# HG changeset patch
# User jjohnson
# Date 1613950876 0
# Node ID 286e35cf3f1c43139211ee5d0b9c4e1401b3a5a0
"planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
diff -r 000000000000 -r 286e35cf3f1c fgbio_sort_bam.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/fgbio_sort_bam.xml Sun Feb 21 23:41:16 2021 +0000
@@ -0,0 +1,34 @@
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+ Sorts a SAM or BAM file
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+ macros.xml
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+
+ fgbio --version
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diff -r 000000000000 -r 286e35cf3f1c macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Sun Feb 21 23:41:16 2021 +0000
@@ -0,0 +1,56 @@
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+ 1.3.0
+ 0
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+ fgbio
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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
+
+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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+ --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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