--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fastqc_contaminants.txt	Mon Jan 27 09:29:14 2014 -0500
@@ -0,0 +1,170 @@
+# This file contains a list of potential contaminants which are
+# frequently found in high throughput sequencing reactions.  These
+# are mostly sequences of adapters / primers used in the various
+# sequencing chemistries.
+# 
+# Please DO NOT rely on these sequences to design your own oligos, some
+# of them are truncated at ambiguous positions, and none of them are
+# definitive sequences from the manufacturers so don't blame us if you
+# try to use them and they don't work.
+#
+# You can add more sequences to the file by putting one line per entry
+# and specifying a name[tab]sequence.  If the contaminant you add is 
+# likely to be of use to others please consider sending it to the FastQ
+# authors, either via a bug report at www.bioinformatics.bbsrc.ac.uk/bugzilla/
+# or by directly emailing simon.andrews@bbsrc.ac.uk so other users of
+# the program can benefit.
+
+Illumina Single End Apapter 1					ACACTCTTTCCCTACACGACGCTGTTCCATCT
+Illumina Single End Apapter 2					CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT
+Illumina Single End PCR Primer 1				AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
+Illumina Single End PCR Primer 2				CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT
+Illumina Single End Sequencing Primer			ACACTCTTTCCCTACACGACGCTCTTCCGATCT
+
+Illumina Paired End Adapter 1					ACACTCTTTCCCTACACGACGCTCTTCCGATCT
+Illumina Paired End Adapter 2					CTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
+Illumina Paried End PCR Primer 1				AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
+Illumina Paired End PCR Primer 2				CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
+Illumina Paried End Sequencing Primer 1			ACACTCTTTCCCTACACGACGCTCTTCCGATCT
+Illumina Paired End Sequencing Primer 2			CGGTCTCGGCATTCCTACTGAACCGCTCTTCCGATCT
+
+Illumina DpnII expression Adapter 1				ACAGGTTCAGAGTTCTACAGTCCGAC
+Illumina DpnII expression Adapter 2				CAAGCAGAAGACGGCATACGA
+Illumina DpnII expression PCR Primer 1			CAAGCAGAAGACGGCATACGA
+Illumina DpnII expression PCR Primer 2			AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA
+Illumina DpnII expression Sequencing Primer		CGACAGGTTCAGAGTTCTACAGTCCGACGATC
+
+Illumina NlaIII expression Adapter 1			ACAGGTTCAGAGTTCTACAGTCCGACATG
+Illumina NlaIII expression Adapter 2			CAAGCAGAAGACGGCATACGA
+Illumina NlaIII expression PCR Primer 1			CAAGCAGAAGACGGCATACGA
+Illumina NlaIII expression PCR Primer 2			AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA
+Illumina NlaIII expression Sequencing Primer	CCGACAGGTTCAGAGTTCTACAGTCCGACATG
+
+Illumina Small RNA Adapter 1					GTTCAGAGTTCTACAGTCCGACGATC
+Illumina Small RNA Adapter 2					TCGTATGCCGTCTTCTGCTTGT
+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
+
+Illumina Multiplexing Adapter 1					GATCGGAAGAGCACACGTCT
+Illumina Multiplexing Adapter 2					ACACTCTTTCCCTACACGACGCTCTTCCGATCT
+Illumina Multiplexing PCR Primer 1.01			AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
+Illumina Multiplexing PCR Primer 2.01			GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
+Illumina Multiplexing Read1 Sequencing Primer	ACACTCTTTCCCTACACGACGCTCTTCCGATCT
+Illumina Multiplexing Index Sequencing Primer	GATCGGAAGAGCACACGTCTGAACTCCAGTCAC
+Illumina Multiplexing Read2 Sequencing Primer	GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
+
+Illumina PCR Primer Index 1						CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTC
+Illumina PCR Primer Index 2						CAAGCAGAAGACGGCATACGAGATACATCGGTGACTGGAGTTC
+Illumina PCR Primer Index 3						CAAGCAGAAGACGGCATACGAGATGCCTAAGTGACTGGAGTTC
+Illumina PCR Primer Index 4						CAAGCAGAAGACGGCATACGAGATTGGTCAGTGACTGGAGTTC
+Illumina PCR Primer Index 5						CAAGCAGAAGACGGCATACGAGATCACTGTGTGACTGGAGTTC
+Illumina PCR Primer Index 6						CAAGCAGAAGACGGCATACGAGATATTGGCGTGACTGGAGTTC
+Illumina PCR Primer Index 7						CAAGCAGAAGACGGCATACGAGATGATCTGGTGACTGGAGTTC
+Illumina PCR Primer Index 8						CAAGCAGAAGACGGCATACGAGATTCAAGTGTGACTGGAGTTC
+Illumina PCR Primer Index 9						CAAGCAGAAGACGGCATACGAGATCTGATCGTGACTGGAGTTC
+Illumina PCR Primer Index 10					CAAGCAGAAGACGGCATACGAGATAAGCTAGTGACTGGAGTTC
+Illumina PCR Primer Index 11					CAAGCAGAAGACGGCATACGAGATGTAGCCGTGACTGGAGTTC
+Illumina PCR Primer Index 12					CAAGCAGAAGACGGCATACGAGATTACAAGGTGACTGGAGTTC
+
+Illumina DpnII Gex Adapter 1					GATCGTCGGACTGTAGAACTCTGAAC
+Illumina DpnII Gex Adapter 1.01					ACAGGTTCAGAGTTCTACAGTCCGAC
+Illumina DpnII Gex Adapter 2					CAAGCAGAAGACGGCATACGA
+Illumina DpnII Gex Adapter 2.01					TCGTATGCCGTCTTCTGCTTG
+Illumina DpnII Gex PCR Primer 1					CAAGCAGAAGACGGCATACGA
+Illumina DpnII Gex PCR Primer 2					AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA
+Illumina DpnII Gex Sequencing Primer			CGACAGGTTCAGAGTTCTACAGTCCGACGATC
+
+Illumina NlaIII Gex Adapter 1.01				TCGGACTGTAGAACTCTGAAC
+Illumina NlaIII Gex Adapter 1.02				ACAGGTTCAGAGTTCTACAGTCCGACATG
+Illumina NlaIII Gex Adapter 2.01				CAAGCAGAAGACGGCATACGA
+Illumina NlaIII Gex Adapter 2.02				TCGTATGCCGTCTTCTGCTTG
+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							TCGTATGCCGTCTTCTGCTTGT
+
+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
+TruSeq Adapter, Index 2							GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 3							GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 4							GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 5							GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 6							GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 7							GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 8							GATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 9							GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 10						GATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 11						GATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCTACATCTCGTATGCCGTCTTCTGCTTG
+TruSeq Adapter, Index 12						GATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAATCTCGTATGCCGTCTTCTGCTTG
+
+Illumina RNA RT Primer							GCCTTGGCACCCGAGAATTCCA
+Illumina RNA PCR Primer							AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGA
+
+RNA PCR Primer, Index 1							CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 2							CAAGCAGAAGACGGCATACGAGATACATCGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 3							CAAGCAGAAGACGGCATACGAGATGCCTAAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 4							CAAGCAGAAGACGGCATACGAGATTGGTCAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 5							CAAGCAGAAGACGGCATACGAGATCACTGTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 6							CAAGCAGAAGACGGCATACGAGATATTGGCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 7							CAAGCAGAAGACGGCATACGAGATGATCTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 8							CAAGCAGAAGACGGCATACGAGATTCAAGTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 9							CAAGCAGAAGACGGCATACGAGATCTGATCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 10						CAAGCAGAAGACGGCATACGAGATAAGCTAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 11						CAAGCAGAAGACGGCATACGAGATGTAGCCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 12						CAAGCAGAAGACGGCATACGAGATTACAAGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 13						CAAGCAGAAGACGGCATACGAGATTTGACTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 14						CAAGCAGAAGACGGCATACGAGATGGAACTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 15						CAAGCAGAAGACGGCATACGAGATTGACATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 16						CAAGCAGAAGACGGCATACGAGATGGACGGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 17						CAAGCAGAAGACGGCATACGAGATCTCTACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 18						CAAGCAGAAGACGGCATACGAGATGCGGACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 19						CAAGCAGAAGACGGCATACGAGATTTTCACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 20						CAAGCAGAAGACGGCATACGAGATGGCCACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 21						CAAGCAGAAGACGGCATACGAGATCGAAACGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 22						CAAGCAGAAGACGGCATACGAGATCGTACGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 23						CAAGCAGAAGACGGCATACGAGATCCACTCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 24						CAAGCAGAAGACGGCATACGAGATGCTACCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 25						CAAGCAGAAGACGGCATACGAGATATCAGTGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 26						CAAGCAGAAGACGGCATACGAGATGCTCATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 27						CAAGCAGAAGACGGCATACGAGATAGGAATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 28						CAAGCAGAAGACGGCATACGAGATCTTTTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 29						CAAGCAGAAGACGGCATACGAGATTAGTTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 30						CAAGCAGAAGACGGCATACGAGATCCGGTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 31						CAAGCAGAAGACGGCATACGAGATATCGTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 32						CAAGCAGAAGACGGCATACGAGATTGAGTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 33						CAAGCAGAAGACGGCATACGAGATCGCCTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 34						CAAGCAGAAGACGGCATACGAGATGCCATGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 35						CAAGCAGAAGACGGCATACGAGATAAAATGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 36						CAAGCAGAAGACGGCATACGAGATTGTTGGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 37						CAAGCAGAAGACGGCATACGAGATATTCCGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 38						CAAGCAGAAGACGGCATACGAGATAGCTAGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 39						CAAGCAGAAGACGGCATACGAGATGTATAGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 40						CAAGCAGAAGACGGCATACGAGATTCTGAGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 41						CAAGCAGAAGACGGCATACGAGATGTCGTCGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 42						CAAGCAGAAGACGGCATACGAGATCGATTAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 43						CAAGCAGAAGACGGCATACGAGATGCTGTAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 44						CAAGCAGAAGACGGCATACGAGATATTATAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 45						CAAGCAGAAGACGGCATACGAGATGAATGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 46						CAAGCAGAAGACGGCATACGAGATTCGGGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 47						CAAGCAGAAGACGGCATACGAGATCTTCGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+RNA PCR Primer, Index 48						CAAGCAGAAGACGGCATACGAGATTGCCGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
+
+ABI Dynabead EcoP Oligo							CTGATCTAGAGGTACCGGATCCCAGCAGT
+ABI Solid3 Adapter A							CTGCCCCGGGTTCCTCATTCTCTCAGCAGCATG
+ABI Solid3 Adapter B							CCACTACGCCTCCGCTTTCCTCTCTATGGGCAGTCGGTGAT
+ABI Solid3 5' AMP Primer						CCACTACGCCTCCGCTTTCCTCTCTATG
+ABI Solid3 3' AMP Primer						CTGCCCCGGGTTCCTCATTCT
+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