Commit dd57a3ed authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 0.11.7+dfsg

parent c00d2b49

.classpath

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<?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

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# 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

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<?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

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#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

+186 −182
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@@ -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