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 -- View it on GitLab: https://salsa.debian.org/med-team/damapper/-/commit/4a503222f97d6a676ea8f71f33cba4f635398971 You're receiving this email because of your account on salsa.debian.org.
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