[med-svn] [pftools] 02/04: Add manpages

[Andreas Tille]

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tille pushed a commit to branch master
in repository pftools.

commit fc9fddfcc449cf98149863dfe0d70118dfeea344
Author: Andreas Tille <tille at debian.org>
Date:   Fri Mar 31 13:06:35 2017 +0200

    Add manpages
---
 debian/manpages     |  1 +
 debian/pfsearch.1   | 67 ++++++++++++++++++++++++++++++++++++++
 debian/pfsearchV3.1 | 93 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 3 files changed, 161 insertions(+)

diff --git a/debian/manpages b/debian/manpages
index 85c5e00..9a00da6 100644
--- a/debian/manpages
+++ b/debian/manpages
@@ -1 +1,2 @@
 man/*
+debian/*.1
\ No newline at end of file
diff --git a/debian/pfsearch.1 b/debian/pfsearch.1
new file mode 100644
index 0000000..161cccb
--- /dev/null
+++ b/debian/pfsearch.1
@@ -0,0 +1,67 @@
+.TH PFSEARCH "1" "March 2017" "pfsearch 3" "User Commands"
+.SH NAME
+pfsearch \- search protein and DNA generalized profiles (legacy)
+.SH SYNOPSIS
+.B pfsearch
+[ \fI\,-abCdfhlLmMkrsuvWxyz \/\fR] [ \fI\,profile-file | - \/\fR] [ \fI\,seq-library-file | - \/\fR] [ \fI\,parameters \/\fR]
+.SH DESCRIPTION
+Build protein and DNA generalized profiles and use them to scan and align sequences,
+and search databases.
+.SH OPTIONS
+.HP
+\fB\-a\fR: report optimal alignment for all sequences.
+.HP
+\fB\-b\fR: search complementary strand of DNA sequences.
+.HP
+\fB\-f\fR: input sequence file is in FASTA format.
+.HP
+\fB\-h\fR: print usage help text.
+.HP
+\fB\-l\fR: indicate highest cut\-off level (number).
+.HP
+\fB\-L\fR: indicate highest cut\-off level (text).
+.HP
+\fB\-m\fR: report individual matches for circular profiles.
+.HP
+\fB\-r\fR: use raw score.
+.HP
+\fB\-u\fR: force profile disjointness to UNIQUE.
+.HP
+\fB\-C\fR<value>:
+.IP
+cut\-off value. An integer value forces \fB\-r\fR. Same as parameter C.
+.HP
+\fB\-M\fR<value>:
+.IP
+set the normalization mode to use for the score computation.
+Overrides the profile PRIORITY parameter.
+.IP
+output modifiers:
+.HP
+\fB\-d\fR: impose length limit on sequence description.
+.HP
+\fB\-k\fR: output using the xPSA header (using keyword=value pairs).
+.HP
+\fB\-s\fR: list sequences of the matched regions.
+.HP
+\fB\-v\fR: suppress warnings on stderr.
+.HP
+\fB\-x\fR: list alignments in PSA format.
+.HP
+\fB\-y\fR: list alignments in human readable form.
+.HP
+\fB\-z\fR: indicate profile start and stop positions.
+.HP
+\fB\-W\fR<value>:
+.IP
+specifies the output width. Same as parameter W.
+.IP
+valid (but deprecated) parameters are:
+.TP
+[C=cut\-off\-value]
+use option \fB\-C\fR instead
+.TP
+[W=output\-width]
+use option \fB\-W\fR instead
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/pfsearchV3.1 b/debian/pfsearchV3.1
new file mode 100644
index 0000000..ad545d9
--- /dev/null
+++ b/debian/pfsearchV3.1
@@ -0,0 +1,93 @@
+.TH PFSEARCHV3 "1" "March 2017" "pfsearchV3 3" "User Commands"
+.SH NAME
+pfsearchV3 \- search protein and DNA generalized profiles (version 3)
+.SH SYNOPSIS
+.B pfsearch
+[options] profile database
+.SH DESCRIPTION
+Build protein and DNA generalized profiles and use them to scan and align sequences,
+and search databases.
+.SH OPTIONS
+.SS Profile
+.TP
+\fB\-\-level\fR
+[\-l] : level to use for cutoff
+.TP
+\fB\-\-mode\fR
+[\-m] : mode to use for normalization
+.SS Database
+.TP
+\fB\-\-create\-index\-database\fR
+[\-c] : output indices to given file
+.TP
+\fB\-\-use\-index\-database\fR
+[\-i] : use indices stored in given file
+.SS Heuristic
+.TP
+\fB\-\-cutoff\fR
+[\-C] : heuristic cutoff value
+.TP
+\fB\-\-dump\-heuristic\-scores\fR
+[\-A] : only print heuristic scores to stdout
+.HP
+\fB\-\-dump\-heuristic\-sequences\fR [\-D] : dump passed heuristic sequences
+.SS Filter
+.TP
+\fB\-\-dump\-filter\-scores\fR
+[\-a] : only print filter scores to stdout
+.TP
+\fB\-\-dump\-filter\-sequences\fR
+[\-d] : dump passed heuristic and filter
+sequences
+.SS Optimizations
+.TP
+\fB\-\-sse2\fR
+[\-s] : enforces SSE 2 only instruction set
+.TP
+\fB\-\-nthreads\fR
+[\-t] : max number of threads to use
+.TP
+\fB\-\-max\-heuristic\-nthreads\fR
+[\-T] : max number of threads to use for
+heuristic phase only. (IO bounds)
+.TP
+\fB\-\-no\-affinity\fR
+[\-f] : disable CPU affinity file
+.TP
+\fB\-\-thread\-affinity\fR
+[\-M] : file containing thread mask,
+one row for one thread
+.TP
+\fB\-\-no\-shared\-core\fR
+[\-k] : Prevent core resource sharing
+.TP
+\fB\-\-split\fR
+[\-b] : if both SSE 2 & 4.1 are available,
+split half\-half using linked resources
+.SS Printing output
+.TP
+\fB\-\-output\-method\fR
+[\-o] : printing output method
+.IP
+== 0 replicates the pfseach output without options (DEFAULT)
+.IP
+== 1 simple ouput
+.IP
+== 2 replicates pfsearch \fB\-lxz\fR output
+.IP
+== 3 replicates pfscan \fB\-lxz\fR output
+.IP
+== 4 tsv output (single line tab delimited)
+.TP
+\fB\-\-output\-length\fR
+[\-W] : maximum number of column for sequence
+ouput printing
+.SS Other
+.TP
+\fB\-\-verbose\fR
+[\-v] : verbose on stderr
+.TP
+\fB\-\-help\fR
+[\-h] : output command help
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

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