[med-svn] [scythe] 01/03: Add hand-made scythe.1 manpage

[Kevin Murray]

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daube-guest pushed a commit to branch master
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commit 8d5d44b510d1fa253d6fab30ef59e650c0a9ea7f
Author: Kevin Murray <spam at kdmurray.id.au>
Date:   Mon May 11 17:06:21 2015 +1000

    Add hand-made scythe.1 manpage
---
 debian/scythe.1 | 41 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)

diff --git a/debian/scythe.1 b/debian/scythe.1
new file mode 100644
index 0000000..1503e01
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+.TH "SCYTHE" "1" "May 2015" "Vince Buffalo" "scythe"
+.
+.SH "NAME"
+\fBscythe\fR \- Bayesian adaptor trimmer
+.
+.SH "SYNOPSIS"
+scythe \-t sanger \-a /path/to/adaptors\.fasta [options] <sequences\.fastq\.gz>
+.
+.P
+Trim 3\'\-end adapter contaminants off sequence files\. If no output file is specified, scythe will use stdout\.
+.
+.SH "USAGE"
+.
+.nf
+ \-p, \-\-prior prior (default: 0\.300)
+ \-q, \-\-quality\-type quality type, either illumina, solexa, or sanger (default: sanger)
+ \-m, \-\-matches\-file matches file (default: no output)
+ \-o, \-\-output\-file output trimmed sequences file (default: stdout)
+ \-t, \-\-tag add a tag to the header indicating Scythe cut a sequence (default: off)
+ \-n, \-\-min\-match smallest contaminant to consider (default: 5)
+ \-M, \-\-min\-keep filter sequences less than or equal to this length (default: 35)
+      \-\-quiet don\'t output statistics about trimming to stdout (default: off)
+      \-\-help display this help and exit
+      \-\-version output version information and exit
+.
+.SH "Quality Schemes"
+.nf
+These are the quality encoding schemes scythe recognises (see \'\-\-quality\')
+
+  phred     PHRED quality scores (e\.g\. from Roche 454)\. ASCII with no
+            offset, range: [4, 60]\.
+  sanger    Sanger are PHRED ASCII qualities with an offset of 33,
+            range: [0, 93]\. From NCBI SRA, or Illumina pipeline 1\.8+\.
+  solexa    Solexa (also very early Illumina \-\- pipeline < 1\.3)\.
+            ASCII offset of 64, range: [\-5, 62]\. Uses a different
+            quality-to-probabilities conversion than other schemes\.
+  illumina  Illumina output from pipeline versions between 1\.3 and 1\.7\.
+            ASCII offset of 64, range: [0, 62]
+.
+.SH "AUTHOR"
+Vince Buffalo, https://github.com/vsbuffalo

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