Mercurial > repos > iuc > bbtools_bbmerge
changeset 1:c05232655d00 draft
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(-) [+] |
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--- /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
--- /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