New upstream version 0.11.9+dfsg

<h2>Failure</h2>

<p>

This module will issue a warning if any tile shows a mean Phred

This module will raise and error if any tile shows a mean Phred

score more than 5 less than the mean for that base across all

tiles. 

</p>

Installing FastQC

-------------------

FastQC is a java application.  In order to run it needs your system to have a suitable

Java Runtime Environment (JRE) installed.  Before you try to run FastQC you should therefore

ensure that you have a suitable JRE.  There are a number of different JREs available

however the ones we have tested are the v1.6-v1.8 JREs from Oracle.  These are available

for a number of different platforms.

Windows/Linux: Go to java.com - click on Free Java Download - DON'T click the large red button

but choose the smaller link to "See all java downloads".  Find your operating system and select

the appropriate offline installer.  If you are using a 64bit operating system (and nearly 

everyone is these days), then make sure you select the 64bit version of the the installer.

OSX: On newer versions of OSX you need to install the Java Development Kit.  The normal Java

runtime environment IS NOT enough.  To get this go to java.com, click "Free java download",

then IGNORE the big red button, and select "See all java downloads", on the next screen select

"Looking for the JDK?" from the left hand menu and select the link to "JDK downloads" in the

first paragraph.  You can then click the "Download" button underneath JDK in the page you are

taken to.  Sorry this is such a pain!

OSX

---

FastQC is distributed as a DMG image file.  Download the image from the project page

and double click it to open it.  You should see the FastQC application appear in a

Finder window.  Drag the application from there to wherever you want to install it 

on your machine.  Once you've copied the application double click it to open it.

FastQC is not a signed application therefore it may initially be blocked by the

Gatekeeper application.  To avoid this open FastQC by right clicking on the app 

and selecting open.  This may prompt you to allow it to open.  If it is still 

blocked go to System Preferences > Security and Privacy and you should see an option

to allow the application to open.  You only need to do this once and the preference

should be remembered by OSX.

Windows and Linux

-----------------

FastQC is a java application.  In order to run it needs your system to have a suitable

Java Runtime Environment (JRE) installed.  Before you try to run FastQC you should 

therefore ensure that you have a suitable JRE.  There are a number of different JREs 

available however the ones we have tested are the latest Oracle runtime environments 

and those from the adoptOpenJDK project (https://adoptopenjdk.net/).  You need to 

download and install a suitable 64-bit JRE and make sure that the java application 

is in your path (most installers will take care of this for you).

On linux most distributions will have java installed already so you might not need to

do anything.  If java isn't installed then you can add it by doing:

If you're not sure whether you have java installed then you can test this from a command

prompt.  To get a command prompt try:

Ubuntu / Mint: sudo apt install default-jre

Windows: Select Start > Run, and type 'cmd' (no quotes) in the box which appears, press OK

CentOS / Redhat: sudo yum install java-1.8.0-openjdk

MaxOSX: Run Applications > Utilities > Terminal

You can check whether java is installed by opening the 'cmd' program on windows, or

any shell on linux and typing:

Linux: From your applications menu look for an application called 'Terminal' or 'Konsole'.

Either of these will give you a usable shell.

java -version

At the command prompt type 'java -version' and press enter.  You should see something like:

You should see something like:

java version "1.8.0_60"

Java(TM) SE Runtime Environment (build 1.8.0_60-b27)

Java HotSpot(TM) 64-Bit Server VM (build 25.60-b23, mixed mode)

>java -version

openjdk version "11.0.2" 2019-01-15

OpenJDK Runtime Environment AdoptOpenJDK (build 11.0.2+9)

OpenJDK 64-Bit Server VM AdoptOpenJDK (build 11.0.2+9, mixed mode)

If you get an error then you don't have java installed.  If the version listed on the first

line is less than 1.6 then you might have problems running FastQC.

Actually installing FastQC is as simple as unzipping the zip file it comes in into a

suitable location.  That's it.  Once unzipped it's ready to go.

shortcut then we've included an icon file in the top level directory so you don't have

to use the generic bat file icon.

MacOSX: There is an application bundle for MacOSX which you can use to install and run

FastQC.  Just drag the application from the disk image to your Applications folder (or

wherever you want to install the program).

MacOSX: Double click on the FastQC application icon.

Linux:  We have included a wrapper script, called 'fastqc' which is the easiest way to 

start the program.  The wrapper is in the top level of the FastQC installation.  You 

RELEASE NOTES FOR FastQC v0.11.9

--------------------------------

This is a bugfix release which resolves some issues with the program;

- We removed the native look and feel from the linux application since

  it's horribly broken

- Fixed a hang if a run terminated from an out-of-memory error

- Fixed a corner case where adapters could occasionally be double-counted

- Updated the fast5 parser to account for the newer format multi-read

  oxford nanopore fast5 files

- Fixed problems if analysing a completely blank file

RELEASE NOTES FOR FastQC v0.11.8

--------------------------------

	$ENV{CLASSPATH} = "$RealBin$delimiter$RealBin/sam-1.103.jar$delimiter$RealBin/jbzip2-0.9.jar$delimiter$RealBin/cisd-jhdf5.jar";

}

# We need to find the java interpreter.  We'll start from the assumption that this

# is included in the path.

my $java_bin = "java";

# We might have bundled a jre with the installation.  If that's the case then we'll

# use the interpreter which is bundled in preference to the system one.

# Windows first

if (-e "$RealBin/jre/bin/java.exe") {

	$java_bin = "$RealBin/jre/bin/java.exe";

}

# Linux

elsif (-e "$RealBin/jre/bin/java") {

	$java_bin = "$RealBin/jre/bin/java";

}

# OSX

elsif (-e "$RealBin/jre/Contents/Home/bin/java") {

	$java_bin = "$RealBin/jre/Contents/Home/bin/java";

}

my @java_args;

my @files;

my $nofilter;

my $kmer_size;

my $temp_directory;

my $java_bin = 'java';

my $min_length;

my $result = GetOptions('version' => \$version,

}

if ($java_bin ne 'java') {

	warn "Java is $java_bin\n";

#	$java_bin =~ s/\\/\//g;

	unless (-e $java_bin) {

import java.util.Iterator;

import java.util.List;

import uk.ac.babraham.FastQC.Modules.BasicStats;

import uk.ac.babraham.FastQC.Modules.QCModule;

import uk.ac.babraham.FastQC.Sequence.Sequence;

import uk.ac.babraham.FastQC.Sequence.SequenceFile;

			}

		}

		// We need to account for their potentially being no sequences

		// in the file.  In this case the BasicStats module never gets 

		// the file name so we need to explicitly pass it.

		if (seqCount == 0) {

			for (int m=0; m<modules.length; m++) {

				if (modules[m] instanceof BasicStats) {

					((BasicStats)modules[m]).setFileName(file.name());

				}

			}

		}

		i = listeners.iterator();

		while (i.hasNext()) {

			i.next().analysisComplete(file,modules);