[med-svn] [kmer-tools] 01/08: Clean up positionDB.1

[Afif Elghraoui]

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commit 413b59c442af3c3cf016bef4de4f144ced64fdaa
Author: Afif Elghraoui <afif at ghraoui.name>
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)

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