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<h3>
Liubov Chuprikova pushed to branch master
at <a href="https://salsa.debian.org/med-team/soapdenovo">Debian Med / soapdenovo</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/soapdenovo/commit/de710ff19760af81a8f03a7f46637a224c4b9d8a">de710ff1</a></strong>
<div>
<span>by Liubov Chuprikova</span>
<i>at 2018-06-09T11:05:55+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix "spelling-error-in-manpage"
</pre>
</li>
</ul>
<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#b580be73eae88696696068fd8821f5b602e3d049">
debian/soapdenovo-127mer.1
</a>
</li>
<li class="file-stats">
<a href="#39f36554100fda8b106ef87be8bc526b39dfeb5c">
debian/soapdenovo-31mer.1
</a>
</li>
<li class="file-stats">
<a href="#7a942462e584f58a6cac0a178c495f469d0d7417">
debian/soapdenovo-63mer.1
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/soapdenovo/commit/de710ff19760af81a8f03a7f46637a224c4b9d8a#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<table class="code white" style="font-family: monospace; font-size: 12px;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">
<tr class="line_holder match" id="" style="line-height: 1.6;">
<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 @@ soapdenovo (1.05-5) UNRELEASED; urgency=medium</td>
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<td class="diff-line-num 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">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * Point Vcs fields to salsa.debian.org</span>
</pre>
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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">
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<td class="diff-line-num new_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">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * Standards-Version: 4.1.4</span>
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<td class="diff-line-num old_line" data-linenumber="12" 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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> * debhelper 11</span>
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<td class="diff-line-num new old_line" data-linenumber="13" 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="13" 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="LC13" class="line" lang="plaintext"> * fix "spelling-error-in-manpage"</span>
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<td class="diff-line-num new_line" data-linenumber="14" 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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="14" 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="diff-line-num new_line" data-linenumber="15" 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="LC15" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> Wed, 06 Sep 2017 23:50:52 +0200</span>
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<td class="diff-line-num old_line" data-linenumber="15" 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="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">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
</pre>
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<br>
</li>
<li id="b580be73eae88696696068fd8821f5b602e3d049">
<a href="https://salsa.debian.org/med-team/soapdenovo/commit/de710ff19760af81a8f03a7f46637a224c4b9d8a#b580be73eae88696696068fd8821f5b602e3d049"><strong>debian/soapdenovo-127mer.1</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="57" 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="57" 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">@@ -57,7 +57,7 @@ pair_num_cutoff</td>
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<td class="diff-line-num old_line" data-linenumber="57" 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="diff-line-num new_line" data-linenumber="57" 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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext">This parameter is the cutoff value of pair number for a reliable connection between two contigs or pre-scaffolds.</span>
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<td class="diff-line-num old_line" data-linenumber="58" 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="diff-line-num new_line" data-linenumber="58" 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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num old_line" data-linenumber="59" 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="diff-line-num new_line" data-linenumber="59" 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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext">map_len</span>
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<td class="diff-line-num old old_line" data-linenumber="60" 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="LC60" class="line" lang="plaintext">This takes effect in the “map” step and is the minimu<span class="idiff left right">n</span> alignment length between a read and a contig required for a reliable read location.</span>
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<td class="diff-line-num new old_line" data-linenumber="61" 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="LC60" class="line" lang="plaintext">This takes effect in the “map” step and is the minimu<span class="idiff left right">m</span> alignment length between a read and a contig required for a reliable read location.</span>
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<td class="diff-line-num old_line" data-linenumber="61" 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="LC61" class="line" lang="plaintext">.P</span>
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<td class="diff-line-num old_line" data-linenumber="62" 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="diff-line-num new_line" data-linenumber="62" 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="LC62" class="line" lang="plaintext">The assembler accepts read file in two formats: FASTA or FASTQ.</span>
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<td class="diff-line-num old_line" data-linenumber="63" 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="LC63" class="line" lang="plaintext">Mate-pair relationship could be indicated in two ways: two sequence files with reads in the same order belonging to a pair, or two adjacent reads in a single file (FASTA only) belonging to a pair. </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="121" 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="121" 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">@@ -121,7 +121,7 @@ strength of merging similar sequences during contiging [default 1, min 0, max 3]</td>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="plaintext">intra-scaffold gap closure [default no]</span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="plaintext">\-u</span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="plaintext">un-mask high coverage contigs before scaffolding [defaut mask]</span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">un-mask high coverage contigs before scaffolding [defau<span class="idiff left right">l</span>t mask]</span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="plaintext">.TP</span>
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126
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="plaintext">\-G</span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="plaintext">INT</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="276" 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">@@ -276,7 +276,7 @@ f=/path/**LIBNAMEB**/fasta_read_single.fa</td>
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="plaintext">.IP "Information for each clone library: insert-size, read index upper bound, rank and pair number cutoff for a reliable link."</span>
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="plaintext">.IP "This file can be revised manually for scaffolding tuning."</span>
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="plaintext">.IP "b. *.readOnContig"</span>
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="plaintext">.IP "Read locations on contigs. Here contigs are referred by their edge index. Howe<span class="idiff left right">r</span>ver about half of them are not listed in the *.contig file for their reverse-complementary counterparts are included already."</span>
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="plaintext">.IP "Read locations on contigs. Here contigs are referred by their edge index. However about half of them are not listed in the *.contig file for their reverse-complementary counterparts are included already."</span>
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="plaintext">.IP "c. *.readInGap"</span>
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="plaintext">.IP "This file includes reads that could be located in gaps between contigs. This information will be used to close gaps in scaffolds."</span>
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/soapdenovo/commit/de710ff19760af81a8f03a7f46637a224c4b9d8a#39f36554100fda8b106ef87be8bc526b39dfeb5c"><strong>debian/soapdenovo-31mer.1</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -57,7 +57,7 @@ pair_num_cutoff</td>
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57
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext">This parameter is the cutoff value of pair number for a reliable connection between two contigs or pre-scaffolds.</span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext">map_len</span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext">This takes effect in the “map” step and is the minimu<span class="idiff left right">n</span> alignment length between a read and a contig required for a reliable read location.</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">This takes effect in the “map” step and is the minimu<span class="idiff left right">m</span> alignment length between a read and a contig required for a reliable read location.</span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext">.P</span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext">The assembler accepts read file in two formats: FASTA or FASTQ.</span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext">Mate-pair relationship could be indicated in two ways: two sequence files with reads in the same order belonging to a pair, or two adjacent reads in a single file (FASTA only) belonging to a pair. </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -121,7 +121,7 @@ strength of merging similar sequences during contiging [default 1, min 0, max 3]</td>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="plaintext">intra-scaffold gap closure [default no]</span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="plaintext">\-u</span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="plaintext">un-mask high coverage contigs before scaffolding [defaut mask]</span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">un-mask high coverage contigs before scaffolding [defau<span class="idiff left right">l</span>t mask]</span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="plaintext">\-G</span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="plaintext">INT</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -276,7 +276,7 @@ f=/path/**LIBNAMEB**/fasta_read_single.fa</td>
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="plaintext">.IP "Information for each clone library: insert-size, read index upper bound, rank and pair number cutoff for a reliable link."</span>
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="plaintext">.IP "This file can be revised manually for scaffolding tuning."</span>
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="plaintext">.IP "b. *.readOnContig"</span>
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="plaintext">.IP "Read locations on contigs. Here contigs are referred by their edge index. Howe<span class="idiff left right">r</span>ver about half of them are not listed in the *.contig file for their reverse-complementary counterparts are included already."</span>
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="plaintext">.IP "Read locations on contigs. Here contigs are referred by their edge index. However about half of them are not listed in the *.contig file for their reverse-complementary counterparts are included already."</span>
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="plaintext">.IP "c. *.readInGap"</span>
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="plaintext">.IP "This file includes reads that could be located in gaps between contigs. This information will be used to close gaps in scaffolds."</span>
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="plaintext"></span>
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<li id="7a942462e584f58a6cac0a178c495f469d0d7417">
<a href="https://salsa.debian.org/med-team/soapdenovo/commit/de710ff19760af81a8f03a7f46637a224c4b9d8a#7a942462e584f58a6cac0a178c495f469d0d7417"><strong>debian/soapdenovo-63mer.1</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -57,7 +57,7 @@ pair_num_cutoff</td>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext">This parameter is the cutoff value of pair number for a reliable connection between two contigs or pre-scaffolds.</span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext">map_len</span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext">This takes effect in the “map” step and is the minimu<span class="idiff left right">n</span> alignment length between a read and a contig required for a reliable read location.</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">This takes effect in the “map” step and is the minimu<span class="idiff left right">m</span> alignment length between a read and a contig required for a reliable read location.</span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext">.P</span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext">The assembler accepts read file in two formats: FASTA or FASTQ.</span>
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63
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext">Mate-pair relationship could be indicated in two ways: two sequence files with reads in the same order belonging to a pair, or two adjacent reads in a single file (FASTA only) belonging to a pair. </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -121,7 +121,7 @@ strength of merging similar sequences during contiging [default 1, min 0, max 3]</td>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="plaintext">intra-scaffold gap closure [default no]</span>
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122
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122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num old_line" data-linenumber="123" 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">
123
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="plaintext">\-u</span>
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124
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="plaintext">un-mask high coverage contigs before scaffolding [defaut mask]</span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">un-mask high coverage contigs before scaffolding [defau<span class="idiff left right">l</span>t mask]</span>
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125
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num old_line" data-linenumber="126" 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">
126
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="plaintext">\-G</span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="plaintext">INT</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="276" 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="276" 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">@@ -276,7 +276,7 @@ f=/path/**LIBNAMEB**/fasta_read_single.fa</td>
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<td class="diff-line-num old_line" data-linenumber="276" 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="LC276" class="line" lang="plaintext">.IP "Information for each clone library: insert-size, read index upper bound, rank and pair number cutoff for a reliable link."</span>
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<td class="diff-line-num old_line" data-linenumber="277" 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="LC277" class="line" lang="plaintext">.IP "This file can be revised manually for scaffolding tuning."</span>
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<td class="diff-line-num old_line" data-linenumber="278" 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="LC278" class="line" lang="plaintext">.IP "b. *.readOnContig"</span>
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<td class="diff-line-num old old_line" data-linenumber="279" 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="LC279" class="line" lang="plaintext">.IP "Read locations on contigs. Here contigs are referred by their edge index. Howe<span class="idiff left right">r</span>ver about half of them are not listed in the *.contig file for their reverse-complementary counterparts are included already."</span>
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<td class="diff-line-num new old_line" data-linenumber="280" 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="LC279" class="line" lang="plaintext">.IP "Read locations on contigs. Here contigs are referred by their edge index. However about half of them are not listed in the *.contig file for their reverse-complementary counterparts are included already."</span>
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<td class="diff-line-num old_line" data-linenumber="280" 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="LC280" class="line" lang="plaintext">.IP "c. *.readInGap"</span>
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<td class="diff-line-num old_line" data-linenumber="281" 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="LC281" class="line" lang="plaintext">.IP "This file includes reads that could be located in gaps between contigs. This information will be used to close gaps in scaffolds."</span>
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<td class="diff-line-num old_line" data-linenumber="282" 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="LC282" class="line" lang="plaintext"></span>
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