[med-svn] [Git][med-team/damapper][master] Write manpages

[Shayan Doust]

Shayan Doust pushed to branch master at Debian Med / damapper


Commits:
4a503222 by Shayan Doust at 2020-08-10T12:34:24+01:00
Write manpages

- - - - -


3 changed files:

- + debian/damapper.manpages
- + debian/mans/HPC.damapper.1
- + debian/mans/damapper.1


Changes:

=====================================
debian/damapper.manpages
=====================================
@@ -0,0 +1 @@
+debian/mans/*.1


=====================================
debian/mans/HPC.damapper.1
=====================================
@@ -0,0 +1,56 @@
+.TH HPC.DAMAPPER "1" "August 2020" "damapper" "User Commands"
+.SH NAME
+HPC.damapper: \- long read to reference genome mapping tool
+.SH DESCRIPTION
+Recognised as the Damapper Library, this is a long read to reference genome mapping tool.
+.PP
+Compared to damapper, this writes a UNIX shell script to the standard output that maps 
+.br
+every read in blocks <first> to <last> of database <reads> to a reference sequence <ref>.
+.SH SYNOPSIS
+.B HPC.damapper
+[\fI\,-vpzCN\/\fR] [\fI\,-k<int(20)>\/\fR] [\fI\,-t<int>\/\fR] [\fI\,-M<int>\/\fR] [\fI\,-e<double(.85)\/\fR] [\fI\,-s<int(100)\/\fR]
+.SH DESCRIPTION
+.TP
+[\-n<double(1.)] [\-m<track>]+ [\-B<int( 4)>] [\-T<int(4)>] [\-f<name>]
+<ref:db|dam> <reads:db|dam> [<first:int>[\-<last:int>]]
+.IP
+Passed through to damapper.
+.HP
+\fB\-k\fR: k\-mer size (must be <= 32).
+.HP
+\fB\-t\fR: Ignore k\-mers that occur >= \fB\-t\fR times in a block.
+.HP
+\fB\-M\fR: Use only \fB\-M\fR GB of memory by ignoring most frequent k\-mers.
+.HP
+\fB\-e\fR: Look for alignments with \fB\-e\fR percent similarity.
+.HP
+\fB\-s\fR: Use \fB\-s\fR as the trace point spacing for encoding alignments.
+.HP
+\fB\-n\fR: Output all matches within this % of the best
+.HP
+\fB\-T\fR: Use \fB\-T\fR threads.
+.HP
+\fB\-P\fR: Do sorts and merges in directory \fB\-P\fR.
+.HP
+\fB\-m\fR: Soft mask the blocks with the specified mask.
+.HP
+\fB\-b\fR: For AT/GC biased data, compensate k\-mer counts (deprecated).
+.HP
+\fB\-z\fR: sort .las by A,B\-read pairs (overlap piles)
+.IP
+off => sort .las by A\-read,A\-position pairs (default for mapping)
+.HP
+\fB\-p\fR: Output repeat profile track
+.HP
+\fB\-C\fR: Output reference vs reads .las.
+.HP
+\fB\-N\fR: Do not output reads vs reference .las.
+.IP
+Script control.
+.HP
+\fB\-v\fR: Verbose mode, output statistics as proceed.
+.HP
+\fB\-B\fR: # of block compares per daligner job
+.HP
+\fB\-f\fR: Place script bundles in separate files with prefix <name>


=====================================
debian/mans/damapper.1
=====================================
@@ -0,0 +1,41 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
+.TH DAMAPPER "1" "August 2020" "damapper" "User Commands"
+.SH NAME
+damapper \- long read to reference genome mapping tool
+.SH DESCRIPTION
+Recognised as the Damapper Library, this is a long read to reference genome mapping command line tool.	
+.SH SYNOPSIS
+.B damapper
+[\fI\,-vpzCN\/\fR] [\fI\,-k<int(20)>\/\fR] [\fI\,-t<int>\/\fR] [\fI\,-M<int>\/\fR] [\fI\,-T<int(4)>\/\fR] 
+[\fI\,-P<dir(/tmp)>\/\fR] [\-e<double(.85)] [\-s<int(100)>] [\-n<double(1.00)>] [\-m<track>]+  
+<reference:dam> <reads:db> ...
+.HP
+\fB\-k\fR: k\-mer size (must be <= 32).
+.HP
+\fB\-t\fR: Ignore k\-mers that occur >= \fB\-t\fR times in a block.
+.HP
+\fB\-M\fR: Use only \fB\-M\fR GB of memory by ignoring most frequent k\-mers.
+.HP
+\fB\-e\fR: Look for alignments with \fB\-e\fR percent similarity.
+.HP
+\fB\-s\fR: Use \fB\-s\fR as the trace point spacing for encoding alignments.
+.HP
+\fB\-n\fR: Output all matches within this % of the best
+.HP
+\fB\-T\fR: Use \fB\-T\fR threads.
+.HP
+\fB\-P\fR: Do sorts and merges in directory \fB\-P\fR.
+.HP
+\fB\-m\fR: Soft mask the blocks with the specified mask.
+.HP
+\fB\-v\fR: Verbose mode, output statistics as proceed.
+.HP
+\fB\-z\fR: sort .las by A,B\-read pairs (overlap piles)
+.IP
+off => sort .las by A\-read,A\-position pairs (default for mapping)
+.HP
+\fB\-p\fR: Output repeat profile track
+.HP
+\fB\-C\fR: Output reference vs reads .las.
+.HP
+\fB\-N\fR: Do not output reads vs reference .las.



View it on GitLab: https://salsa.debian.org/med-team/damapper/-/commit/4a503222f97d6a676ea8f71f33cba4f635398971

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