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<h3>
Sascha Steinbiss pushed to branch master
at <a href="https://salsa.debian.org/med-team/genomethreader">Debian Med / genomethreader</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/genomethreader/commit/1b0b8408826c7c509cead9a8621d9fd68c57d8a7">1b0b8408</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2020-01-09T22:10:38+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add man page building
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/genomethreader/commit/f30ceda835d1092e825b2091846aa8d7216c354f">f30ceda8</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2020-01-09T22:16:20+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">install manpages
</pre>
</li>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
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<li class="file-stats">
<a href="#7f0bd295ad7a659111b14e983d999cdaed9b6986">
<span class="new-file">
+
debian/genomethreader.manpages
</span>
</a>
</li>
<li class="file-stats">
<a href="#66c09cd9f59ee022bf29300bdf6a29ca59d35df2">
<span class="new-file">
+
debian/man_src/gth.1.adoc
</span>
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</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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</li>
</ul>
<h4>Changes:</h4>
<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/genomethreader/compare/205e56590886042ee3bc74df524597cbbc284a12...f30ceda835d1092e825b2091846aa8d7216c354f#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -39,7 +39,7 @@ Copyright: (c) 2003-2009 Gordon Gremme <gordon@gremme.org></td>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"> (c) 2003-2008 Center for Bioinformatics, University of Hamburg</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">License: ISC</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"></span>
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<td class="diff-line-num old old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext">File: src/gth/editoperation.h</span>
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<td class="diff-line-num new old_line" data-linenumber="43" 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="LC42" class="line" lang="plaintext">File<span class="idiff left right">s</span>: src/gth/editoperation.h</span>
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<td class="diff-line-num old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext">Copyright: (c) 2003-2009 Gordon Gremme <gordon@gremme.org></span>
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<td class="diff-line-num old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"> (c) 2003 Stefan Kurtz <kurtz@zbh.uni-hamburg.de></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"> (c) 2003-2007 Center for Bioinformatics, University of Hamburg</span>
</pre>
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</li>
<li id="7f0bd295ad7a659111b14e983d999cdaed9b6986">
<a href="https://salsa.debian.org/med-team/genomethreader/compare/205e56590886042ee3bc74df524597cbbc284a12...f30ceda835d1092e825b2091846aa8d7216c354f#7f0bd295ad7a659111b14e983d999cdaed9b6986"><strong>debian/genomethreader.manpages</strong></a>
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<td class="diff-line-num new new_line" data-linenumber="1" 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="LC1" class="line" lang="plaintext">debian/man/*.1</span></pre>
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<li id="66c09cd9f59ee022bf29300bdf6a29ca59d35df2">
<a href="https://salsa.debian.org/med-team/genomethreader/compare/205e56590886042ee3bc74df524597cbbc284a12...f30ceda835d1092e825b2091846aa8d7216c354f#66c09cd9f59ee022bf29300bdf6a29ca59d35df2"><strong>debian/man_src/gth.1.adoc</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># gth(1)</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">## NAME</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">gth - calculate genome structures</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">## SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">*gth* [option ...] -genomic file [...] -cdna file [...] -protein file [...]</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">## DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Computes similarity-based gene structure predictions (spliced alignments)</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">using cDNA/EST and/or protein sequences and assemble the resulting spliced</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">alignments to consensus spliced alignments.</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">## OPTIONS</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">-genomic specify input files containing genomic sequences</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> mandatory option</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">-cdna specify input files containing cDNA/EST sequences</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">-protein specify input files containing protein sequences</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">-species specify species to select splice site model which is most</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> appropriate; possible species:</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> "human"</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> "mouse"</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> "rat"</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> "chicken"</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> "drosophila"</span>
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30
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> "nematode"</span>
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<td class="diff-line-num new new_line" data-linenumber="31" 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">
31
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> "fission_yeast"</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> "aspergillus"</span>
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33
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> "arabidopsis"</span>
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34
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> "maize"</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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35
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> "rice"</span>
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<td class="diff-line-num new new_line" data-linenumber="36" 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">
36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> "medicago"</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> default: undefined</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">-bssm read bssm parameter from file in the path given by the</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> environment variable BSSMDIR</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> default: undefined</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">-scorematrix read amino acid substitution scoring matrix from file in the</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> path given by the environment variable GTHDATADIR</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> default: BLOSUM62</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">-translationtable set the codon translation table used for codon translation in</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> matching, DP, and output</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> default: 1</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">-f analyze only forward strand of genomic sequences</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> default: no</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">-r analyze only reverse strand of genomic sequences</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> default: no</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">-cdnaforward align only forward strand of cDNAs</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> default: no</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">-frompos analyze genomic sequence from this position</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> requires -topos or -width; counting from 1 on</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> default: 0</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">-topos analyze genomic sequence to this position</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> requires -frompos; counting from 1 on</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> default: 0</span>
</pre>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">-width analyze only this width of genomic sequence</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> requires -frompos</span>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> default: 0</span>
</pre>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">-v be verbose</span>
</pre>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> default: no</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">-xmlout show output in XML format</span>
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<td class="diff-line-num new new_line" data-linenumber="65" 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">
65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"> default: no</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="66" 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">
66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">-gff3out show output in GFF3 format</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="67" 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">
67
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"> default: no</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="68" 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">
68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">-md5ids show MD5 fingerprints as sequence IDs</span>
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<td class="diff-line-num new new_line" data-linenumber="69" 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">
69
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"> default: no</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="70" 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">
70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">-o redirect output to specified file</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="71" 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">
71
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> default: undefined</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="72" 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">
72
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">-gzip write gzip compressed output file</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="73" 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">
73
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"> default: no</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="74" 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">
74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">-bzip2 write bzip2 compressed output file</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="75" 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">
75
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"> default: no</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="76" 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">
76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">-force force writing to output file</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="77" 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">
77
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"> default: no</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="78" 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">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">-gs2out output in old GeneSeqer2 format</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="79" 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">
79
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"> default: no</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="80" 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">
80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">-minmatchlen specify minimum match length (cDNA matching)</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="81" 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">
81
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"> default: 20</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="82" 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">
82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">-seedlength specify the seed length (cDNA matching)</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="83" 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">
83
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext"> default: 18</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="84" 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">
84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">-exdrop specify the Xdrop value for edit distance extension (cDNA</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="85" 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">
85
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext"> matching)</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="86" 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">
86
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext"> default: 2</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="87" 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">
87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">-prminmatchlen specify minimum match length (protein matches)</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="88" 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">
88
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext"> default: 24</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="89" 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">
89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">-prseedlength specify seed length (protein matching)</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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<td class="diff-line-num new new_line" data-linenumber="90" 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">
90
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext"> default: 10</span>
</pre>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">-prhdist specify Hamming distance (protein matching)</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext"> default: 4</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">-gcmaxgapwidth set the maximum gap width for global chains</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext"> defines approximately the maximum intron length</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext"> set to 0 to allow for unlimited length</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"> in order to avoid false-positive exons (lonely exons) at the</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext"> sequence ends, it is very important to set this parameter</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext"> appropriately!</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext"> default: 1000000</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">-gcmincoverage set the minimum coverage of global chains regarding to the</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext"> reference sequence</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext"> default: 50</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">-paralogs compute paralogous genes (different chaining procedure)</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext"> default: no</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext">-introncutout enable the intron cutout technique</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext"> default: no</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">-fastdp use jump table to increase speed of DP calculation</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext"> default: no</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext">-autointroncutout set the automatic intron cutout matrix size in megabytes and</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext"> enable the automatic intron cutout technique</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext"> default: 0</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext">-intermediate stop after calculation of spliced alignments and output</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext"> results in reusable XML format. Do not process this output</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext"> yourself, use the ``normal'' XML output instead!</span>
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<td class="diff-line-num new new_line" data-linenumber="115" 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">
115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext"> default: no</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext">-first set the maximum number of spliced alignments per genomic DNA</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext"> input. Set to 0 for unlimited number.</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext"> default: 0</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext">-help display help for basic options and exit</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext">-help+ display help for all options and exit</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext">-version display version information and exit</span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/genomethreader/compare/205e56590886042ee3bc74df524597cbbc284a12...f30ceda835d1092e825b2091846aa8d7216c354f#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,6 +10,7 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all</td>
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10
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">override_dh_clean:</span>
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<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> dh_clean</span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> rm -rf bin/bssm debian/bssm bin/gthdata debian/gthdata</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> rm -rf $(CURDIR)/debian/man</span>
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13
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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14
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">override_dh_auto_build:</span>
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15
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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> make licensemanager=no opt=yes 64bit=yes</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -26,7 +27,7 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</td>
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26
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">endif</span>
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27
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">override_dh_installman:</span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"> <span class="idiff left right">#</span>mkdir -p $(CURDIR)/debian/man</span>
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30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"> <span class="idiff left right">#</span>asciidoctor -a docdate='' -b manpage $(CURDIR)/debian/man_src/*.adoc</span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"> <span class="idiff left right">#</span>cp $(CURDIR)/debian/man_src/*.? $(CURDIR)/debian/man</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> mkdir -p $(CURDIR)/debian/man</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> asciidoctor -a docdate='' -b manpage $(CURDIR)/debian/man_src/*.adoc</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> cp $(CURDIR)/debian/man_src/*.? $(CURDIR)/debian/man</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> dh_installman --</span></pre>
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