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commit 413b59c442af3c3cf016bef4de4f144ced64fdaa Author: Afif Elghraoui <[email protected]> Date: Sat May 23 14:50:59 2015 -0700 Clean up positionDB.1 --- debian/positionDB.1 | 83 ++++++++++++++++++++++++++++++----------------------- 1 file changed, 47 insertions(+), 36 deletions(-) diff --git a/debian/positionDB.1 b/debian/positionDB.1 index ce397f3..97d01bf 100644 --- a/debian/positionDB.1 +++ b/debian/positionDB.1 @@ -1,67 +1,78 @@ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4. .TH POSITIONDB "1" "May 2015" "positionDB 0~20150520+2004" "User Commands" .SH NAME -positionDB \- manual page for positionDB 0~20150520+2004 -.SH DESCRIPTION -usage: ./positionDB [args] +positionDB \- management of posDB files +.SH SYNOPSIS +.B positionDB +[\fB\-mersize\fR \fIk\fR] +[\fB\-merskip\fR \fIk\fR] +[\fB\-use\fR \fIa\fR\-\fIb\fR,\fIc\fR] +[\fB\-merbegin\fR \fIb\fR] +[\fB\-merend\fR \fIe\fR] +\fB\-sequence\fR \fIs.fasta\fR +\fB\-output\fR \fIp.posDB\fR +.PP +.B positionDB +\fB\-dump\fR \fIdatafile\fR +.PP +.B positionDB +\fB\-test1\fR \fIsequence.fasta\fR +.PP +.B positionDB +\fB\-test2\fR \fIdb.fasta\fR \fIsequence.fasta\fR +.SH OPTIONS +.SS Building a table .TP -\fB\-mersize\fR k +\fB\-mersize\fR \fIk\fR The size of the mers, default=20. .TP -\fB\-merskip\fR k +\fB\-merskip\fR \fIk\fR The skip between mers, default=0 .TP -\fB\-use\fR a\-b,c +\fB\-use\fR \fIa\fR\-\fIb\fR,\fIc\fR Specify which sequences to use, default=all .TP -\fB\-merbegin\fR b +\fB\-merbegin\fR \fIb\fR Build on a subset of the mers, starting at mer #b, default=all mers .TP -\fB\-merend\fR e +\fB\-merend\fR \fIe\fR Build on a subset of the mers, ending at mer #e, default=all mers .TP -\fB\-sequence\fR s.fasta +\fB\-sequence\fR \fIs.fasta\fR Input sequences. .TP -\fB\-output\fR p.posDB +\fB\-output\fR \fIp.posDB\fR Output filename. .IP -To dump information about an image: +.SS Dumping information about an image .HP -\fB\-dump\fR datafile +\fB\-dump\fR \fIdatafile.posDB\fR .IP -To run sanity tests: -.HP -\fB\-buildonly\fR [build opts] sequence.fasta +.SS Running sanity tests .TP -\fB\-\-\fR +\fB\-buildonly\fR [build opts] \fIsequence.fasta\fR just builds a table and exits -.HP -\fB\-existence\fR [build opts] sequence.fasta .TP -\fB\-\-\fR -builds (or reads) a table reports if any mers -in sequence.fasta cannot be found -.HP -\fB\-extra\fR [build opts] sequence.fasta +\fB\-existence\fR [build opts] \fIsequence.fasta\fR +builds (or reads) a table and reports if any mers +in \fIsequence.fasta\fR cannot be found .TP -\fB\-\-\fR -builds (or reads) a table reports if any mers -NOT in sequence.fasta are be found -.HP -\fB\-test1\fR sequence.fasta +\fB\-extra\fR [build opts] \fIsequence.fasta\fR +builds (or reads) a table and reports if any mers +NOT in \fIsequence.fasta\fR are found .TP -\fB\-\-\fR +\fB\-test1\fR \fIsequence.fasta\fR Tests if each and every mer is found in the -positionDB. Reports if it doesn't find a mer +\fBpositionDB\fR. Reports if it doesn't find a mer at the correct position. Doesn't report if table has too much stuff. -.HP -\fB\-test2\fR db.fasta sequence.fasta .TP -\fB\-\-\fR -Builds a positionDB from db.fasta, then searches -the table for each mer in sequence.fasta. Reports +\fB\-test2\fR \fIdb.fasta\fR \fIsequence.fasta\fR +Builds a \fBpositionDB\fR from \fIdb.fasta\fR, then searches +the table for each mer in \fIsequence.fasta\fR. Reports all mers it finds. .IP -\fB\-\-\fR This is a silly test and you shouldn't do it. +This is a silly test and you shouldn't do it. +.SH SEE ALSO +.BR existDB (1), +.BR meryl (1) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/kmer-tools.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
