[med-svn] [kmer-tools] 05/08: Polish the remaining man-pages
Afif Elghraoui
afif-guest at moszumanska.debian.org
Sun May 24 09:29:41 UTC 2015
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository kmer-tools.
commit ca2cfe9f3bd7046bb6441e57b26da8a23d5ba4e4
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Sun May 24 01:08:01 2015 -0700
Polish the remaining man-pages
Fix formatting and add content to the remaining man pages.
---
debian/kmer-mask.1 | 114 +++++++++++-----
debian/mapMers-depth.1 | 52 ++++---
debian/mapMers.1 | 34 ++++-
debian/meryl.1 | 361 ++++++++++++++++++++++++++++++-------------------
debian/positionDB.1 | 2 +-
5 files changed, 369 insertions(+), 194 deletions(-)
diff --git a/debian/kmer-mask.1 b/debian/kmer-mask.1
index b9ae5b0..20c5746 100644
--- a/debian/kmer-mask.1
+++ b/debian/kmer-mask.1
@@ -1,69 +1,119 @@
.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
.TH KMER-MASK "1" "May 2015" "kmer-mask 0~20150520+2004" "User Commands"
.SH NAME
-kmer-mask \- manual page for kmer-mask 0~20150520+2004
+kmer-mask \- mask and filter set of nucleotide sequences by kmer content
+.SH SYNOPSIS
+.B kmer\-mask
+.RB { \-novel | \-confirmed }
+.RB [ \-mdb
+.IR mer-database ]
+.RB [ \-ms
+.IR mer-size ]
+.RB [ \-edb
+.IR exist-database ]
+.RB [ \-m
+.IR min-size ]
+.RB [ \-e
+.IR extend-size]
+.RB [ \-lowthreshold
+.IR l ]
+.RB [ \-highthreshold
+.IR h ]
+.RB [ \-t
+.IR threads ]
+.RB [ \-v ]
+.RB [ \-h
+.IR histogram ]
+.RB [ \-promote | \-demote | \-discard ]
+.BI \-1 \0in.1.fastq
+.RB [ \-2
+.IR in.2.fastq ]
+.BI \-o \0output-prefix
.SH DESCRIPTION
-usage: ./kmer\-mask [\-novel | \fB\-confirmed]\fR ...
+Mask and filter set of sequences (presumed to be reads) by kmer content.
+Masking can be done to retain novel sequence not in the database, or to retain
+confirmed sequence present in the database.
+Filtering will segregate sequences fully, partially or not masked.
+.SH OPTIONS
.TP
-\fB\-mdb\fR mer\-database
-load masking kmers from meryl 'mer\-database'
+.BI \-mdb \0mer\-database
+load masking kmers from
+.BR meryl (1)
+.I mer\-database
.TP
-\fB\-ms\fR
-mer\-size
+.BI \-ms \0mer\-size
.TP
-\fB\-edb\fR exist\-database
-save masking kmers to 'exist\-database' for faster restarts
+.BI \-edb \0exist\-database
+save masking kmers to an
+.BR existDB (1)
+file
+.I exist\-database
+for faster restarts
.TP
-\fB\-1\fR in.1.fastq
-input reads \- fastq, fastq.gz, fastq.bz2 or fastq.xz
-.HP
-\fB\-2\fR in.2.fastq \- (optional, but if not present, messes up the output classification)
+.BI \-1 \0in.1.fastq
.TP
-\fB\-o\fR
-out output reads:
-out.fullymasked.[12].fastq \- reads with below 'lowthreshold' bases retained
-out.partiallymasked.[12].fastq \- reads in between
-out.retained.[12].fastq \- reads with more than 'hightreshold' bases retained
-out.discarded.[12].fastq \- reads with conflicting status
+.BI \-2 \0in.2.fastq
+input reads files in fastq, fastq.gz, fastq.bz2 or fastq.xz format.
+The second is optional, but messes up the output classification if not present.
.TP
-\fB\-m\fR min\-size
+.BI \-o \0out
+.RS
+prefix for output reads
+.TP
+\fIout\fR.fullymasked.[12].fastq
+reads with below 'lowthreshold' bases retained
+.TP
+.IR out .partiallymasked.[12].fastq
+reads in between
+.TP
+.IR out .retained.[12].fastq
+reads with more than 'hightreshold' bases retained
+.TP
+.IR out .discarded.[12].fastq
+reads with conflicting status
+.RE
+.TP
+.BI \-m \0min\-size
ignore database hits below this many consecutive kmers (0)
.TP
-\fB\-e\fR extend\-size
+.BI \-e \0extend\-size
extend database hits across this many missing kmers (0)
.TP
-\fB\-novel\fR
+.B \-novel
RETAIN novel sequence not present in the database
.TP
-\fB\-confirmed\fR
+.B \-confirmed
RETAIN confirmed sequence present in the database
.TP
-\fB\-promote\fR
+.B \-promote
promote the lesser RETAINED read to the status of the more RETAINED read
read1=fullymasked and read2=partiallymasked \-> both are partiallymasked
.TP
-\fB\-demote\fR
+.B \-demote
demote the more RETAINED read to the status of the lesser RETAINED read
read1=fullymasked and read2=partiallymasked \-> both are fullymasked
.TP
-\fB\-discard\fR
+.B \-discard
discard pairs with conflicting status (DEFAULT)
read1=fullymasked and read2=partiallymasked \-> both are discarded
.SS "stats on stderr, number of sequences with amount RETAINED:"
.TP
-\fB\-lowthreshold\fR t
+.BI \-lowthreshold \0t
(0.3333)
.TP
-\fB\-highthreshold\fR t
+.BI \-highthreshold \0t
(0.6667)
.TP
-\fB\-h\fR histogram
+.BI \-h \0histogram
write a histogram of the amount of sequence RETAINED
.TP
-\fB\-t\fR t
-use 't' compute threads
+.BI \-t \0t
+use
+.I t
+compute threads
.TP
\fB\-v\fR
show progress
-.PP
-ERROR: exactly one of \fB\-novel\fR and \fB\-confirmed\fR must be supplied.
+.SH SEE ALSO
+.BR meryl (1)
+.BR existDB (1)
diff --git a/debian/mapMers-depth.1 b/debian/mapMers-depth.1
index 8c2e73a..f77e71d 100644
--- a/debian/mapMers-depth.1
+++ b/debian/mapMers-depth.1
@@ -1,28 +1,44 @@
.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
.TH MAPMERS-DEPTH "1" "May 2015" "mapMers-depth 0~20150520+2004" "User Commands"
.SH NAME
-mapMers-depth \- manual page for mapMers-depth 0~20150520+2004
-.SH DESCRIPTION
-unknown option ''
-usage: ./mapMers\-depth \fB\-mers\fR MERYL \fB\-m\fR MERSIZE \fB\-seq\fR IN.FASTA [\-count | \fB\-depth\fR | \fB\-stats]\fR > output
-.PP
+mapMers-depth \- report information about mapping kmers to sequences
+.SH SYNOPSIS
+.B mapMers\-depth
+.RB { \-count | \-depth | \-stats }
+.BI \-mers \0MERYL
+.BI \-m \0MERSIZE
+.BI \-seq \0IN.FASTA
+.SH OPTIONS
+.SS
+Modes of operation
For sequence ordinal 's' and position in that sequence 'p':
-.HP
-\fB\-count\fR \- report the count (c) of the single kmer that starts at position (p).
+.TP
+.B \-count
+reports the count (c) of the single kmer that starts at position (p).
.IP
Format: 's p c'
.TP
-\fB\-depth\fR \- report the number (n) of kmers that span position (p).
+.B \-depth
+reports the number (n) of kmers that span position (p).
+.IP
Format: 's p n'
-.HP
-\fB\-stats\fR \- report the min (m), max (M), ave (a) count of all mers that span
.TP
-position (p).
-Format: 's p m M a t n'
+.B \-stats
+reports the minimum (m), maximum (M), and average (a) count of all mers that span position (p). also reports total count (t) and number of kmers (n)
.IP
-(also reports total count (t) and number of kmers (n))
-.PP
-ERROR: No mer size (\fB\-m\fR) suppled.
-ERROR: No fasta input (\fB\-seq\fR) suppled.
-ERROR: No meryl database (\fB\-mers\fR) suppled.
-ERROR: Exactly one of \fB\-count\fR, \fB\-depth\fR and \fB\-stats\fR may be supplied.
+Format: 's p m M a t n'
+.SS General
+.TP
+.BI \-m \0MERSIZE
+.TP
+.BI \-mers \0MERYL
+.BR meryl (1)
+database
+.TP
+.BI \-seq \0IN.FASTA
+fasta input sequence
+.SH SEE ALSO
+.BR meryl (1),
+.BR mapMers (1)
+
+
diff --git a/debian/mapMers.1 b/debian/mapMers.1
index 976229d..4a1fbd6 100644
--- a/debian/mapMers.1
+++ b/debian/mapMers.1
@@ -1,7 +1,33 @@
.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
.TH MAPMERS "1" "May 2015" "mapMers 0~20150520+2004" "User Commands"
.SH NAME
-mapMers \- manual page for mapMers 0~20150520+2004
-.SH DESCRIPTION
-unknown option ''
-usage: ./mapMers [\-stats | \fB\-regions\fR | \fB\-details]\fR \fB\-m\fR mersize \fB\-mers\fR mers \fB\-seq\fR fasta > output
+mapMers \- report statistics of mapping kmers to sequences
+.SH SYNOPSIS
+.B mapMers
+.RB { \-stats | \-regions | \-details }
+.BI \-m \0mersize
+.BI \-mers \0mers
+.BI \-seq \0fasta
+.SH OPTIONS
+.TP
+.B \-stats
+reports the mean, minimum, and maximum for each sequence, along with a log2 histogram of the counts
+.TP
+.B \-regions
+reports regions with kmer coverage
+.TP
+.B \-details
+reports the forward and reverse count in the database for each kmer in the sequence
+.TP
+.BI \-m \0mersize
+.TP
+.BI \-mers \0mers
+the
+.BR meryl (1)
+database
+.TP
+.BI \-seq \0fasta
+input sequence file
+.SH SEE ALSO
+.BR meryl (1),
+.BR mapMers-depth (1)
diff --git a/debian/meryl.1 b/debian/meryl.1
index f9e94af..01ef7d7 100644
--- a/debian/meryl.1
+++ b/debian/meryl.1
@@ -1,230 +1,293 @@
.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
.TH MERYL "1" "May 2015" "meryl 0~20150520+2004" "User Commands"
.SH NAME
-meryl \- manual page for meryl 0~20150520+2004
+meryl \- in- and out-of-core kmer counting and utilities
+.SH SYNOPSIS
+.SS Estimating memory requirements
+.PP
+.B meryl \-P
+.BI -m \0kmersize
+.RB [ \-c
+.IR # ]
+.RB [ \-p ]
+.BI \-s \0seq.fasta
+.PP
+.B meryl \-P
+.BI \-m \0kmersize
+.RB [ \-c
+.IR # ]
+.RB [ \-p ]
+.BI \-n \0mercount
+.SS Building a table
+.B meryl \-B
+.BI -m \0kmersize
+.RB [ \-c
+.IR # ]
+.RB [ \-p ]
+.RB [ \-v ]
+.RB [ \-f | \-r | \-C ]
+.RB [ \-L
+.IR minoccurrence ]
+.RB [ \-U
+.IR maxoccurrence ]
+.RB [ \-threads
+.IR n \0|
+.RB { \-segments
+.IR segments \0|
+.BI \-memory \0megabytes \fR}
+.RB [ \-configbatch \0[ \-sge
+.IR jobname ]]]
+.BI \-s \0seq.fasta
+.BI \-o \0tblprefix
+.PP
+.B meryl
+.BI \-countbatch \0number
+.RB [ \-sgebuild
+\fR"\fIqsuboptionstring\fR"]
+.BI \-o \0tblprefix
+.PP
+.B meryl
+.BI \-mergebatch \0number
+.RB [ \-sgemerge
+\fR"\fIqsuboptionstring\fR"]
+.BI \-o \0tblprefix
+.SS Performing operations on a table
+.B meryl
+.BI -M \0operation
+.RB [ \-v ]
+.BI \-s \0tblprefix
+.RB [ \-s
+.IR \0tblprefix2 \0...]
+.BI \-o \0output
+.SS Dumping a table
+.B meryl \-Dh
+.BI \-s \0tblprefix
+.PP
+.B meryl \-Dt
+.BI \-n \0mincount
+.BI \-s \0tblprefix
.SH DESCRIPTION
-usage: ./meryl [personality] [global options] [options]
-.SS "where personality is:"
-.HP
-\fB\-P\fR \fB\-\-\fR compute parameters
-.HP
-\fB\-B\fR \fB\-\-\fR build table
-.HP
-\fB\-S\fR \fB\-\-\fR scan table
-.HP
-\fB\-M\fR \fB\-\-\fR "math" operations
-.HP
-\fB\-D\fR \fB\-\-\fR dump table
+\fBmeryl\fR computes the kmer content of genomic sequences.
+Kmer content is represented as a list of kmers and the number of times each occurs in the input sequences.
+The kmer can be restricted to only the forward kmer, only the reverse kmer, or the canonical kmer (lexicographically smaller of the forward and reverse kmer at each location).
+\fBMeryl\fR can report the histogram of counts, the list of kmers and their counts, or can perform mathematical and set operations on the processed data files.
.PP
-\fB\-P\fR: Given a sequence file (\fB\-s\fR) or an upper limit on the
-.IP
-number of mers in the file (\fB\-n\fR), compute the table size
-(\fB\-t\fR in build) to minimize the memory usage.
+The output of
+.B meryl
+is two binary files, called a meryl database, which can be
+quickly dumped to provide a histogram of counts, or the actual counts.
+A C++ library is supplied for direct access to the files.
+.SH OPTIONS
.TP
-\fB\-m\fR #
-(size of a mer; required)
+.B \-P
+Estimate memory requirements. Given a sequence file (\fB\-s\fR) or an upper limit on the number of mers in the file (\fB\-n\fR), compute the table size
+(\fB\-t\fR in build) to minimize the memory usage. This mode recognizes the following options:
+.RS
.TP
-\fB\-c\fR #
-(homopolymer compression; optional)
+.BI \-m \0#
+size of a mer (required)
.TP
-\fB\-p\fR
-(enable positions)
+.BI \-c \0#
+homopolymer compression (optional)
.TP
-\fB\-s\fR seq.fasta
-(seq.fasta is scanned to determine the number of mers)
+.B \-p
+enable positions
.TP
-\fB\-n\fR #
-(compute params assuming file with this many mers in it)
+.BI \-s \0seq.fasta
+Sequence file to be scanned to determine the number of mers
.TP
-Only one of \fB\-s\fR, \fB\-n\fR need to be specified.
-If both are given
-.HP
-\fB\-s\fR takes priority.
+.BI \-n \0#
+compute params assuming file with this many mers in it
.PP
-\fB\-B\fR: Given a sequence file (\fB\-s\fR) and lots of parameters, compute
+Only one of \fB\-s\fR, \fB\-n\fR need to be specified.
+If both are given, \fB\-s\fR takes priority.
+.RE
.TP
-the mer\-count tables.
+.B \-B
+Compute the mer-count tables given a sequence file (\fB\-s\fR) and lots of parameters.
By default, both strands are processed.
+.RS
.TP
-\fB\-f\fR
-(only build for the forward strand)
+.B \-f
+only build for the forward strand
.TP
-\fB\-r\fR
-(only build for the reverse strand)
+.B \-r
+only build for the reverse strand
.TP
-\fB\-C\fR
-(use canonical mers, assumes both strands)
+.B \-C
+use canonical mers (assumes both strands)
.TP
-\fB\-L\fR #
-(DON'T save mers that occur less than # times)
+.BI \-L \0#
+DON'T save mers that occur less than # times
.TP
-\fB\-U\fR #
-(DON'T save mers that occur more than # times)
+.BI \-U \0#
+DON'T save mers that occur more than # times
.TP
-\fB\-m\fR #
-(size of a mer; required)
+.BI \-m \0#
+size of a mer (required)
.TP
-\fB\-c\fR #
-(homopolymer compression; optional)
+.BI \-c \0#
+homopolymer compression (optional)
.TP
-\fB\-p\fR
-(enable positions)
+.B \-p
+enable positions
.TP
-\fB\-s\fR seq.fasta
-(sequence to build the table for)
+.BI \-s \0seq.fasta
+sequence to build the table for
.TP
-\fB\-o\fR tblprefix
-(output table prefix)
+.BI \-o \0tblprefix
+output table prefix
.TP
\fB\-v\fR
-(entertain the user)
-.IP
+entertain the user
+.PP
+The
+.B meryl
+process can run in one large memory batch, in many small memory batches, or under SGE control, all with or without using multiple CPU cores.
By default, the computation is done as one large sequential process.
Multi\-threaded operation is possible, at additional memory expense, as
is segmented operation, at additional I/O expense.
-.IP
-Threaded operation: Split the counting in to n almost\-equally sized
-pieces. This uses an extra h MB (from \fB\-P\fR) per thread.
-.TP
-\fB\-threads\fR n
-(use n threads to build)
-.IP
-Segmented, sequential operation: Split the counting into pieces that
+.TP
+.B Threaded operation
+Split the counting in to n almost\-equally sized pieces.
+This uses an extra h MB (from \fB\-P\fR) per thread.
+.RS
+.TP
+.BI \-threads \0n
+use
+.I n
+threads to build
+.RE
+.TP
+.B Segmented, sequential operation
+Split the counting into pieces that
will fit into no more than m MB of memory, or into n equal sized pieces.
Each piece is computed sequentially, and the results are merged at the end.
Only one of \fB\-memory\fR and \fB\-segments\fR is needed.
+.RS
+.TP
+.BI \-memory \0m
+use at most \fIm\fR MB of memory per segment
.TP
-\fB\-memory\fR mMB
-(use at most m MB of memory per segment)
+.BI \-segments \0n
+use \fIn\fR segments
+.PP
+.RE
.TP
-\fB\-segments\fR n
-(use n segments)
-.IP
-Segmented, batched operation: Same as sequential, except this allows
-each segment to be manually executed in parallel.
+.B Segmented, batched operation
+Same as sequential, except this allows each segment to be manually executed
+in parallel.
Only one of \fB\-memory\fR and \fB\-segments\fR is needed.
+Also see the
+.I EXAMPLE
+section on this page.
+.RS
.TP
-\fB\-memory\fR mMB
-(use at most m MB of memory per segment)
+.BI \-memory \0m
+use at most \fIm\fR MB of memory per segment
.TP
-\fB\-segments\fR n
-(use n segments)
+.BI \-segments \0n
+use \fIn\fR segments
.TP
-\fB\-configbatch\fR
-(create the batches)
+.B \-configbatch
+create the batches
.TP
-\fB\-countbatch\fR n
-(run batch number n)
+.BI \-countbatch \0n
+run batch number \fIn\fR
.TP
-\fB\-mergebatch\fR
-(merge the batches)
-.IP
-Initialize the compute with \fB\-configbatch\fR, which needs all the build options.
-Execute all \fB\-countbatch\fR jobs, then \fB\-mergebatch\fR to complete.
-.IP
-meryl \fB\-configbatch\fR \fB\-B\fR [options] \fB\-o\fR file
-meryl \fB\-countbatch\fR 0 \fB\-o\fR file
-meryl \fB\-countbatch\fR 1 \fB\-o\fR file
-\&...
-meryl \fB\-countbatch\fR N \fB\-o\fR file
-meryl \fB\-mergebatch\fR N \fB\-o\fR file
-.IP
+.B \-mergebatch
+merge the batches
+.PP
Batched mode can run on the grid.
.TP
-\fB\-sge\fR
-jobname unique job name for this execution. Meryl will submit
-jobs with name mpjobname, ncjobname, nmjobname, for
+.BI \-sge \0jobname
+unique job name for this execution.
+\fBMeryl\fR will submit jobs with name mp\fIjobname\fR, nc\fIjobname\fR, nm\fIjobname\fR, for
phases prepare, count and merge.
.TP
-\fB\-sgebuild\fR "options"
-any additional options to sge, e.g.,
+.BI \-sgebuild \0"options"
.TP
-\fB\-sgemerge\fR "options"
-"\-p \fB\-153\fR \fB\-pe\fR thread 2 \fB\-A\fR merylaccount"
+.BI \-sgemerge \0"options"
+any additional options to
+.BR qsub (1)
+(e.g., "\-p \fB\-153\fR \fB\-pe\fR thread 2 \fB\-A\fR merylaccount")
N.B. \- \fB\-N\fR will be ignored
N.B. \- be sure to quote the options
-.PP
-\fB\-M\fR: Given a list of tables, perform a math, logical or threshold operation.
-.IP
+.RE
+.RE
+.TP
+.B \-M
+Given a list of tables, perform a math, logical or threshold operation.
Unless specified, all operations take any number of databases.
-.IP
Math operations are:
+.RS
.TP
-min
+.B min
count is the minimum count for all databases. If the mer
does NOT exist in all databases, the mer has a zero count, and
is NOT in the output.
.TP
-minexist
+.B minexist
count is the minimum count for all databases that contain the mer
.TP
-max
+.B max
count is the maximum count for all databases
.TP
-add
+.B add
count is sum of the counts for all databases
.TP
-sub
+.B sub
count is the first minus the second (binary only)
.TP
-abs
+.B abs
count is the absolute value of the first minus the second (binary only)
-.IP
+.PP
Logical operations are:
.TP
-and
+.B and
outputs mer iff it exists in all databases
.TP
-nand
+.B nand
outputs mer iff it exists in at least one, but not all, databases
.TP
-or
+.B or
outputs mer iff it exists in at least one database
.TP
-xor
+.B xor
outputs mer iff it exists in an odd number of databases
-.IP
+.PP
Threshold operations are:
.TP
-lessthan x
+.BI lessthan \0x
outputs mer iff it has count < x
.TP
-lessthanorequal x
+.BI lessthanorequal \0x
outputs mer iff it has count <= x
.TP
-greaterthan x
+.BI greaterthan \0x
outputs mer iff it has count > x
.TP
-greaterthanorequal x
+.BI greaterthanorequal \0x
outputs mer iff it has count >= x
.TP
-equal x
+.BI equal \0x
outputs mer iff it has count == x
-.IP
+.PP
Threshold operations work on exactly one database.
.TP
-\fB\-s\fR tblprefix
-(use tblprefix as a database)
+.BI \-s \0tblprefix
+use \fItblprefix\fR as a database
.TP
-\fB\-o\fR tblprefix
-(create this output)
+.BI \-o \0tblprefix
+create this output
.TP
\fB\-v\fR
-(entertain the user)
-.TP
-NOTE:
-Multiple tables are specified with multiple \fB\-s\fR switches; e.g.:
-.IP
-\&./meryl \fB\-M\fR add \fB\-s\fR 1 \fB\-s\fR 2 \fB\-s\fR 3 \fB\-s\fR 4 \fB\-o\fR all
-.TP
-NOTE:
-It is NOT possible to specify more than one operation:
-.IP
-\&./meryl \fB\-M\fR add \fB\-s\fR 1 \fB\-s\fR 2 \fB\-sub\fR \fB\-s\fR 3
-.IP
-will NOT work.
-.PP
-\fB\-D\fR: Dump the table (not all of these work).
+entertain the user
+.RE
+.TP
+.B \-D
+Dump table (not all of these work)
+.RS
.TP
\fB\-Dd\fR
Dump a histogram of the distance between the same mers.
@@ -240,3 +303,23 @@ Dump (to stdout) a histogram of mer counts.
.TP
\fB\-s\fR
Read the count table from here (leave off the .mcdat or .mcidx).
+.RE
+.SH EXAMPLE
+.SS Batch creation of a table
+Initialize the compute with \fB\-configbatch\fR, which needs all the build options.
+Execute all \fB\-countbatch\fR jobs, then \fB\-mergebatch\fR to complete.
+.PP
+.nf
+.RS
+meryl \fB\-configbatch\fR \fB\-B\fR [options] \fB\-o\fR file
+meryl \fB\-countbatch\fR 0 \fB\-o\fR file
+meryl \fB\-countbatch\fR 1 \fB\-o\fR file
+\&...
+meryl \fB\-countbatch\fR N \fB\-o\fR file
+meryl \fB\-mergebatch\fR N \fB\-o\fR file
+.RE
+.fi
+.SH SEE ALSO
+.BR mapMers (1),
+.BR mapMers-depth (1),
+.BR kmer-mask (1)
diff --git a/debian/positionDB.1 b/debian/positionDB.1
index 70c3008..980451a 100644
--- a/debian/positionDB.1
+++ b/debian/positionDB.1
@@ -21,7 +21,7 @@ positionDB \- management of posDB files
.B positionDB
\fB\-test2\fR \fIdb.fasta\fR \fIsequence.fasta\fR
.SH OPTIONS
-.SS Building a table
+.SS Building an image
.TP
\fB\-mersize\fR \fIk\fR
The size of the mers, default=20.
--
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