[med-svn] [mhap] 05/07: Update manpage

[Afif Elghraoui]

This is an automated email from the git hooks/post-receive script.

afif pushed a commit to branch master
in repository mhap.

commit 6dca11eba4eb2ceb36a0947740c8d7fb17dec7b1
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Wed Jul 13 00:40:45 2016 -0700

    Update manpage
---
 debian/mhap.1 | 96 +++++++++++------------------------------------------------
 1 file changed, 18 insertions(+), 78 deletions(-)

diff --git a/debian/mhap.1 b/debian/mhap.1
index ea438fa..52594d5 100644
--- a/debian/mhap.1
+++ b/debian/mhap.1
@@ -1,83 +1,23 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.2.
-.TH MHAP "1" "September 2015" "mhap 1.6" "User Commands"
+.TH MHAP "1" "July 2016" "mhap" "User Commands"
 .SH NAME
 mhap \- probabilistic sequence overlapping
+.SH SYNOPSIS
+.B mhap
+\fB\-s\fR<fasta/dat from/self file> [\-q<fasta/dat to file>] [\-f<kmer filter list, must be sorted>]
+.br
+.B java
+\fB\-server\fR \fB\-Xmx\fR<memory> \fB\-jar\fR $(which mhap) \fB\-s\fR<fasta/dat from/self file> [\-q<fasta/dat to file>] [\-f<kmer filter list, must be sorted>]
+.br
+generate precomputed binaries:
+.br
+.B java
+\fB\-server\fR \fB\-Xmx\fR<memory> \fB\-jar\fR $(which mhap) \fB\-p\fR<directory of fasta files> \fB\-q\fR <output directory> [\-f<kmer filter list, must be sorted>]
 .SH DESCRIPTION
-Please set the \fB\-s\fR or the \fB\-p\fR options. See options below:
-MHAP: MinHash Alignment Protocol. A tool for finding overlaps of long\-read sequences (such as PacBio or Nanopore) in bioinformatics.
-.IP
-Version: 1.6, Build time: 09/12/2015 11:46 PM
-Usage 1 (direct execution): java \fB\-server\fR \fB\-Xmx\fR<memory> \fB\-jar\fR <MHAP jar> \fB\-s\fR<fasta/dat from/self file> [\-q<fasta/dat to file>] [\-f<kmer filter list, must be sorted>]
-Usage 2 (generate precomputed binaries): java \fB\-server\fR \fB\-Xmx\fR<memory> \fB\-jar\fR <MHAP jar> \fB\-p\fR<directory of fasta files> \fB\-q\fR <output directory> [\-f<kmer filter list, must be sorted>]
+MHAP (MinHash Alignment Protocol) is a tool for finding overlaps of long\-read sequences (such as PacBio or Nanopore) in bioinformatics.
+.SH OPTIONS
 .TP
-\fB\-\-alignment\fR, default = false
-Experimental option.
+.B \-h \-\-help
+Show summary of available options.
 .TP
-\fB\-\-alignment\-offset\fR, default = \fB\-0\fR.535
-The offset to account for the variance in the alignment match score.
-.TP
-\fB\-\-alignment\-score\fR, default = 1.0E\-6
-The cutoff score for alignment matches.
-.TP
-\fB\-\-filter\-threshold\fR, default = 1.0E\-5
-[double], the cutoff at which the k\-mer in the k\-mer filter file is considered repetitive. This value for a specific k\-mer is specified in the second column in the filter file. If no filter file is provided, this option is ignored.
-.TP
-\fB\-\-help\fR, default = false
-Displays the help menu.
-.TP
-\fB\-\-max\-shift\fR, default = 0.2
-[double], region size to the left and right of the estimated overlap, as derived from the median shift and sequence length, where a k\-mer matches are still considered valid. Second stage filter only.
-.TP
-\fB\-\-min\-store\-length\fR, default = 0
-[int], The minimum length of the read that is stored in the box. Used to filter out short reads from FASTA file.
-.TP
-\fB\-\-nanopore\-fast\fR, default = false
-Set all the parameters for the Nanopore fast settings. This is the current best guidance, and could change at any time without warning.
-.TP
-\fB\-\-no\-self\fR, default = false
-Do not compute the overlaps between sequences inside a box. Should be used when the to and from sequences are coming from different files.
-.TP
-\fB\-\-num\-hashes\fR, default = 512
-[int], number of min\-mers to be used in MinHashing.
-.TP
-\fB\-\-num\-min\-matches\fR, default = 3
-[int], minimum # min\-mer that must be shared before computing second stage filter. Any sequences below that value are considered non\-overlapping.
-.TP
-\fB\-\-num\-threads\fR, default = 12
-[int], number of threads to use for computation. Typically set to 2 x #cores.
-.TP
-\fB\-\-pacbio\-fast\fR, default = false
-Set all the parameters for the PacBio fast setting. This is the current best guidance, and could change at any time without warning.
-.TP
-\fB\-\-pacbio\-sensitive\fR, default = false
-Set all the parameters for the PacBio sensitive settings. This is the current best guidance, and could change at any time without warning.
-.TP
-\fB\-\-store\-full\-id\fR, default = false
-Store full IDs as seen in FASTA file, rather than storing just the sequence position in the file. Some FASTA files have long IDS, slowing output of results. This options is ignored when using compressed file format.
-.TP
-\fB\-\-threshold\fR, default = 0.04
-[double], the threshold similarity score cutoff for the second stage sort\-merge filter. This is based on the average number of k\-mers matching in the overlapping region.
-.TP
-\fB\-\-version\fR, default = false
-Displays the version and build time.
-.TP
-\fB\-\-weighted\fR, default = false
-Perform weighted MinHashing.
-.TP
-\fB\-f\fR, default = ""
-k\-mer filter file used for filtering out highly repetative k\-mers. Must be sorted in descending order of frequency (second column).
-.TP
-\fB\-h\fR, default = false
-Displays the help menu.
-.TP
-\fB\-k\fR, default = 16
-[int], k\-mer size used for MinHashing. The k\-mer size for second stage filter is separate, and cannot be modified.
-.TP
-\fB\-p\fR, default = ""
-Usage 2 only. The directory containing FASTA files that should be converted to binary format for storage.
-.TP
-\fB\-q\fR, default = ""
-Usage 1: The FASTA file of reads, or a directory of files, that will be compared to the set of reads in the box (see \fB\-s\fR). Usage 2: The output directory for the binary formatted dat files.
-.TP
-\fB\-s\fR, default = ""
-Usage 1 only. The FASTA or binary dat file (see Usage 2) of reads that will be stored in a box, and that all subsequent reads will be compared to.
+.B \-\-version
+Displays the version.

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/mhap.git