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commit bb1cf761fa662d9ae6b5ecec4f3d8815c66de34a Author: Kevin Murray <[email protected]> Date: Mon May 11 17:16:50 2015 +1000 Minor re-write of scythe.1 - Be consistent with use of adaptor vs adapter (-or is the go-between, -er is something which adapts) - Use OPTIONS not USAGE - Add FILES section & description of adaptor FASTA file --- debian/scythe.1 | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/debian/scythe.1 b/debian/scythe.1 index 1503e01..ad1d07d 100644 --- a/debian/scythe.1 +++ b/debian/scythe.1 @@ -7,9 +7,9 @@ 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\. +Trim 3\'-end adaptor contaminants off sequence files\. If no output file is specified, scythe will use stdout\. . -.SH "USAGE" +.SH "OPTIONS" . .nf \-p, \-\-prior prior (default: 0\.300) @@ -22,8 +22,7 @@ Trim 3\'\-end adapter contaminants off sequence files\. If no output file is spe \-\-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\') @@ -37,5 +36,12 @@ These are the quality encoding schemes scythe recognises (see \'\-\-quality\') illumina Illumina output from pipeline versions between 1\.3 and 1\.7\. ASCII offset of 64, range: [0, 62] . +.SH "FILES" +.nf + +adaptors\.fasta: Provide contaminant sequences as a fasta-formatted file\. + See \'/usr/share/doc/scythe/illumina_adaptors\.fa\'\. + N\.B\.: Index/Barcode sequences should be substituted for Ns in + the example adaptor file. .SH "AUTHOR" Vince Buffalo, https://github.com/vsbuffalo -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/scythe.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
