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changeset 1:c05232655d00 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 35db9ac8668f3e376886ea09de63c87dce93e1ce
author iuc
date Tue, 30 May 2023 09:03:04 +0000
parents fc029a9b4d07
children 6d084528a6f1
files readme.rst test-data/bbnorm/discarded.fastq test-data/bbnorm/input_R1.fastq test-data/bbnorm/input_R1.fastq.gz test-data/bbnorm/input_R2.fastq test-data/bbnorm/input_interleaved.fastq test-data/bbnorm/kmer_hist_input.tabular test-data/bbnorm/kmer_hist_output.tabular test-data/bbnorm/normalised_R1.fastq test-data/bbnorm/normalised_R2.fastq test-data/bbnorm/normalised_interleaved.fastq
diffstat 11 files changed, 316 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.rst	Tue May 30 09:03:04 2023 +0000
@@ -0,0 +1,18 @@
+
+=================
+IMPORTANT NOTE REGARDING SYSTEM CONFIGURATION
+=================
+
+All of the Galaxy wrappers contained herein call the respective bbtools' shell wrapper, which calls the underlying java-based tool. Unlike a C-based program, java will grab a pre-determined amount of memory at the very beginning of the execution.
+
+Some of the algorithms (e.g. bbnorm) utilise a hash table, and potential collusions can decrease the numeric accuracy of the output. This problem is expected to become more pronounced if the fraction of the memory occupied w.r.t. allocated memory becomes high, i.e. when the available memory is low and/or the input file is big. If the tool generates a warning to stderr, and will be caught by the Galaxy wrapper resulting in a failed job. However, `count min sketch <https://en.wikipedia.org/wiki/Count%E2%80%93min_sketch>` does not run out of memory, this is a gradual effect, and will NOT trigger a fatal error unless the load reaches this critically high level. You can read more about the implications of this at the `BBtools manual <https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbnorm-guide/>`
+
+If you are administering a heteregenous computing environment with multiple nodes of very different quantities of physically available RAM, it is recommended to define a global cap on the RAM to be used to avoid introducing run-to-run bias by exporting an environmental variable, by something like:
+export _JAVA_OPTIONS="-Xmx2048m -Xms256m"
+
+The tool currently considers the following limits, in the given priority order:
+1) _JAVA_OPTIONS
+2) JAVA_TOOL_OPTIONS
+3) GALAXY_MEMORY_MB
+4) 4 GB
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bbnorm/discarded.fastq	Tue May 30 09:03:04 2023 +0000
@@ -0,0 +1,32 @@
+@read1:duplicateA 1:N:0:ATCGTCTC+NTAACCGA
+GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read1:duplicateA 2:N:0:ATCGTCTC+NTAACCGA
+TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read5:duplicateA 1:N:0:ATCGTCTC+NTAACCGA
+GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read5:duplicateA 2:N:0:ATCGTCTC+NTAACCGA
+TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read7:duplicateB 1:N:0:ATCGTCTC+NTAACCGA
+AAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAACGCGCGAGTCGGCATGCTGATGCACGATGCTAGCTGAGCATGCTAGTCGAGCAGTCGT
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read7:duplicateB 2:N:0:ATCGTCTC+NTAACCGA
+ACGACTGCTCGACTAGCATGCTCAGCTAGCATCGTGCATCAGCATGCCGACTCGCGCGTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTT
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read8:duplicateB 1:N:0:ATCGTCTC+NTAACCGA
+AAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAACGCGCGAGTCGGCATGCTGATGCACGATGCTAGCTGAGCATGCTAGTCGAGCAGTCGT
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read8:duplicateB 2:N:0:ATCGTCTC+NTAACCGA
+ACGACTGCTCGACTAGCATGCTCAGCTAGCATCGTGCATCAGCATGCCGACTCGCGCGTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTT
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bbnorm/input_R1.fastq	Tue May 30 09:03:04 2023 +0000
@@ -0,0 +1,40 @@
+@read1:duplicateA 1:N:0:ATCGTCTC+NTAACCGA
+GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read2:duplicateA 1:N:0:ATCGTCTC+NTAACCGA
+GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read3:duplicateA 1:N:0:ATCGTCTC+NTAACCGA
+GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read4:duplicateA 1:N:0:ATCGTCTC+NTAACCGA
+GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read5:duplicateA 1:N:0:ATCGTCTC+NTAACCGA
+GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read6:duplicateA 1:N:0:ATCGTCTC+NTAACCGA
+GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read7:duplicateB 1:N:0:ATCGTCTC+NTAACCGA
+AAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAACGCGCGAGTCGGCATGCTGATGCACGATGCTAGCTGAGCATGCTAGTCGAGCAGTCGT
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read8:duplicateB 1:N:0:ATCGTCTC+NTAACCGA
+AAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAACGCGCGAGTCGGCATGCTGATGCACGATGCTAGCTGAGCATGCTAGTCGAGCAGTCGT
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read9:duplicateC 1:N:0:ATCGTCTC+NTAACCGA
+ACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAACGCGCGAGTCGGCATGCTGATGCACGATGCTAGCTGAGCATGCTAGTCGAGCAGTCGTAGCGCGCGCGCTATCGCGATCGCGATCGGCATCGGAGCTACGGAATA
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read10:duplicateC 1:N:0:ATCGTCTC+NTAACCGA
+ACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAACGCGCGAGTCGGCATGCTGATGCACGATGCTAGCTGAGCATGCTAGTCGAGCAGTCGTAGCGCGCGCGCTATCGCGATCGCGATCGGCATCGGAGCTACGGAATA
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
Binary file test-data/bbnorm/input_R1.fastq.gz has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bbnorm/input_R2.fastq	Tue May 30 09:03:04 2023 +0000
@@ -0,0 +1,40 @@
+@read1:duplicateA 2:N:0:ATCGTCTC+NTAACCGA
+TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read2:duplicateA 2:N:0:ATCGTCTC+NTAACCGA
+TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read3:duplicateA 2:N:0:ATCGTCTC+NTAACCGA
+TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read4:duplicateA 2:N:0:ATCGTCTC+NTAACCGA
+TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read5:duplicateA 2:N:0:ATCGTCTC+NTAACCGA
+TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read6:duplicateA 2:N:0:ATCGTCTC+NTAACCGA
+TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read7:duplicateB 2:N:0:ATCGTCTC+NTAACCGA
+ACGACTGCTCGACTAGCATGCTCAGCTAGCATCGTGCATCAGCATGCCGACTCGCGCGTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTT
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read8:duplicateB 2:N:0:ATCGTCTC+NTAACCGA
+ACGACTGCTCGACTAGCATGCTCAGCTAGCATCGTGCATCAGCATGCCGACTCGCGCGTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTT
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read9:duplicateC 2:N:0:ATCGTCTC+NTAACCGA
+TATTCCGTAGCTCCGATGCCGATCGCGATCGCGATAGCGCGCGCGCTACGACTGCTCGACTAGCATGCTCAGCTAGCATCGTGCATCAGCATGCCGACTCGCGCGTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGT
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read10:duplicateC 2:N:0:ATCGTCTC+NTAACCGA
+TATTCCGTAGCTCCGATGCCGATCGCGATCGCGATAGCGCGCGCGCTACGACTGCTCGACTAGCATGCTCAGCTAGCATCGTGCATCAGCATGCCGACTCGCGCGTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGT
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bbnorm/input_interleaved.fastq	Tue May 30 09:03:04 2023 +0000
@@ -0,0 +1,80 @@
+@read1:duplicateA 1:N:0:ATCGTCTC+NTAACCGA
+GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read1:duplicateA 2:N:0:ATCGTCTC+NTAACCGA
+TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read2:duplicateA 1:N:0:ATCGTCTC+NTAACCGA
+GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read2:duplicateA 2:N:0:ATCGTCTC+NTAACCGA
+TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read3:duplicateA 1:N:0:ATCGTCTC+NTAACCGA
+GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read3:duplicateA 2:N:0:ATCGTCTC+NTAACCGA
+TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read4:duplicateA 1:N:0:ATCGTCTC+NTAACCGA
+GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read4:duplicateA 2:N:0:ATCGTCTC+NTAACCGA
+TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read5:duplicateA 1:N:0:ATCGTCTC+NTAACCGA
+GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read5:duplicateA 2:N:0:ATCGTCTC+NTAACCGA
+TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read6:duplicateA 1:N:0:ATCGTCTC+NTAACCGA
+GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read6:duplicateA 2:N:0:ATCGTCTC+NTAACCGA
+TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read7:duplicateB 1:N:0:ATCGTCTC+NTAACCGA
+AAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAACGCGCGAGTCGGCATGCTGATGCACGATGCTAGCTGAGCATGCTAGTCGAGCAGTCGT
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read7:duplicateB 2:N:0:ATCGTCTC+NTAACCGA
+ACGACTGCTCGACTAGCATGCTCAGCTAGCATCGTGCATCAGCATGCCGACTCGCGCGTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTT
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read8:duplicateB 1:N:0:ATCGTCTC+NTAACCGA
+AAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAACGCGCGAGTCGGCATGCTGATGCACGATGCTAGCTGAGCATGCTAGTCGAGCAGTCGT
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read8:duplicateB 2:N:0:ATCGTCTC+NTAACCGA
+ACGACTGCTCGACTAGCATGCTCAGCTAGCATCGTGCATCAGCATGCCGACTCGCGCGTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTT
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read9:duplicateC 1:N:0:ATCGTCTC+NTAACCGA
+ACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAACGCGCGAGTCGGCATGCTGATGCACGATGCTAGCTGAGCATGCTAGTCGAGCAGTCGTAGCGCGCGCGCTATCGCGATCGCGATCGGCATCGGAGCTACGGAATA
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read9:duplicateC 2:N:0:ATCGTCTC+NTAACCGA
+TATTCCGTAGCTCCGATGCCGATCGCGATCGCGATAGCGCGCGCGCTACGACTGCTCGACTAGCATGCTCAGCTAGCATCGTGCATCAGCATGCCGACTCGCGCGTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGT
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read10:duplicateC 1:N:0:ATCGTCTC+NTAACCGA
+ACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAACGCGCGAGTCGGCATGCTGATGCACGATGCTAGCTGAGCATGCTAGTCGAGCAGTCGTAGCGCGCGCGCTATCGCGATCGCGATCGGCATCGGAGCTACGGAATA
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read10:duplicateC 2:N:0:ATCGTCTC+NTAACCGA
+TATTCCGTAGCTCCGATGCCGATCGCGATCGCGATAGCGCGCGCGCTACGACTGCTCGACTAGCATGCTCAGCTAGCATCGTGCATCAGCATGCCGACTCGCGCGTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGT
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bbnorm/kmer_hist_input.tabular	Tue May 30 09:03:04 2023 +0000
@@ -0,0 +1,6 @@
+#Depth	Raw_Count	Unique_Kmers
+2	188	94
+4	472	118
+6	708	118
+8	752	94
+10	300	30
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bbnorm/kmer_hist_output.tabular	Tue May 30 09:03:04 2023 +0000
@@ -0,0 +1,4 @@
+#Depth	Raw_Count	Unique_Kmers
+2	424	212
+4	848	212
+6	180	30
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bbnorm/normalised_R1.fastq	Tue May 30 09:03:04 2023 +0000
@@ -0,0 +1,24 @@
+@read2:duplicateA 1:N:0:ATCGTCTC+NTAACCGA
+GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read3:duplicateA 1:N:0:ATCGTCTC+NTAACCGA
+GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read4:duplicateA 1:N:0:ATCGTCTC+NTAACCGA
+GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read6:duplicateA 1:N:0:ATCGTCTC+NTAACCGA
+GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read9:duplicateC 1:N:0:ATCGTCTC+NTAACCGA
+ACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAACGCGCGAGTCGGCATGCTGATGCACGATGCTAGCTGAGCATGCTAGTCGAGCAGTCGTAGCGCGCGCGCTATCGCGATCGCGATCGGCATCGGAGCTACGGAATA
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read10:duplicateC 1:N:0:ATCGTCTC+NTAACCGA
+ACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAACGCGCGAGTCGGCATGCTGATGCACGATGCTAGCTGAGCATGCTAGTCGAGCAGTCGTAGCGCGCGCGCTATCGCGATCGCGATCGGCATCGGAGCTACGGAATA
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bbnorm/normalised_R2.fastq	Tue May 30 09:03:04 2023 +0000
@@ -0,0 +1,24 @@
+@read2:duplicateA 2:N:0:ATCGTCTC+NTAACCGA
+TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read3:duplicateA 2:N:0:ATCGTCTC+NTAACCGA
+TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read4:duplicateA 2:N:0:ATCGTCTC+NTAACCGA
+TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read6:duplicateA 2:N:0:ATCGTCTC+NTAACCGA
+TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read9:duplicateC 2:N:0:ATCGTCTC+NTAACCGA
+TATTCCGTAGCTCCGATGCCGATCGCGATCGCGATAGCGCGCGCGCTACGACTGCTCGACTAGCATGCTCAGCTAGCATCGTGCATCAGCATGCCGACTCGCGCGTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGT
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read10:duplicateC 2:N:0:ATCGTCTC+NTAACCGA
+TATTCCGTAGCTCCGATGCCGATCGCGATCGCGATAGCGCGCGCGCTACGACTGCTCGACTAGCATGCTCAGCTAGCATCGTGCATCAGCATGCCGACTCGCGCGTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGT
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bbnorm/normalised_interleaved.fastq	Tue May 30 09:03:04 2023 +0000
@@ -0,0 +1,48 @@
+@read2:duplicateA 1:N:0:ATCGTCTC+NTAACCGA
+GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read2:duplicateA 2:N:0:ATCGTCTC+NTAACCGA
+TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read3:duplicateA 1:N:0:ATCGTCTC+NTAACCGA
+GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read3:duplicateA 2:N:0:ATCGTCTC+NTAACCGA
+TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read4:duplicateA 1:N:0:ATCGTCTC+NTAACCGA
+GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read4:duplicateA 2:N:0:ATCGTCTC+NTAACCGA
+TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read6:duplicateA 1:N:0:ATCGTCTC+NTAACCGA
+GATCTCATTCCTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGCCGGGCGACGATCATGAGCGTTTAAGAGCTATGCTGGAAACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAA
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read6:duplicateA 2:N:0:ATCGTCTC+NTAACCGA
+TTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGTTTCCAGCATAGCTCTTAAACGCTCATGATCGTCGCCCGGCGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATACTTTCAAGGAATGAGATC
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read9:duplicateC 1:N:0:ATCGTCTC+NTAACCGA
+ACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAACGCGCGAGTCGGCATGCTGATGCACGATGCTAGCTGAGCATGCTAGTCGAGCAGTCGTAGCGCGCGCGCTATCGCGATCGCGATCGGCATCGGAGCTACGGAATA
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read9:duplicateC 2:N:0:ATCGTCTC+NTAACCGA
+TATTCCGTAGCTCCGATGCCGATCGCGATCGCGATAGCGCGCGCGCTACGACTGCTCGACTAGCATGCTCAGCTAGCATCGTGCATCAGCATGCCGACTCGCGCGTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGT
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read10:duplicateC 1:N:0:ATCGTCTC+NTAACCGA
+ACAGCATAGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAACGCGCGAGTCGGCATGCTGATGCACGATGCTAGCTGAGCATGCTAGTCGAGCAGTCGTAGCGCGCGCGCTATCGCGATCGCGATCGGCATCGGAGCTACGGAATA
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
+@read10:duplicateC 2:N:0:ATCGTCTC+NTAACCGA
+TATTCCGTAGCTCCGATGCCGATCGCGATCGCGATAGCGCGCGCGCTACGACTGCTCGACTAGCATGCTCAGCTAGCATCGTGCATCAGCATGCCGACTCGCGCGTTTCAAGTTGATAACGGACTAGCCTTATTTAAACTTGCTATGCTGT
++
+EFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF