
*.rar
# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
hs_err_pid*
.project 0 → 100644
View file @ 30567660
<?xml version="1.0" encoding="UTF-8"?>
<projectDescription>
<name>FastQC</name>
<comment></comment>
<projects>
</projects>
<buildSpec>
<buildCommand>
<name>org.eclipse.jdt.core.javabuilder</name>
<arguments>
</arguments>
</buildCommand>
</buildSpec>
<natures>
<nature>org.eclipse.jdt.core.javanature</nature>
</natures>
</projectDescription>
.settings/org.eclipse.jdt.core.prefs 0 → 100644
View file @ 30567660
#Tue Nov 23 20:41:22 GMT 2010
eclipse.preferences.version=1
org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.5
org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
org.eclipse.jdt.core.compiler.compliance=1.5
org.eclipse.jdt.core.compiler.debug.lineNumber=generate
org.eclipse.jdt.core.compiler.debug.localVariable=generate
org.eclipse.jdt.core.compiler.debug.sourceFile=generate
org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
org.eclipse.jdt.core.compiler.source=1.5
Configuration/contaminant_list.txt
View file @ 30567660
......@@ -43,7 +43,6 @@ Illumina NlaIII expression Sequencing Primer CCGACAGGTTCAGAGTTCTACAGTCCGACATG
Illumina Small RNA Adapter 1 GTTCAGAGTTCTACAGTCCGACGATC
Illumina Small RNA Adapter 2 TGGAATTCTCGGGTGCCAAGG
Illumina Small RNA RT Primer CAAGCAGAAGACGGCATACGA
Illumina Small RNA PCR Primer 1 CAAGCAGAAGACGGCATACGA
Illumina Small RNA PCR Primer 2 AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA
Illumina Small RNA Sequencing Primer CGACAGGTTCAGAGTTCTACAGTCCGACGATC
......@@ -84,14 +83,11 @@ Illumina NlaIII Gex PCR Primer 1 CAAGCAGAAGACGGCATACGA
Illumina NlaIII Gex PCR Primer 2 AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA
Illumina NlaIII Gex Sequencing Primer CCGACAGGTTCAGAGTTCTACAGTCCGACATG
Illumina Small RNA RT Primer CAAGCAGAAGACGGCATACGA
Illumina 5p RNA Adapter GTTCAGAGTTCTACAGTCCGACGATC
Illumina RNA Adapter1 TGGAATTCTCGGGTGCCAAGG
Illumina Small RNA 3p Adapter 1 ATCTCGTATGCCGTCTTCTGCTTG
Illumina Small RNA PCR Primer 1 CAAGCAGAAGACGGCATACGA
Illumina Small RNA PCR Primer 2 AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA
Illumina Small RNA Sequencing Primer CGACAGGTTCAGAGTTCTACAGTCCGACGATC
TruSeq Universal Adapter AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
TruSeq Adapter, Index 1 GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG
......@@ -180,3 +176,11 @@ ABI Solid3 EF1 alpha Sense Primer CATGTGTGTTGAGAGCTTC
ABI Solid3 EF1 alpha Antisense Primer GAAAACCAAAGTGGTCCAC
ABI Solid3 GAPDH Forward Primer TTAGCACCCCTGGCCAAGG
ABI Solid3 GAPDH Reverse Primer CTTACTCCTTGGAGGCCATG
Clontech Universal Primer Mix Short CTAATACGACTCACTATAGGGC
Clontech Universal Primer Mix Long CTAATACGACTCACTATAGGGCAAGCAGTGGTATCAACGCAGAGT
Clontech SMARTer II A Oligonucleotide AAGCAGTGGTATCAACGCAGAGTAC
Clontech SMART CDS Primer II A AAGCAGTGGTATCAACGCAGAGTACT
Configuration/limits.txt
View file @ 30567660
......@@ -2,7 +2,7 @@
# module at all by setting the value below to 1 for the
# modules you want to remove.
duplication ignore 0
kmer ignore 0
kmer ignore 1
n_content ignore 0
overrepresented ignore 0
quality_base ignore 0
......
Help/3 Analysis Modules/12 Per Tile Sequence Quality.html
View file @ 30567660
......@@ -22,7 +22,7 @@ with only one part of the flowcell.
<p>
The plot shows the deviation from the average quality for each tile.
The colours are on a cold to hot scale, with cold colours being
positions where the quality was at or below the average for that
positions where the quality was at or above the average for that
base in the run, and hotter colours indicate that a tile had worse
qualities than other tiles for that base. In the example below you
can see that certain tiles show consistently poor quality. A good
......
INSTALL.txt
View file @ 30567660
......@@ -119,6 +119,14 @@ streaming uncompressed fastq format data to the program. For example:
zcat *fastq.gz | fastqc stdin
If you want the results from a streamed analysis sent to a file with a name other than
stdin then you can add a colon and put the file name you want, for example:
zcat *fastq.gz | fastqc stdin:my_results
..would write results to my_result.html and my_results.zip.
Customising the report output
-----------------------------
......
LICENSE 0 → 100644
View file @ 30567660
GNU GENERAL PUBLIC LICENSE
Version 2, June 1991
Copyright (C) 1989, 1991 Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
Preamble
The licenses for most software are designed to take away your
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TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
0. This License applies to any program or other work which contains
a notice placed by the copyright holder saying it may be distributed
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POSSIBILITY OF SUCH DAMAGES.
END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest
possible use to the public, the best way to achieve this is to make it
free software which everyone can redistribute and change under these terms.
To do so, attach the following notices to the program. It is safest
to attach them to the start of each source file to most effectively
convey the exclusion of warranty; and each file should have at least
the "copyright" line and a pointer to where the full notice is found.
<one line to give the program's name and a brief idea of what it does.>
Copyright (C) <year> <name of author>
This program 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 2 of the License, or
(at your option) any later version.
This program 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 this program; if not, write to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
Also add information on how to contact you by electronic and paper mail.
If the program is interactive, make it output a short notice like this
when it starts in an interactive mode:
Gnomovision version 69, Copyright (C) year name of author
Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
The hypothetical commands `show w' and `show c' should show the appropriate
parts of the General Public License. Of course, the commands you use may
be called something other than `show w' and `show c'; they could even be
mouse-clicks or menu items--whatever suits your program.
You should also get your employer (if you work as a programmer) or your
school, if any, to sign a "copyright disclaimer" for the program, if
necessary. Here is a sample; alter the names:
Yoyodyne, Inc., hereby disclaims all copyright interest in the program
`Gnomovision' (which makes passes at compilers) written by James Hacker.
<signature of Ty Coon>, 1 April 1989
Ty Coon, President of Vice
This General Public License does not permit incorporating your program into
proprietary programs. If your program is a subroutine library, you may
consider it more useful to permit linking proprietary applications with the
library. If this is what you want to do, use the GNU Lesser General
Public License instead of this License.
README.md 0 → 100644
View file @ 30567660
# FastQC
FastQC is a program designed to spot potential problems in high througput sequencing datasets. It runs a set of analyses on one or more raw sequence files in fastq or bam format and produces a report which summarises the results.
![FastQC Screenshot](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc.png)
FastQC will highlight any areas where this library looks unusual and where you should take a closer look. The program is not tied to any specific type of sequencing technique and can be used to look at libraries coming from a large number of different experiment types (Genomic Sequencing, ChIP-Seq, RNA-Seq, BS-Seq etc etc).
This project page contains the source code for the application and is only really useful only to people wanting to develop new functionality or trace bugs in FastQC. If you just want to run the program then you want to go to the [**project web page**](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) where you can download the compiled pacakges for Windows, OSX and Linux.
README.txt
View file @ 30567660
......@@ -37,8 +37,8 @@ instructions in the INSTALL.txt document to tell you how to get a
suitable java version to run FastQC on your system.
If you have any comments about FastQC we would like to hear them. You
can either enter them in our bug tracking system at:
can either enter them into the github bug tracker at:
http://www.bioinformatics.babraham.ac.uk/bugzilla/
https://github.com/s-andrews/FastQC/issues/
..or send them directly to simon.andrews@babraham.ac.uk.
RELEASE_NOTES.txt
View file @ 30567660
RELEASE NOTES FOR FastQC v0.11.7
--------------------------------
This is a bugfix release for a bug introduced in 0.11.6. Specifically
this version would crash if the first sequence in a file was <12bp
(or less than the length of the longest adapter if a custom adapters
file was being used).
RELEASE NOTES FOR FastQC v0.11.6
--------------------------------
This update fixes some bugs and updates some of the functionality to
accommodate changes in some of the sequencing platforms.
There is one major change which is that by default we now disable the
kmer module. With the inclusion of the adapter plot the value of the
information in the Kmer plot is often not great, and it is easy to
confound it if there are any over-represented sequences, or primer
compositional bias. Overall therefore we consider it best to not
routinely include this module.
If you want to turn this module back on, then simply edit the
limits.txt file in the Configuration folder of the FastQC installation
and change the line near the top which says:
kmer ignore 1
..to..
kmer ignore 0
..and the module will be re-enabled.
Other changes in this release are:
1) Fixed a bug which prematurely abandoned the adapter content plot
when long custom adapters were being used.
2) Changed the cutoff for the maximum number of tiles to allow for
the novaseq which has lots of them.
3) Fixed a bug in the parsing of tile numbers on some illumina
sequencers
4) Added some new Clontech sequences to the contaminants list.
5) Made the --nanopore option work with the new multi-folder ONT
folder structure
6) Added an option to specify a file name when streaming data into
FastQC
7) Added new RDF paths to check for fastq data in nanopore fast5 files
8) Fix parsing of newer nanopore base names to correctly collate sequences
9) Fixed a typo in the documentation for the per tile plot documentation
10) Added a --min-length option to ignore short sequences making it easier
to generate directly comparable statistics between runs.
RELEASE NOTES FOR FastQC v0.11.5
--------------------------------
......
debian/changelog
View file @ 30567660
fastqc (0.11.5+dfsg-7) UNRELEASED; urgency=medium
fastqc (0.11.7+dfsg-1) unstable; urgency=medium
[ Steffen Moeller ]
* debian/upstream/metadata: Added references to
OMICtools, SciCrunch, bio.tools registries
[ Andreas Tille ]
* New upstream version
* Standards-Version: 4.1.4
* Point Vcs-fields to Salsa
* debhelper 11
* Depends: libfindbin-libs-perl
Closes: #896931
* Drop alternative Depends: java7-runtime
* Set Java 9 as build target
-- Andreas Tille <tille@debian.org> Fri, 27 Apr 2018 07:14:43 +0200
-- Andreas Tille <tille@debian.org> Fri, 27 Apr 2018 08:31:31 +0200
fastqc (0.11.5+dfsg-6) unstable; urgency=medium
......
debian/patches/drop-fast5.patch
View file @ 30567660
......@@ -23,7 +23,7 @@ Description: HDF5 1.10 is about to transition into unstable, and unfortunately
my $nofilter;
my $kmer_size;
my $temp_directory;
@@ -91,7 +90,6 @@ my $result = GetOptions('version' => \$v
@@ -92,7 +91,6 @@ my $result = GetOptions('version' => \$v
'threads=i' => \$threads,
'kmers=i' => \$kmer_size,
'casava' => \$casava,
......@@ -31,7 +31,7 @@ Description: HDF5 1.10 is about to transition into unstable, and unfortunately
'nofilter' => \$nofilter,
'contaminants=s' => \$contaminant,
'adapters=s' => \$adapter,
@@ -183,10 +181,6 @@ if ($casava) {
@@ -189,10 +187,6 @@ if ($casava) {
push @java_args ,"-Dfastqc.casava=true";
}
......@@ -42,7 +42,7 @@ Description: HDF5 1.10 is about to transition into unstable, and unfortunately
if ($nofilter) {
push @java_args ,"-Dfastqc.nofilter=true";
@@ -320,11 +314,6 @@ DESCRIPTION
@@ -326,11 +320,6 @@ DESCRIPTION
(including being gzipped and ending with .gz) otherwise they
won't be grouped together correctly.
......@@ -54,23 +54,11 @@ Description: HDF5 1.10 is about to transition into unstable, and unfortunately
--nofilter If running with --casava then don't remove read flagged by
casava as poor quality when performing the QC analysis.
--- a/uk/ac/babraham/FastQC/Sequence/SequenceFactory.java
+++ b/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);
}
--- a/uk/ac/babraham/FastQC/Sequence/Fast5File.java
+++ /dev/null
@@ -1,89 +0,0 @@
@@ -1,107 +0,0 @@
-/**
- * Copyright Copyright 2010-15 Simon Andrews
- * Copyright Copyright 2010-17 Simon Andrews
- *
- * This file is part of FastQC.
- *
......@@ -109,9 +97,20 @@ Description: HDF5 1.10 is about to transition into unstable, and unfortunately
-
- IHDF5SimpleReader reader = HDF5Factory.openForReading(file);
-
- if (reader.exists("Analyses/Basecall_2D_000/BaseCalled_template/Fastq")) {
- String [] rdfPaths = new String [] {
- "Analyses/Basecall_2D_000/BaseCalled_template/Fastq",
- "Analyses/Basecall_2D_000/BaseCalled_2D/Fastq",
- "Analyses/Basecall_1D_000/BaseCalled_template/Fastq",
- "Analyses/Basecall_1D_000/BaseCalled_1D/Fastq"
- };
-
- String fastq = reader.readString("Analyses/Basecall_2D_000/BaseCalled_template/Fastq");
- boolean foundPath = false;
- for (int r=0;r<rdfPaths.length;r++) {
-
- if (reader.exists(rdfPaths[r])) {
-
- foundPath = true;
- String fastq = reader.readString(rdfPaths[r]);
-
- String [] sections = fastq.split("\\n");
-
......@@ -120,9 +119,16 @@ Description: HDF5 1.10 is about to transition into unstable, and unfortunately
- }
-
- nextSequence = new Sequence(this, sections[1].toUpperCase(),sections[3], sections[0]);
- break;
- }
- }
-
- reader.close();
-
- if (!foundPath) {
- throw new SequenceFormatException("No valid fastq paths found in "+file);
- }
-
- }
-
- public String name() {
......@@ -158,3 +164,18 @@ Description: HDF5 1.10 is about to transition into unstable, and unfortunately
- }
-
-}
--- a/uk/ac/babraham/FastQC/Sequence/SequenceFactory.java
+++ b/uk/ac/babraham/FastQC/Sequence/SequenceFactory.java
@@ -99,9 +99,9 @@ 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 if (file.getName().toLowerCase().endsWith(".fast5")) {
+// return new Fast5File(file);
+// }
else {
return new FastQFile(config,file);
}
debian/patches/fastqc.patch
View file @ 30567660
......@@ -3,7 +3,7 @@ Subject: Ensure proper CLASSPATH according to location of Debian JARs
--- a/fastqc
+++ b/fastqc
@@ -33,16 +33,15 @@
@@ -33,16 +33,15 @@ if (-e "$RealBin/uk/ac/babraham/FastQC/F
}
my $delimiter = ':';
......@@ -23,7 +23,7 @@ Subject: Ensure proper CLASSPATH according to location of Debian JARs
}
my @java_args;
@@ -271,10 +270,10 @@
@@ -277,10 +276,10 @@ if (@files or $version or $help) {
if ($java_bin ne 'java') {
......@@ -36,7 +36,7 @@ Subject: Ensure proper CLASSPATH according to location of Debian JARs
}
__DATA__
@@ -392,4 +391,3 @@
@@ -405,4 +404,3 @@ BUGS
Any bugs in fastqc should be reported either to simon.andrews@babraham.ac.uk
or in www.bioinformatics.babraham.ac.uk/bugzilla/
......
debian/patches/fix-help-call.patch
View file @ 30567660
From: Andreas Tille <tille@debian.org>
Subject: The original way to open Help text ends up in an exception
Setting the explicite file name as well as avoiding the call to
Setting the explicit file name as well as avoiding the call to
ClassLoader.getSystemResource
helps fixing this. Specifically the later is important, see
https://lists.debian.org/debian-med/2012/11/msg00073.html
......