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<h3>
Shayan Doust pushed to branch master
at <a href="https://salsa.debian.org/med-team/damapper">Debian Med / damapper</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/damapper/-/commit/4a503222f97d6a676ea8f71f33cba4f635398971">4a503222</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2020-08-10T12:34:24+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Write manpages
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<h4>3 changed files:</h4>
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<a href="#68f77f618ec5163f6f652cbc559f17f7c192f557">
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debian/damapper.manpages
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debian/mans/HPC.damapper.1
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debian/mans/damapper.1
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<h4>Changes:</h4>
<li id="68f77f618ec5163f6f652cbc559f17f7c192f557">
<a href="https://salsa.debian.org/med-team/damapper/-/commit/4a503222f97d6a676ea8f71f33cba4f635398971#68f77f618ec5163f6f652cbc559f17f7c192f557"><strong>debian/damapper.manpages</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/mans/*.1</span></pre>
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<a href="https://salsa.debian.org/med-team/damapper/-/commit/4a503222f97d6a676ea8f71f33cba4f635398971#e26881879d4bc5f0323e4efa5f0d1bdefe991163"><strong>debian/mans/HPC.damapper.1</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.TH HPC.DAMAPPER "1" "August 2020" "damapper" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">HPC.damapper: \- long read to reference genome mapping tool</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Recognised as the Damapper Library, this is a long read to reference genome mapping tool.</span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.PP</span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Compared to damapper, this writes a UNIX shell script to the standard output that maps </span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.br</span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">every read in blocks <first> to <last> of database <reads> to a reference sequence <ref>.</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.B HPC.damapper</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">[\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]</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">[\-n<double(1.)] [\-m<track>]+ [\-B<int( 4)>] [\-T<int(4)>] [\-f<name>]</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"><ref:db|dam> <reads:db|dam> [<first:int>[\-<last:int>]]</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Passed through to damapper.</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">\fB\-k\fR: k\-mer size (must be <= 32).</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">\fB\-t\fR: Ignore k\-mers that occur >= \fB\-t\fR times in a block.</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.HP</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">\fB\-M\fR: Use only \fB\-M\fR GB of memory by ignoring most frequent k\-mers.</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">.HP</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">\fB\-e\fR: Look for alignments with \fB\-e\fR percent similarity.</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">.HP</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">\fB\-s\fR: Use \fB\-s\fR as the trace point spacing for encoding alignments.</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">.HP</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">\fB\-n\fR: Output all matches within this % of the best</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">.HP</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">\fB\-T\fR: Use \fB\-T\fR threads.</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">.HP</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">\fB\-P\fR: Do sorts and merges in directory \fB\-P\fR.</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">\fB\-m\fR: Soft mask the blocks with the specified mask.</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">\fB\-b\fR: For AT/GC biased data, compensate k\-mer counts (deprecated).</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">.HP</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">\fB\-z\fR: sort .las by A,B\-read pairs (overlap piles)</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">.IP</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">off => sort .las by A\-read,A\-position pairs (default for mapping)</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">\fB\-p\fR: Output repeat profile track</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">\fB\-C\fR: Output reference vs reads .las.</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">\fB\-N\fR: Do not output reads vs reference .las.</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">Script control.</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">\fB\-v\fR: Verbose mode, output statistics as proceed.</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">\fB\-B\fR: # of block compares per daligner job</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">\fB\-f\fR: Place script bundles in separate files with prefix <name></span></pre>
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<li id="a3c5acb100a60e29fb348d29b2243a6dcf67d75c">
<a href="https://salsa.debian.org/med-team/damapper/-/commit/4a503222f97d6a676ea8f71f33cba4f635398971#a3c5acb100a60e29fb348d29b2243a6dcf67d75c"><strong>debian/mans/damapper.1</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH DAMAPPER "1" "August 2020" "damapper" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">damapper \- long read to reference genome mapping tool</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Recognised as the Damapper Library, this is a long read to reference genome mapping command line tool. </span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.B damapper</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">[\fI\,-vpzCN\/\fR] [\fI\,-k<int(20)>\/\fR] [\fI\,-t<int>\/\fR] [\fI\,-M<int>\/\fR] [\fI\,-T<int(4)>\/\fR] </span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">[\fI\,-P<dir(/tmp)>\/\fR] [\-e<double(.85)] [\-s<int(100)>] [\-n<double(1.00)>] [\-m<track>]+ </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"><reference:dam> <reads:db> ...</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">\fB\-k\fR: k\-mer size (must be <= 32).</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">\fB\-t\fR: Ignore k\-mers that occur >= \fB\-t\fR times in a block.</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">.HP</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">\fB\-M\fR: Use only \fB\-M\fR GB of memory by ignoring most frequent k\-mers.</span>
</pre>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">.HP</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">\fB\-e\fR: Look for alignments with \fB\-e\fR percent similarity.</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">.HP</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">\fB\-s\fR: Use \fB\-s\fR as the trace point spacing for encoding alignments.</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">.HP</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">\fB\-n\fR: Output all matches within this % of the best</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">.HP</span>
</pre>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">\fB\-T\fR: Use \fB\-T\fR threads.</span>
</pre>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">.HP</span>
</pre>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">\fB\-P\fR: Do sorts and merges in directory \fB\-P\fR.</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">.HP</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">\fB\-m\fR: Soft mask the blocks with the specified mask.</span>
</pre>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">.HP</span>
</pre>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">\fB\-v\fR: Verbose mode, output statistics as proceed.</span>
</pre>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">.HP</span>
</pre>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">\fB\-z\fR: sort .las by A,B\-read pairs (overlap piles)</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">.IP</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">off => sort .las by A\-read,A\-position pairs (default for mapping)</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">.HP</span>
</pre>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">\fB\-p\fR: Output repeat profile track</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">.HP</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">\fB\-C\fR: Output reference vs reads .las.</span>
</pre>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">.HP</span>
</pre>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">\fB\-N\fR: Do not output reads vs reference .las.</span></pre>
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