# HG changeset patch
# User jjohnson
# Date 1629386035 0
# Node ID 099a35a39c298139fed26f25d701613867023276
"planemo upload commit 77a5370a0978b5332bb3a9f063588a52a468ea08"
diff -r 000000000000 -r 099a35a39c29 fgbio_sort_fastq.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/fgbio_sort_fastq.xml Thu Aug 19 15:13:55 2021 +0000
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+ Sorts the records in a FASTQ file based on the lexicographic ordering of their read names
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+ macros.xml
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+ fgbio --version
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diff -r 000000000000 -r 099a35a39c29 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Thu Aug 19 15:13:55 2021 +0000
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+ 1.3.0
+ 1
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+ fgbio
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+ @online{fgbio,
+ author = {Tim Fennell, Nils Homer},
+ title = {fgbio},
+ year = 2015,
+ url = {https://github.com/fulcrumgenomics/fgbio},
+ urldate = {2021-03-01}
+ }
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+ (([1-9][0-9]*[TBMS])*([+]|[1-9][0-9]*)[TBMS])
+ @READ_STRUCTURE_PATTERN@(\s@READ_STRUCTURE_PATTERN@)*
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+ ^@READ_STRUCTURES_PATTERN@$
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+ ^[A-Za-z][A-Za-z]$
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+ pairs much like the CIGAR string in BAM files. Four kinds of operators are recognized:
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+ - T identifies a template read
+ - B identifies a sample barcode read
+ - M identifies a unique molecular index read
+ - S identifies a set of bases that should be skipped or ignored
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+The last pair may be specified using a + sign instead of number to denote “all remaining bases”. This is useful if, e.g., fastqs have been trimmed and contain reads of varying length. For example to convert a paired-end run with an index read and where the first 5 bases of R1 are a UMI and the second five bases are monotemplate you might specify:
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+::
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+ --input r1.fq r2.fq i1.fq --read-structures 5M5S+T +T +B
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+Alternative if you know your reads are of fixed length you could specify:
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+::
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+ --input r1.fq r2.fq i1.fq --read-structures 5M5S65T 75T 8B
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+]]>
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