# HG changeset patch
# User jjohnson
# Date 1613950809 0
# Node ID ee774248788f0a47bfbb27059846f6c01b5ac45e
"planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
diff -r 000000000000 -r ee774248788f fgbio_fastq_to_bam.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/fgbio_fastq_to_bam.xml Sun Feb 21 23:40:09 2021 +0000
@@ -0,0 +1,91 @@
+
+ Generates an unmapped BAM file from fastq files
+
+ macros.xml
+
+
+ fgbio --version
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r 000000000000 -r ee774248788f macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Sun Feb 21 23:40:09 2021 +0000
@@ -0,0 +1,56 @@
+
+ 1.3.0
+ 0
+
+
+ fgbio
+
+
+
+ (([1-9][0-9]*[TBMS])*([+]|[1-9][0-9]*)[TBMS])
+ @READ_STRUCTURE_PATTERN@(\s@READ_STRUCTURE_PATTERN@)*
+
+ ^@READ_STRUCTURES_PATTERN@$
+
+
+ ^[A-Za-z][A-Za-z]$
+
+
+
+
+
+
+
+
+
+
+ pairs much like the CIGAR string in BAM files. Four kinds of operators are recognized:
+
+ 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:
+
+::
+
+ --input r1.fq r2.fq i1.fq --read-structures 5M5S+T +T +B
+
+Alternative if you know your reads are of fixed length you could specify:
+
+::
+
+ --input r1.fq r2.fq i1.fq --read-structures 5M5S65T 75T 8B
+
+
+]]>
+
+
+
+
+
+