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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/dwgsim">Debian Med / dwgsim</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/dwgsim/-/commit/04b98d101bf82362b705e761c6e2a763db32d94a">04b98d10</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-01-16T17:01:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/dwgsim/-/commit/386d48d63429e49e80d06b119dfa4689747ea353">386d48d6</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-01-16T17:01:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.1.13</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/dwgsim/-/commit/44333b85b8b94e928c5ef37f8643e7f53465b80b">44333b85</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-01-16T17:01:27+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/0.1.13'
Update to upstream version '0.1.13'
with Debian dir 9f02bf31b8aa5c62bf604c292a3b00213d080a8c</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/dwgsim/-/commit/07297ec17ed31fc7c5f86664bebf58b4e7d97f41">07297ec1</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-01-16T17:01:34+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add missing build dependency on dh addon.
Changes-By: lintian-brush
Fixes: lintian: missing-build-dependency-for-dh_-command
See-also: https://lintian.debian.org/tags/missing-build-dependency-for-dh_-command.html
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/dwgsim/-/commit/7534a223e8bb361975a11eed3e82273b9853f5ff">7534a223</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-01-16T17:11:53+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update patch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/dwgsim/-/commit/cc1268699bc3c40e6be51d57622451add0c4856e">cc126869</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-01-16T17:15:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">TODO: Autopkgtest failure
</pre>
</li>
</ul>
<h4>12 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
Makefile
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
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<li class="file-stats">
<a href="#28dca8d5f5dfe1a58b3f2e3f71c103fe9de27e50">
debian/patches/0001-Debian-ise-makefile.patch
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<li class="file-stats">
<a href="#845bb8884d201d561aac46a5d3bc664c47cad3ec">
src/dwgsim.c
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<li class="file-stats">
<a href="#8b1a544f9bdc749248298113fcdb4d61b8852b21">
src/dwgsim_opt.c
</a>
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<li class="file-stats">
<a href="#39520621c459de4e7f9bbce08e8cb714f082ccb8">
src/dwgsim_opt.h
</a>
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<li class="file-stats">
<a href="#018f262518f189e45af7e9d496e0bc11d93d630d">
src/mut_txt.c
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<li class="file-stats">
<a href="#db76ac610a956949061eae8c4e730e9501549237">
testdata/ex1.test.bfast.fastq.gz
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<li class="file-stats">
<a href="#c7f2e76f5da5a77a0dddbdad52567902afe25ac7">
testdata/ex1.test.bwa.read1.fastq.gz
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<li class="file-stats">
<a href="#93ae750d120630d2cd0ca837997f528701dc0465">
testdata/ex1.test.bwa.read2.fastq.gz
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<li class="file-stats">
<a href="#98f89ee23327a234265305cd43afeeef63f0025b">
testdata/test.sh
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</ul>
<h4>Changes:</h4>
<li id="836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
<a href="https://salsa.debian.org/med-team/dwgsim/-/compare/7dd19c7c56b00cbd3ecf5c57cd1fa13bd5ee8658...cc1268699bc3c40e6be51d57622451add0c4856e#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c"><strong>Makefile</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="make"><span class="nv" style="color: #008080;">PACKAGE_VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"0.1.1<span class="idiff left right">1</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="make"><span class="nv" style="color: #008080;">PACKAGE_VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"0.1.1<span class="idiff left right">3</span>"</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="make"><span class="nv" style="color: #008080;">CC</span><span class="o" style="font-weight: 600;">=</span> gcc</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="3" 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="LC3" class="line" lang="make"><span class="nv" style="color: #008080;">CFLAGS</span><span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-g</span> <span class="nt" style="color: #000080;">-Wall</span> <span class="nt" style="color: #000080;">-O3</span> <span class="c" style="color: #998; font-style: italic;">#-m64 #-arch ppc</span></span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="make"><span class="nv" style="color: #008080;">DFLAGS</span><span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-D_FILE_OFFSET_BITS</span><span class="o" style="font-weight: 600;">=</span>64 <span class="nt" style="color: #000080;">-D_LARGEFILE64_SOURCE</span> <span class="nt" style="color: #000080;">-D_USE_KNETFILE</span> <span class="nt" style="color: #000080;">-DPACKAGE_VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="se" style="color: #d14;">\\\"</span><span class="nv" style="color: #008080;">${PACKAGE_VERSION}</span><span class="se" style="color: #d14;">\\\"</span></span>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/dwgsim/-/compare/7dd19c7c56b00cbd3ecf5c57cd1fa13bd5ee8658...cc1268699bc3c40e6be51d57622451add0c4856e#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">dwgsim (0.1.13-1) UNRELEASED; urgency=medium</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"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Add missing build dependency on dh addon.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> TODO: Autopkgtest fails with</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> [dwgsim_core] Complete!</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> TAKE DIFF FOR CORRECT OUTPUT</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> diff: tmp/ex1.test.bfast.fastq: No such file or directory</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"> -- Andreas Tille <tille@debian.org> Sun, 16 Jan 2022 17:01:24 +0100</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">dwgsim (0.1.12-5) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> * Team upload.</span>
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<a href="https://salsa.debian.org/med-team/dwgsim/-/compare/7dd19c7c56b00cbd3ecf5c57cd1fa13bd5ee8658...cc1268699bc3c40e6be51d57622451add0c4856e#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -6,7 +6,8 @@ Priority: optional</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> samtools,</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> markdown,</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> zlib1g-dev</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> zlib1g-dev,</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> debhelper</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Standards-Version: 4.6.0</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/dwgsim</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/dwgsim.git</span>
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<a href="https://salsa.debian.org/med-team/dwgsim/-/compare/7dd19c7c56b00cbd3ecf5c57cd1fa13bd5ee8658...cc1268699bc3c40e6be51d57622451add0c4856e#28dca8d5f5dfe1a58b3f2e3f71c103fe9de27e50"><strong>debian/patches/0001-Debian-ise-makefile.patch</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">@@ -8,12 +8,10 @@ Fix parts of the makefile patching</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> Makefile | 84 ++++++++++++++++------------------------------------------------</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> 1 file changed, 21 insertions(+), 63 deletions(-)</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff">diff --git a/Makefile b/Makefile</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gh" style="color: #800080; font-weight: 600;">index 0d5b9ec..e4f7134 100644</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff">--- a/Makefile</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="p">@@ -1,7<span class="idiff left right">3</span> +1,31 @@</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-PACKAGE_VERSION="0.1.1<span class="idiff left right">1</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="p">@@ -1,7<span class="idiff left right">6</span> +1,31 @@</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-PACKAGE_VERSION="0.1.1<span class="idiff left right">3</span>"</span></span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CC= gcc</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CFLAGS= -g -Wall -O3 #-m64 #-arch ppc</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -DPACKAGE_VERSION=\\\"${PACKAGE_VERSION}\\\"</span></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">@@ -31,23 +29,22 @@ index 0d5b9ec..e4f7134 100644</td>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CLEAN_SUBDIRS= samtools src</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-LIBPATH=</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+PACKAGE_VERSION=$(shell dpkg-parsechangelog | egrep '^Version:' | cut -f 2 -d ' ')</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CC ?=<span class="idiff left right"> </span>gcc</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CFLAGS +=<span class="idiff left right"> </span>-Wall -O3 -I.</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CPPFLAGS +=<span class="idiff left right"> </span>-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -DPACKAGE_VERSION=\"${PACKAGE_VERSION}\"</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+PROG<span class="idiff left right"> </span>= dwgsim</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CC ?=<span class="idiff left right"> </span>gcc</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CFLAGS +=<span class="idiff left right"> </span>-Wall -O3 -I.</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CPPFLAGS +=<span class="idiff left right"> </span>-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -DPACKAGE_VERSION=\"${PACKAGE_VERSION}\"</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+PROG=<span class="idiff left right"> </span> dwgsim</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+DWGSIM_AOBJS =<span class="idiff left right"> </span>src/dwgsim_opt.o \</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+<span class="idiff left right"> </span>src/mut.o \</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+<span class="idiff left right"> </span>src/contigs.o \</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+<span class="idiff left right"> </span>src/regions_bed.o \</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+<span class="idiff left right"> </span>src/mut_txt.o \</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+<span class="idiff left right"> </span>src/mut_bed.o \</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+<span class="idiff left right"> </span>src/mut_vcf.o \</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+<span class="idiff left right"> </span>src/mut_input.o \</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+<span class="idiff left right"> </span>src/dwgsim.o</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+DWGSIM_AOBJS =<span class="idiff left right"> </span>src/dwgsim_opt.o \</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+<span class="idiff left right"> </span>src/mut.o \</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+<span class="idiff left right"> </span>src/contigs.o \</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+<span class="idiff left right"> </span>src/regions_bed.o \</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+<span class="idiff left right"> </span>src/mut_txt.o \</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+<span class="idiff left right"> </span>src/mut_bed.o \</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+<span class="idiff left right"> </span>src/mut_vcf.o \</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+<span class="idiff left right"> </span>src/mut_input.o \</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+<span class="idiff left right"> </span>src/dwgsim.o</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="diff"> .SUFFIXES:.c .o</span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.PHONY:all clean cleanlocal</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="diff"> .c.o:</span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -61,7 +58,7 @@ index 0d5b9ec..e4f7134 100644</td>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cd $$wdir; \</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- done;</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CC) -c $(CFLAGS) $(CPPFLAGS) $< -o $@</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <span class="idiff left right"> </span>$(CC) -c $(CFLAGS) $(CPPFLAGS) $< -o $@</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="diff"> all:$(PROG)</span>
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="73" 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">@@ -76,7 +73,7 @@ index 0d5b9ec..e4f7134 100644</td>
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76
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+dwgsim: $(DWGSIM_AOBJS)</span></span>
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77
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(DWGSIM_AOBJS) -lm -lz -lpthread</span></span>
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78
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="diff"> </span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="diff"><span class="idiff left right"> </span>cleanlocal:</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;"><span class="idiff left right">-</span>cleanlocal:</span></span>
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80
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- rm -vfr gmon.out *.o a.out *.exe *.dSYM razip bgzip $(PROG) *~ *.a *.so.* *.so *.dylib; \</span></span>
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81
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- wdir=`pwd`; \</span></span>
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82
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- list='$(CLEAN_SUBDIRS)'; for subdir in $$list; do \</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="89" 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="86" 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">@@ -89,8 +86,7 @@ index 0d5b9ec..e4f7134 100644</td>
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89
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- done;</span></span>
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90
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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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91
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88
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-clean:cleanlocal-recur</span></span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ rm -vfr gmon.out *.o a.out *.exe *.dSYM razip bgzip $(PROG) *~ *.a *.so.* *.so *.dylib;</span></span>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="diff"> </span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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94
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-dist:clean</span></span>
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95
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if [ -f dwgsim-${PACKAGE_VERSION}.tar.gz ]; then \</span></span>
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<td class="old_line diff-line-num" data-linenumber="96" 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">
96
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92
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- rm -rv dwgsim-${PACKAGE_VERSION}.tar.gz; \</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -106,4 +102,8 @@ index 0d5b9ec..e4f7134 100644</td>
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<td class="old_line diff-line-num" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
106
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- tar -vcf dwgsim-${PACKAGE_VERSION}.tar dwgsim-${PACKAGE_VERSION}; \</span></span>
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<td class="old_line diff-line-num" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
107
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- gzip -9 dwgsim-${PACKAGE_VERSION}.tar; \</span></span>
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<td class="old_line diff-line-num" data-linenumber="108" 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">
108
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- rm -rv dwgsim-${PACKAGE_VERSION};</span></span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+clean:cleanlocal</span></span></pre>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+clean:</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ rm -vfr gmon.out *.o a.out *.exe *.dSYM razip bgzip $(PROG) *~ *.a *.so.* *.so *.dylib;</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> </span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"> test:</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> if [ -d tmp ]; then rm -r tmp; fi</span></pre>
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<a href="https://salsa.debian.org/med-team/dwgsim/-/compare/7dd19c7c56b00cbd3ecf5c57cd1fa13bd5ee8658...cc1268699bc3c40e6be51d57622451add0c4856e#845bb8884d201d561aac46a5d3bc664c47cad3ec"><strong>src/dwgsim.c</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">@@ -41,6 +41,7 @@</td>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stdint.h></span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <ctype.h></span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <string.h></span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <zlib.h></span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "contigs.h"</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "mut.h"</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "mut_txt.h"</span></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">@@ -71,33 +72,33 @@ uint8_t nst_nt4_table[256] = {</td>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="c"> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="c"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define __gen_read(x, start, iter) do {<span class="idiff left right"> </span>\</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> for (i = (start), k = 0, ext_coor[x] = -10; i >= 0 && i < seq.l && k < s[x]; iter) {<span class="idiff left right"> </span>\</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> mut_t c = currseq->s[i], mut_type = c & mutmsk;<span class="idiff left right"> </span>\</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if (ext_coor[x] < 0) {<span class="idiff left right"> </span>\</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define __gen_read(x, start, iter) do {<span class="idiff left right"> </span>\</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> for (i = (start), k = 0, ext_coor[x] = -10; i >= 0 && i < seq.l && k < s[x]; iter) {<span class="idiff left right"> </span>\</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> mut_t c = currseq->s[i], mut_type = c & mutmsk;<span class="idiff left right"> </span>\</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if (ext_coor[x] < 0) {<span class="idiff left right"> </span>\</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if (mut_type != NOCHANGE && mut_type != SUBSTITUTE) continue; \</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> ext_coor[x] = i;<span class="idiff left right"> </span>\</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> ext_coor[x] = i;<span class="idiff left right"> </span>\</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if(1 == strand[x]) ext_coor[x] -= s[x]-1; \</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> }<span class="idiff left right"> </span>\</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> }<span class="idiff left right"> </span>\</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if (mut_type == DELETE) { \</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> ++n_indel[x];<span class="idiff left right"> </span>\</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> ++n_indel[x];<span class="idiff left right"> </span>\</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if(1 == strand[x]) ext_coor[x]--; \</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if(0 == k) n_indel_first[x]++; \</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> } \</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> else if (mut_type == NOCHANGE || mut_type == SUBSTITUTE) { \</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> tmp_seq[x][k++] = c & 0xf;<span class="idiff left right"> </span>\</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> tmp_seq[x][k++] = c & 0xf;<span class="idiff left right"> </span>\</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if (mut_type == SUBSTITUTE) { \</span></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> ++n_sub[x];<span class="idiff left right"> </span>\</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> ++n_sub[x];<span class="idiff left right"> </span>\</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if(0 == k) n_sub_first[x]++; \</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> } <span class="idiff left right"> </span>\</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> } else {<span class="idiff left right"> </span>\</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> mut_t n, ins;<span class="idiff left right"> </span>\</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> } <span class="idiff left right"> </span>\</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> } else {<span class="idiff left right"> </span>\</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> mut_t n, ins;<span class="idiff left right"> </span>\</span></span>
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96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> assert(mut_type == INSERT); \</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> ++n_indel[x];<span class="idiff left right"> </span>\</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> n_indel_first[x]++;<span class="idiff left right"> </span>\</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> ++n_indel[x];<span class="idiff left right"> </span>\</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> n_indel_first[x]++;<span class="idiff left right"> </span>\</span></span>
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if(1 == mut_get_ins(currseq, i, &n, &ins)) { \</span></span>
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99
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if(0 == strand[x]) { \</span></span>
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100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if(k < s[x]) tmp_seq[x][k++] = c & 0xf;<span class="idiff left right"> </span>\</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if(k < s[x]) tmp_seq[x][k++] = c & 0xf;<span class="idiff left right"> </span>\</span></span>
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101
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> while(n > 0 && k < s[x]) { \</span></span>
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> tmp_seq[x][k++] = ins & 0x3; \</span></span>
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103
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> --n, ins >>= 2; \</span></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">@@ -108,7 +109,7 @@ uint8_t nst_nt4_table[256] = {</td>
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108
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> tmp_seq[x][k++] = (ins >> ((n-1) << 1) & 0x3); \</span></span>
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109
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> --n; \</span></span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> } \</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if (k < s[x]) tmp_seq[x][k++] = c & 0xf;<span class="idiff left right"> </span>\</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if (k < s[x]) tmp_seq[x][k++] = c & 0xf;<span class="idiff left right"> </span>\</span></span>
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112
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> } \</span></span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> } else { \</span></span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> int32_t byte_index, bit_index; \</span></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">@@ -117,7 +118,7 @@ uint8_t nst_nt4_table[256] = {</td>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> insertion = mut_get_ins_long_n(currseq->ins[ins], &num_ins); \</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if(0 == strand[x]) { \</span></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> byte_index = mut_packed_len(num_ins) - 1; bit_index = (num_ins-1) & 0x3 ; \</span></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if(k < s[x]) tmp_seq[x][k++] = c & 0xf;<span class="idiff left right"> </span>\</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if(k < s[x]) tmp_seq[x][k++] = c & 0xf;<span class="idiff left right"> </span>\</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> while(num_ins > 0 && k < s[x]) { \</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> assert(0 <= byte_index); \</span></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> tmp_seq[x][k++] = (insertion[byte_index] >> (bit_index << 1)) & 0x3; \</span></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">@@ -140,19 +141,18 @@ uint8_t nst_nt4_table[256] = {</td>
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> byte_index++; \</span></span>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> } \</span></span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> } \</span></span>
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if (k < s[x]) tmp_seq[x][k++] = c & 0xf;<span class="idiff left right"> </span>\</span></span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if (k < s[x]) tmp_seq[x][k++] = c & 0xf;<span class="idiff left right"> </span>\</span></span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> } \</span></span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> }<span class="idiff left right"> </span>\</span></span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> }<span class="idiff left right"> </span>\</span></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> } \</span></span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> }<span class="idiff left right"> </span>\</span></span>
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if (k != s[x]) ext_coor[x] = -10;<span class="idiff left right"> </span>\</span></span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> }<span class="idiff left right"> </span>\</span></span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if (k != s[x]) ext_coor[x] = -10;<span class="idiff left right"> </span>\</span></span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if (1 == strand[x]) { \</span></span>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> for (k = 0; k < s[x]; ++k) tmp_seq[x][k] = tmp_seq[x][k] < 4? 3 - tmp_seq[x][k] : 4; \</span></span>
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> } <span class="idiff left right"> </span>\</span></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> } <span class="idiff left right"> </span>\</span></span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">} while (0)</span></span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* Simple normal random number generator, copied from genran.c */</span></span>
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">ran_normal</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="c"><span class="p">{</span> </span>
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">iset</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> </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">@@ -174,6 +174,11 @@ double ran_normal()</td>
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">unreachable</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">message</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">[dwgsim_core] Error: %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">message</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="nf" style="color: #900; font-weight: 600;">ran_num</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">prob</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">n</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">;</span></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">@@ -532,8 +537,7 @@ void dwgsim_core(dwgsim_opt_t * opt)</td>
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<pre style="margin: 0;"> <span id="LC537" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC538" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC539" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC535" class="line" lang="c"></span>
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536
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<pre style="margin: 0;">-<span id="LC536" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">muts_only</span><span class="p">)</span> <span class="p">{</span></span>
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540
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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537
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541
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<pre style="margin: 0;"> <span id="LC541" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">n_ref</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">C</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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538
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542
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<pre style="margin: 0;"> <span id="LC542" class="line" lang="c"> <span class="n" style="color: #333;">n_pairs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">N</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">n_sim</span><span class="p">;</span></span>
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543
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<pre style="margin: 0;"> <span id="LC543" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="605" 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="609" 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">@@ -605,6 +609,7 @@ void dwgsim_core(dwgsim_opt_t * opt)</td>
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605
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609
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<pre style="margin: 0;"> <span id="LC609" class="line" lang="c"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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606
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610
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<pre style="margin: 0;"> <span id="LC610" class="line" lang="c"> <span class="p">}</span></span>
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607
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611
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<pre style="margin: 0;"> <span id="LC611" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">n_pairs</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// NB: this should not happen</span></span>
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612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"[dwgsim_core] #4 skip sequence '%s' as not enough pairs found</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">);</span></span>
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608
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613
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<pre style="margin: 0;"> <span id="LC613" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// not enough pairs</span></span>
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614
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<pre style="margin: 0;"> <span id="LC614" class="line" lang="c"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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610
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615
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<pre style="margin: 0;"> <span id="LC615" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="617" 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="622" 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">@@ -617,6 +622,7 @@ void dwgsim_core(dwgsim_opt_t * opt)</td>
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617
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622
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<pre style="margin: 0;"> <span id="LC622" class="line" lang="c"> <span class="n" style="color: #333;">mut_print</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">mutseq</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">mutseq</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_mut</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_vcf</span><span class="p">);</span></span>
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618
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623
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<pre style="margin: 0;"> <span id="LC623" class="line" lang="c"></span>
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619
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624
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<pre style="margin: 0;"> <span id="LC624" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">muts_only</span><span class="p">)</span> <span class="p">{</span></span>
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625
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">num_failed</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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620
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626
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<pre style="margin: 0;"> <span id="LC626" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">ii</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">ii</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">n_pairs</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">ii</span><span class="p">,</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">ctr</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// the core loop</span></span>
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<pre style="margin: 0;"> <span id="LC627" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="n" style="color: #333;">ctr</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">10000</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC628" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\r</span><span class="s" style="color: #d14;">[dwgsim_core] %llu"</span><span class="p">,</span></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">@@ -685,23 +691,27 @@ void dwgsim_core(dwgsim_opt_t * opt)</td>
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<pre style="margin: 0;"> <span id="LC691" class="line" lang="c"> <span class="n" style="color: #333;">n_sub_first</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n_sub_first</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n_indel_first</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n_indel_first</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n_err_first</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n_err_first</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC692" class="line" lang="c"> <span class="n" style="color: #333;">num_n</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">num_n</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC693" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC688" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// strand</span></span>
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<pre style="margin: 0;">-<span id="LC689" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">strandedness</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">strandedness</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">ILLUMINA</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data_type</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC690" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// opposite strand by default for Illumina</span></span>
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<pre style="margin: 0;">-<span id="LC691" class="line" lang="c"> <span class="n" style="color: #333;">strand</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">strand</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> </span>
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<pre style="margin: 0;">-<span id="LC692" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC693" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">strandedness</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">strandedness</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">SOLID</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data_type</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">IONTORRENT</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data_type</span><span class="p">)))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC694" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// same strands by default for SOLiD</span></span>
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<pre style="margin: 0;">-<span id="LC695" class="line" lang="c"> <span class="n" style="color: #333;">strand</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">strand</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> </span>
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<pre style="margin: 0;">-<span id="LC696" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC697" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC698" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// should not reach here</span></span>
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<pre style="margin: 0;">-<span id="LC699" class="line" lang="c"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// set read one's strand</span></span>
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695
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="c"> <span class="k" style="font-weight: 600;">switch</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_one_strand</span><span class="p">)</span> <span class="p">{</span></span>
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696
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<pre style="margin: 0;">+<span id="LC696" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span> <span class="n" style="color: #333;">strand</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">drand48</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">5</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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697
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span> <span class="n" style="color: #333;">strand</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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698
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">2</span><span class="p">:</span> <span class="n" style="color: #333;">strand</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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699
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="c"> <span class="nl">default:</span> <span class="n" style="color: #333;">unreachable</span><span class="p">(</span><span class="s" style="color: #d14;">"read strand was not between 0-2"</span><span class="p">);</span></span>
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700
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<pre style="margin: 0;"> <span id="LC700" class="line" lang="c"> <span class="p">}</span></span>
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701
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<pre style="margin: 0;">-<span id="LC701" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">drand48</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">5</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// which strand ?</span></span>
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702
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<pre style="margin: 0;">-<span id="LC702" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Flip strands </span></span>
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703
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<pre style="margin: 0;">-<span id="LC703" class="line" lang="c"> <span class="n" style="color: #333;">strand</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">strand</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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704
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<pre style="margin: 0;">-<span id="LC704" class="line" lang="c"> <span class="n" style="color: #333;">strand</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">strand</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC701" class="line" lang="c"></span>
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702
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// set read two's strand</span></span>
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703
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="c"> <span class="k" style="font-weight: 600;">switch</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">strandedness</span><span class="p">)</span> <span class="p">{</span></span>
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704
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;">// default to data type</span></span>
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705
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="c"> <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data_type</span><span class="p">)</span> <span class="p">{</span></span>
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706
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ILLUMINA</span><span class="p">:</span> <span class="n" style="color: #333;">strand</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">strand</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// paired end for Illumina (opposite strand)</span></span>
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707
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">SOLID</span><span class="p">:</span> </span>
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708
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">IONTORRENT</span><span class="p">:</span> <span class="n" style="color: #333;">strand</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strand</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// mate pair for SOLiD and IonTorrent (same strand)</span></span>
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709
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="c"> <span class="nl">default:</span> <span class="n" style="color: #333;">unreachable</span><span class="p">(</span><span class="s" style="color: #d14;">"data type was not between 0-2"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC711" class="line" lang="c"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span> <span class="n" style="color: #333;">strand</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strand</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// mate pair (same strand)</span></span>
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">2</span><span class="p">:</span> <span class="n" style="color: #333;">strand</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">strand</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// paired end (opposite strand)</span></span>
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="c"> <span class="nl">default:</span> <span class="n" style="color: #333;">unreachable</span><span class="p">(</span><span class="s" style="color: #d14;">"strandedness was not between 0-2"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC715" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC716" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC717" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// generate the reads in base space</span></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">@@ -712,12 +722,8 @@ void dwgsim_core(dwgsim_opt_t * opt)</td>
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<pre style="margin: 0;"> <span id="LC722" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * 5' E2 -----> .... E1 -----> 3'</span></span>
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<pre style="margin: 0;"> <span id="LC723" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * 3' .... 5'</span></span>
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<pre style="margin: 0;"> <span id="LC724" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC715" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_inner</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC716" class="line" lang="c"> <span class="n" style="color: #333;">__gen_read</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">);</span> </span>
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<pre style="margin: 0;">-<span id="LC717" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC718" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC719" class="line" lang="c"> <span class="n" style="color: #333;">__gen_read</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">);</span> </span>
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<pre style="margin: 0;">-<span id="LC720" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC725" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">r0_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_inner</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="p">(</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="o" style="font-weight: 600;">:</span> <span class="p">(</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC726" class="line" lang="c"> <span class="n" style="color: #333;">__gen_read</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">r0_pos</span><span class="p">,</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">);</span> </span>
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<pre style="margin: 0;"> <span id="LC727" class="line" lang="c"> <span class="n" style="color: #333;">__gen_read</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC728" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC729" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// - strand</span></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">@@ -725,13 +731,9 @@ void dwgsim_core(dwgsim_opt_t * opt)</td>
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<pre style="margin: 0;"> <span id="LC731" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * 3' .... 5'</span></span>
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<pre style="margin: 0;"> <span id="LC732" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * 5' <----- E1 .... <----- E2 3'</span></span>
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<pre style="margin: 0;"> <span id="LC733" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC728" class="line" lang="c"> <span class="n" style="color: #333;">__gen_read</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC729" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_inner</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC730" class="line" lang="c"> <span class="n" style="color: #333;">__gen_read</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC731" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC732" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC733" class="line" lang="c"> <span class="n" style="color: #333;">__gen_read</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC734" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC734" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">r1_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_inner</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="p">(</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="p">(</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC735" class="line" lang="c"> <span class="n" style="color: #333;">__gen_read</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="c"> <span class="n" style="color: #333;">__gen_read</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">r1_pos</span><span class="p">,</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC737" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC738" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC739" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// opposite strand</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="742" 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">@@ -740,25 +742,17 @@ void dwgsim_core(dwgsim_opt_t * opt)</td>
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<pre style="margin: 0;"> <span id="LC742" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * 5' E1 -----> .... 3'</span></span>
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<pre style="margin: 0;"> <span id="LC743" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * 3' .... <----- E2 5'</span></span>
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<pre style="margin: 0;"> <span id="LC744" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">r1_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_inner</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="p">(</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="p">(</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC746" class="line" lang="c"> <span class="n" style="color: #333;">__gen_read</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC744" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_inner</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC745" class="line" lang="c"> <span class="n" style="color: #333;">__gen_read</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC746" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC747" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC748" class="line" lang="c"> <span class="n" style="color: #333;">__gen_read</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC749" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="c"> <span class="n" style="color: #333;">__gen_read</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">r1_pos</span><span class="p">,</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC748" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC749" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// - strand</span></span>
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<pre style="margin: 0;"> <span id="LC750" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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<pre style="margin: 0;"> <span id="LC751" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * 5' E2 -----> .... 3'</span></span>
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<pre style="margin: 0;"> <span id="LC752" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * 3' .... <----- E1 5'</span></span>
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<pre style="margin: 0;"> <span id="LC753" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC756" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_inner</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC757" class="line" lang="c"> <span class="n" style="color: #333;">__gen_read</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC758" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC759" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC760" class="line" lang="c"> <span class="n" style="color: #333;">__gen_read</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">i</span><span class="p">);</span> </span>
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761
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<pre style="margin: 0;">-<span id="LC761" class="line" lang="c"> <span class="p">}</span></span>
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754
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">r0_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_inner</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="p">(</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="p">(</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span> </span>
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755
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<pre style="margin: 0;">+<span id="LC755" class="line" lang="c"> <span class="n" style="color: #333;">__gen_read</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">r0_pos</span><span class="p">,</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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756
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<pre style="margin: 0;"> <span id="LC756" class="line" lang="c"> <span class="n" style="color: #333;">__gen_read</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">);</span></span>
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763
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757
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<pre style="margin: 0;"> <span id="LC757" class="line" lang="c"> <span class="p">}</span></span>
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758
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<pre style="margin: 0;"> <span id="LC758" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="785" 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>
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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">@@ -785,8 +779,14 @@ void dwgsim_core(dwgsim_opt_t * opt)</td>
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785
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779
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<pre style="margin: 0;"> <span id="LC779" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ext_coor</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">ext_coor</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max_n</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">num_n</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max_n</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">num_n</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// fail to generate the read(s)</span></span>
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786
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780
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<pre style="margin: 0;"> <span id="LC780" class="line" lang="c"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">ii</span><span class="p">;</span></span>
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787
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781
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<pre style="margin: 0;"> <span id="LC781" class="line" lang="c"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">ctr</span><span class="p">;</span></span>
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782
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<pre style="margin: 0;">+<span id="LC782" class="line" lang="c"> <span class="n" style="color: #333;">num_failed</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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783
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<pre style="margin: 0;">+<span id="LC783" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">num_failed</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">10000</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="784" 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">
784
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<pre style="margin: 0;">+<span id="LC784" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\r</span><span class="s" style="color: #d14;">[dwgsim_core] failed to generate a read after %d trials</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">num_failed</span><span class="p">);</span></span>
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785
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<pre style="margin: 0;">+<span id="LC785" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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786
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<pre style="margin: 0;">+<span id="LC786" class="line" lang="c"> <span class="p">}</span></span>
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788
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787
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<pre style="margin: 0;"> <span id="LC787" class="line" lang="c"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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789
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788
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<pre style="margin: 0;"> <span id="LC788" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC789" class="line" lang="c"> <span class="n" style="color: #333;">num_failed</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC790" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC791" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">SOLID</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data_type</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC792" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Convert to color sequence, use the first base as the adaptor</span></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">@@ -858,61 +858,65 @@ void dwgsim_core(dwgsim_opt_t * opt)</td>
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858
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858
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<pre style="margin: 0;"> <span id="LC858" class="line" lang="c"> <span class="n" style="color: #333;">qstr</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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859
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859
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<pre style="margin: 0;"> <span id="LC859" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// BWA</span></span>
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860
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860
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<pre style="margin: 0;"> <span id="LC860" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fpo</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bwa1</span><span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bwa2</span><span class="p">;</span></span>
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861
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<pre style="margin: 0;">-<span id="LC861" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">ILLUMINA</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data_type</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">IONTORRENT</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data_type</span><span class="p">)</span> <span class="p">{</span></span>
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862
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<pre style="margin: 0;">-<span id="LC862" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fpo</span><span class="p">,</span> <span class="s" style="color: #d14;">"@%s%s%s_%u_%u_%1u_%1u_%1u_%1u_%d:%d:%d_%d:%d:%d_%llx/%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> </span>
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863
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<pre style="margin: 0;">-<span id="LC863" class="line" lang="c"> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_prefix</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_prefix</span><span class="p">,</span></span>
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864
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<pre style="margin: 0;">-<span id="LC864" class="line" lang="c"> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_prefix</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"_"</span><span class="p">,</span></span>
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865
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<pre style="margin: 0;">-<span id="LC865" class="line" lang="c"> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">ext_coor</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">ext_coor</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">strand</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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866
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<pre style="margin: 0;">-<span id="LC866" class="line" lang="c"> <span class="n" style="color: #333;">n_err</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">n_sub</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">n_indel</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span></span>
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867
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<pre style="margin: 0;">-<span id="LC867" class="line" lang="c"> <span class="n" style="color: #333;">n_err</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">n_sub</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span><span class="n" style="color: #333;">n_indel</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span></span>
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868
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<pre style="margin: 0;">-<span id="LC868" class="line" lang="c"> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">)</span><span class="n" style="color: #333;">ii</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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869
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<pre style="margin: 0;">-<span id="LC869" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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870
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<pre style="margin: 0;">-<span id="LC870" class="line" lang="c"> <span class="n" style="color: #333;">fputc</span><span class="p">(</span><span class="s" style="color: #d14;">"ACGTN"</span><span class="p">[(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">tmp_seq</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">]],</span> <span class="n" style="color: #333;">fpo</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC871" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fpo</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">qstr</span><span class="p">);</span></span>
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861
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<pre style="margin: 0;">+<span id="LC861" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">fpo</span><span class="p">)</span> <span class="p">{</span></span>
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862
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<pre style="margin: 0;">+<span id="LC862" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">ILLUMINA</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data_type</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">IONTORRENT</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data_type</span><span class="p">)</span> <span class="p">{</span></span>
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863
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<pre style="margin: 0;">+<span id="LC863" class="line" lang="c"> <span class="n" style="color: #333;">gzprintf</span><span class="p">(</span><span class="n" style="color: #333;">fpo</span><span class="p">,</span> <span class="s" style="color: #d14;">"@%s%s%s_%u_%u_%1u_%1u_%1u_%1u_%d:%d:%d_%d:%d:%d_%llx/%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> </span>
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864
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<pre style="margin: 0;">+<span id="LC864" class="line" lang="c"> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_prefix</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_prefix</span><span class="p">,</span></span>
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865
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<pre style="margin: 0;">+<span id="LC865" class="line" lang="c"> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_prefix</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"_"</span><span class="p">,</span></span>
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866
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<pre style="margin: 0;">+<span id="LC866" class="line" lang="c"> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">ext_coor</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">ext_coor</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">strand</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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867
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<pre style="margin: 0;">+<span id="LC867" class="line" lang="c"> <span class="n" style="color: #333;">n_err</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">n_sub</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">n_indel</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span></span>
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868
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<pre style="margin: 0;">+<span id="LC868" class="line" lang="c"> <span class="n" style="color: #333;">n_err</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">n_sub</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span><span class="n" style="color: #333;">n_indel</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span></span>
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869
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<pre style="margin: 0;">+<span id="LC869" class="line" lang="c"> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">)</span><span class="n" style="color: #333;">ii</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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870
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<pre style="margin: 0;">+<span id="LC870" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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871
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<pre style="margin: 0;">+<span id="LC871" class="line" lang="c"> <span class="n" style="color: #333;">gzputc</span><span class="p">(</span><span class="n" style="color: #333;">fpo</span><span class="p">,</span> <span class="s" style="color: #d14;">"ACGTN"</span><span class="p">[(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">tmp_seq</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">]]);</span></span>
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872
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<pre style="margin: 0;">+<span id="LC872" class="line" lang="c"> <span class="n" style="color: #333;">gzprintf</span><span class="p">(</span><span class="n" style="color: #333;">fpo</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">qstr</span><span class="p">);</span></span>
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873
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<pre style="margin: 0;">+<span id="LC873" class="line" lang="c"> <span class="p">}</span></span>
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874
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<pre style="margin: 0;">+<span id="LC874" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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875
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<pre style="margin: 0;">+<span id="LC875" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Note: BWA ignores the adapter and the first color, so this is a misrepresentation </span></span>
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876
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<pre style="margin: 0;">+<span id="LC876" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// in samtools. We must first skip the first color. Basically, a 50 color read is a </span></span>
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877
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<pre style="margin: 0;">+<span id="LC877" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// 49 color read for BWA.</span></span>
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878
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<pre style="margin: 0;">+<span id="LC878" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<pre style="margin: 0;">+<span id="LC879" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Note: BWA outputs F3 to read1, annotated as read "2", and outputs R3 to read2,</span></span>
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880
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<pre style="margin: 0;">+<span id="LC880" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// annotated as read "1".</span></span>
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881
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<pre style="margin: 0;">+<span id="LC881" class="line" lang="c"> <span class="n" style="color: #333;">gzprintf</span><span class="p">(</span><span class="n" style="color: #333;">fpo</span><span class="p">,</span> <span class="s" style="color: #d14;">"@%s%s%s_%u_%u_%1u_%1u_%1u_%1u_%d:%d:%d_%d:%d:%d_%llx/%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> </span>
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882
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<pre style="margin: 0;">+<span id="LC882" class="line" lang="c"> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_prefix</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_prefix</span><span class="p">,</span></span>
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883
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<pre style="margin: 0;">+<span id="LC883" class="line" lang="c"> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_prefix</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"_"</span><span class="p">,</span></span>
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884
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<pre style="margin: 0;">+<span id="LC884" class="line" lang="c"> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">ext_coor</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">ext_coor</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">strand</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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885
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<pre style="margin: 0;">+<span id="LC885" class="line" lang="c"> <span class="n" style="color: #333;">n_err</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">n_err_first</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">n_sub</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">n_sub_first</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">n_indel</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">n_indel_first</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> </span>
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886
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<pre style="margin: 0;">+<span id="LC886" class="line" lang="c"> <span class="n" style="color: #333;">n_err</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">n_err_first</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">n_sub</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">n_sub_first</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">n_indel</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">n_indel_first</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span></span>
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887
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<pre style="margin: 0;">+<span id="LC887" class="line" lang="c"> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">)</span><span class="n" style="color: #333;">ii</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">j</span><span class="p">);</span></span>
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888
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<pre style="margin: 0;">+<span id="LC888" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//gzputc(fpo, 'A');</span></span>
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889
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<pre style="margin: 0;">+<span id="LC889" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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890
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<pre style="margin: 0;">+<span id="LC890" class="line" lang="c"> <span class="n" style="color: #333;">gzputc</span><span class="p">(</span><span class="n" style="color: #333;">fpo</span><span class="p">,</span> <span class="s" style="color: #d14;">"ACGTN"</span><span class="p">[(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">tmp_seq</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">]]);</span></span>
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891
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<pre style="margin: 0;">+<span id="LC891" class="line" lang="c"> <span class="n" style="color: #333;">gzprintf</span><span class="p">(</span><span class="n" style="color: #333;">fpo</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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892
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<pre style="margin: 0;">+<span id="LC892" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> </span>
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893
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<pre style="margin: 0;">+<span id="LC893" class="line" lang="c"> <span class="n" style="color: #333;">gzputc</span><span class="p">(</span><span class="n" style="color: #333;">fpo</span><span class="p">,</span> <span class="n" style="color: #333;">qstr</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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894
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<pre style="margin: 0;">+<span id="LC894" class="line" lang="c"> <span class="n" style="color: #333;">gzprintf</span><span class="p">(</span><span class="n" style="color: #333;">fpo</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC895" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC896" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC873" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC874" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Note: BWA ignores the adapter and the first color, so this is a misrepresentation </span></span>
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<pre style="margin: 0;">-<span id="LC875" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// in samtools. We must first skip the first color. Basically, a 50 color read is a </span></span>
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<pre style="margin: 0;">-<span id="LC876" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// 49 color read for BWA.</span></span>
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<pre style="margin: 0;">-<span id="LC877" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<pre style="margin: 0;">-<span id="LC878" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Note: BWA outputs F3 to read1, annotated as read "2", and outputs R3 to read2,</span></span>
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<pre style="margin: 0;">-<span id="LC879" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// annotated as read "1".</span></span>
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<pre style="margin: 0;">-<span id="LC880" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fpo</span><span class="p">,</span> <span class="s" style="color: #d14;">"@%s%s%s_%u_%u_%1u_%1u_%1u_%1u_%d:%d:%d_%d:%d:%d_%llx/%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> </span>
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<pre style="margin: 0;">+<span id="LC897" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC898" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// BFAST output</span></span>
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899
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<pre style="margin: 0;">+<span id="LC899" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bfast</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC900" class="line" lang="c"> <span class="n" style="color: #333;">gzprintf</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bfast</span><span class="p">,</span> <span class="s" style="color: #d14;">"@%s%s%s_%u_%u_%1u_%1u_%1u_%1u_%d:%d:%d_%d:%d:%d_%llx</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> </span>
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<pre style="margin: 0;"> <span id="LC901" class="line" lang="c"> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_prefix</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_prefix</span><span class="p">,</span></span>
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882
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902
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<pre style="margin: 0;"> <span id="LC902" class="line" lang="c"> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_prefix</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"_"</span><span class="p">,</span></span>
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883
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903
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<pre style="margin: 0;"> <span id="LC903" class="line" lang="c"> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">ext_coor</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">ext_coor</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">strand</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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884
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<pre style="margin: 0;">-<span id="LC884" class="line" lang="c"> <span class="n" style="color: #333;">n_err</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">n_err_first</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">n_sub</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">n_sub_first</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">n_indel</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">n_indel_first</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> </span>
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<pre style="margin: 0;">-<span id="LC885" class="line" lang="c"> <span class="n" style="color: #333;">n_err</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">n_err_first</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">n_sub</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">n_sub_first</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">n_indel</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">n_indel_first</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span></span>
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886
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<pre style="margin: 0;">-<span id="LC886" class="line" lang="c"> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">)</span><span class="n" style="color: #333;">ii</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">j</span><span class="p">);</span></span>
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887
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<pre style="margin: 0;">-<span id="LC887" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//fputc('A', fpo);</span></span>
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888
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<pre style="margin: 0;">-<span id="LC888" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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889
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<pre style="margin: 0;">-<span id="LC889" class="line" lang="c"> <span class="n" style="color: #333;">fputc</span><span class="p">(</span><span class="s" style="color: #d14;">"ACGTN"</span><span class="p">[(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">tmp_seq</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">]],</span> <span class="n" style="color: #333;">fpo</span><span class="p">);</span></span>
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890
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<pre style="margin: 0;">-<span id="LC890" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fpo</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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891
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<pre style="margin: 0;">-<span id="LC891" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> </span>
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892
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<pre style="margin: 0;">-<span id="LC892" class="line" lang="c"> <span class="n" style="color: #333;">fputc</span><span class="p">(</span><span class="n" style="color: #333;">qstr</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">fpo</span><span class="p">);</span></span>
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893
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<pre style="margin: 0;">-<span id="LC893" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fpo</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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894
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<pre style="margin: 0;">-<span id="LC894" class="line" lang="c"> <span class="p">}</span></span>
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895
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<td class="new_line diff-line-num old" data-linenumber="904" 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="LC895" class="line" lang="c"></span>
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<td class="old_line diff-line-num old" data-linenumber="896" 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">
896
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<pre style="margin: 0;">-<span id="LC896" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// BFAST output</span></span>
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897
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<pre style="margin: 0;">-<span id="LC897" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bfast</span><span class="p">,</span> <span class="s" style="color: #d14;">"@%s%s%s_%u_%u_%1u_%1u_%1u_%1u_%d:%d:%d_%d:%d:%d_%llx</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> </span>
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<td class="old_line diff-line-num old" data-linenumber="898" 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">
898
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<td class="new_line diff-line-num old" data-linenumber="904" 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="LC898" class="line" lang="c"> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_prefix</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_prefix</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="899" 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">
899
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<td class="new_line diff-line-num old" data-linenumber="904" 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="LC899" class="line" lang="c"> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_prefix</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"_"</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="900" 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">
900
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<pre style="margin: 0;">-<span id="LC900" class="line" lang="c"> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">ext_coor</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">ext_coor</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">strand</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="901" 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">
901
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<pre style="margin: 0;">-<span id="LC901" class="line" lang="c"> <span class="n" style="color: #333;">n_err</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">n_sub</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">n_indel</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">n_err</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">n_sub</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">n_indel</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span></span>
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902
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<pre style="margin: 0;">-<span id="LC902" class="line" lang="c"> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">)</span><span class="n" style="color: #333;">ii</span><span class="p">);</span></span>
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903
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<pre style="margin: 0;">-<span id="LC903" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">ILLUMINA</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data_type</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">IONTORRENT</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data_type</span><span class="p">)</span> <span class="p">{</span></span>
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904
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<pre style="margin: 0;">-<span id="LC904" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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905
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<pre style="margin: 0;">-<span id="LC905" class="line" lang="c"> <span class="n" style="color: #333;">fputc</span><span class="p">(</span><span class="s" style="color: #d14;">"ACGTN"</span><span class="p">[(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">tmp_seq</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">]],</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bfast</span><span class="p">);</span></span>
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906
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<pre style="margin: 0;">-<span id="LC906" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bfast</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">qstr</span><span class="p">);</span></span>
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907
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<td class="new_line diff-line-num old" data-linenumber="904" 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="LC907" class="line" lang="c"> <span class="p">}</span></span>
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908
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<td class="new_line diff-line-num old" data-linenumber="904" 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="LC908" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="909" 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">
909
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<td class="new_line diff-line-num old" data-linenumber="904" 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="LC909" class="line" lang="c"> <span class="n" style="color: #333;">fputc</span><span class="p">(</span><span class="sc" style="color: #d14;">'A'</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bfast</span><span class="p">);</span></span>
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910
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<td class="new_line diff-line-num old" data-linenumber="904" 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="LC910" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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911
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<pre style="margin: 0;">-<span id="LC911" class="line" lang="c"> <span class="n" style="color: #333;">fputc</span><span class="p">(</span><span class="s" style="color: #d14;">"01234"</span><span class="p">[(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">tmp_seq</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">]],</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bfast</span><span class="p">);</span></span>
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912
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<pre style="margin: 0;">-<span id="LC912" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bfast</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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913
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<pre style="margin: 0;">-<span id="LC913" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> </span>
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914
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<pre style="margin: 0;">-<span id="LC914" class="line" lang="c"> <span class="n" style="color: #333;">fputc</span><span class="p">(</span><span class="n" style="color: #333;">qstr</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bfast</span><span class="p">);</span></span>
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915
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<pre style="margin: 0;">-<span id="LC915" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bfast</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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904
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<pre style="margin: 0;">+<span id="LC904" class="line" lang="c"> <span class="n" style="color: #333;">n_err</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">n_sub</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">n_indel</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">n_err</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">n_sub</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">n_indel</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span></span>
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905
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<pre style="margin: 0;">+<span id="LC905" class="line" lang="c"> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">)</span><span class="n" style="color: #333;">ii</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="906" 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">
906
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<pre style="margin: 0;">+<span id="LC906" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">ILLUMINA</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data_type</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">IONTORRENT</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data_type</span><span class="p">)</span> <span class="p">{</span></span>
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907
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<pre style="margin: 0;">+<span id="LC907" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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908
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<pre style="margin: 0;">+<span id="LC908" class="line" lang="c"> <span class="n" style="color: #333;">gzputc</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bfast</span><span class="p">,</span> <span class="s" style="color: #d14;">"ACGTN"</span><span class="p">[(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">tmp_seq</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">]]);</span></span>
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909
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<pre style="margin: 0;">+<span id="LC909" class="line" lang="c"> <span class="n" style="color: #333;">gzprintf</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bfast</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">qstr</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="910" 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">
910
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<pre style="margin: 0;">+<span id="LC910" class="line" lang="c"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="911" 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">
911
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<pre style="margin: 0;">+<span id="LC911" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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912
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<pre style="margin: 0;">+<span id="LC912" class="line" lang="c"> <span class="n" style="color: #333;">gzputc</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bfast</span><span class="p">,</span> <span class="sc" style="color: #d14;">'A'</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="913" 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">
913
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<pre style="margin: 0;">+<span id="LC913" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="914" 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">
914
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<pre style="margin: 0;">+<span id="LC914" class="line" lang="c"> <span class="n" style="color: #333;">gzputc</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bfast</span><span class="p">,</span> <span class="s" style="color: #d14;">"01234"</span><span class="p">[(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">tmp_seq</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">]]);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="915" 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">
915
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<pre style="margin: 0;">+<span id="LC915" class="line" lang="c"> <span class="n" style="color: #333;">gzprintf</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bfast</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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916
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<pre style="margin: 0;">+<span id="LC916" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> </span>
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917
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<pre style="margin: 0;">+<span id="LC917" class="line" lang="c"> <span class="n" style="color: #333;">gzputc</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bfast</span><span class="p">,</span> <span class="n" style="color: #333;">qstr</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="918" 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">
918
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<pre style="margin: 0;">+<span id="LC918" class="line" lang="c"> <span class="n" style="color: #333;">gzprintf</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bfast</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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919
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<pre style="margin: 0;">+<span id="LC919" class="line" lang="c"> <span class="p">}</span></span>
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916
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920
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<pre style="margin: 0;"> <span id="LC920" class="line" lang="c"> <span class="p">}</span></span>
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917
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921
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<pre style="margin: 0;"> <span id="LC921" class="line" lang="c"> <span class="p">}</span></span>
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918
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922
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<pre style="margin: 0;"> <span id="LC922" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="962" 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="966" 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">@@ -962,61 +966,65 @@ void dwgsim_core(dwgsim_opt_t * opt)</td>
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962
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966
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<pre style="margin: 0;"> <span id="LC966" class="line" lang="c"> <span class="p">}</span></span>
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963
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967
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<pre style="margin: 0;"> <span id="LC967" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// BWA</span></span>
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<td class="old_line diff-line-num" data-linenumber="964" 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">
964
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968
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<pre style="margin: 0;"> <span id="LC968" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fpo</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bwa1</span><span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bwa2</span><span class="p">;</span></span>
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965
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<pre style="margin: 0;">-<span id="LC965" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">ILLUMINA</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data_type</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">IONTORRENT</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data_type</span><span class="p">)</span> <span class="p">{</span></span>
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966
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<td class="new_line diff-line-num old" data-linenumber="969" 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="LC966" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fpo</span><span class="p">,</span> <span class="s" style="color: #d14;">"@%s%s%s_%u_%u_%1u_%1u_%1u_%1u_%d:%d:%d_%d:%d:%d_%llx/%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> </span>
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<td class="old_line diff-line-num old" data-linenumber="967" 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">
967
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<td class="new_line diff-line-num old" data-linenumber="969" 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="LC967" class="line" lang="c"> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_prefix</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_prefix</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="968" 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">
968
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<td class="new_line diff-line-num old" data-linenumber="969" 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="LC968" class="line" lang="c"> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_prefix</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"_"</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="969" 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">
969
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<td class="new_line diff-line-num old" data-linenumber="969" 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="LC969" class="line" lang="c"> <span class="s" style="color: #d14;">"rand"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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970
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<td class="new_line diff-line-num old" data-linenumber="969" 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="LC970" class="line" lang="c"> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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971
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<td class="new_line diff-line-num old" data-linenumber="969" 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="LC971" class="line" lang="c"> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">)</span><span class="n" style="color: #333;">rand_ii</span><span class="p">,</span></span>
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972
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<td class="new_line diff-line-num old" data-linenumber="969" 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="LC972" class="line" lang="c"> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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973
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<td class="new_line diff-line-num old" data-linenumber="969" 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="LC973" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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974
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<td class="new_line diff-line-num old" data-linenumber="969" 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="LC974" class="line" lang="c"> <span class="n" style="color: #333;">fputc</span><span class="p">(</span><span class="s" style="color: #d14;">"ACGTN"</span><span class="p">[(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">tmp_seq</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">]],</span> <span class="n" style="color: #333;">fpo</span><span class="p">);</span></span>
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975
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<td class="new_line diff-line-num old" data-linenumber="969" 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="LC975" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fpo</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">qstr</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="969" 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">
969
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<pre style="margin: 0;">+<span id="LC969" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">fpo</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="970" 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">
970
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<pre style="margin: 0;">+<span id="LC970" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">ILLUMINA</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data_type</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">IONTORRENT</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data_type</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="971" 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">
971
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<pre style="margin: 0;">+<span id="LC971" class="line" lang="c"> <span class="n" style="color: #333;">gzprintf</span><span class="p">(</span><span class="n" style="color: #333;">fpo</span><span class="p">,</span> <span class="s" style="color: #d14;">"@%s%s%s_%u_%u_%1u_%1u_%1u_%1u_%d:%d:%d_%d:%d:%d_%llx/%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="972" 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">
972
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<pre style="margin: 0;">+<span id="LC972" class="line" lang="c"> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_prefix</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_prefix</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="973" 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">
973
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<pre style="margin: 0;">+<span id="LC973" class="line" lang="c"> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_prefix</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"_"</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="974" 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">
974
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<pre style="margin: 0;">+<span id="LC974" class="line" lang="c"> <span class="s" style="color: #d14;">"rand"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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975
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<pre style="margin: 0;">+<span id="LC975" class="line" lang="c"> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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976
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<pre style="margin: 0;">+<span id="LC976" class="line" lang="c"> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">)</span><span class="n" style="color: #333;">rand_ii</span><span class="p">,</span></span>
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977
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<pre style="margin: 0;">+<span id="LC977" class="line" lang="c"> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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978
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<pre style="margin: 0;">+<span id="LC978" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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979
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<pre style="margin: 0;">+<span id="LC979" class="line" lang="c"> <span class="n" style="color: #333;">gzputc</span><span class="p">(</span><span class="n" style="color: #333;">fpo</span><span class="p">,</span> <span class="s" style="color: #d14;">"ACGTN"</span><span class="p">[(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">tmp_seq</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">]]);</span></span>
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980
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<pre style="margin: 0;">+<span id="LC980" class="line" lang="c"> <span class="n" style="color: #333;">gzprintf</span><span class="p">(</span><span class="n" style="color: #333;">fpo</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">qstr</span><span class="p">);</span></span>
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981
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<pre style="margin: 0;">+<span id="LC981" class="line" lang="c"> <span class="p">}</span></span>
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982
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<pre style="margin: 0;">+<span id="LC982" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="983" 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">
983
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<pre style="margin: 0;">+<span id="LC983" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Note: BWA ignores the adapter and the first color, so this is a misrepresentation </span></span>
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<td class="new_line diff-line-num new" data-linenumber="984" 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">
984
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<pre style="margin: 0;">+<span id="LC984" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// in samtools. We must first skip the first color. Basically, a 50 color read is a </span></span>
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985
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<pre style="margin: 0;">+<span id="LC985" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// 49 color read for BWA.</span></span>
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986
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<pre style="margin: 0;">+<span id="LC986" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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987
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<pre style="margin: 0;">+<span id="LC987" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Note: BWA outputs F3 to read1, annotated as read "2", and outputs R3 to read2,</span></span>
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988
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<pre style="margin: 0;">+<span id="LC988" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// annotated as read "1".</span></span>
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989
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<pre style="margin: 0;">+<span id="LC989" class="line" lang="c"> <span class="n" style="color: #333;">gzprintf</span><span class="p">(</span><span class="n" style="color: #333;">fpo</span><span class="p">,</span> <span class="s" style="color: #d14;">"@%s%s%s_%u_%u_%1u_%1u_%1u_%1u_%d:%d:%d_%d:%d:%d_%llx/%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> </span>
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990
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<pre style="margin: 0;">+<span id="LC990" class="line" lang="c"> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_prefix</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_prefix</span><span class="p">,</span></span>
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991
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<pre style="margin: 0;">+<span id="LC991" class="line" lang="c"> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_prefix</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"_"</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="992" 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">
992
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<pre style="margin: 0;">+<span id="LC992" class="line" lang="c"> <span class="s" style="color: #d14;">"rand"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="993" 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">
993
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<pre style="margin: 0;">+<span id="LC993" class="line" lang="c"> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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994
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<pre style="margin: 0;">+<span id="LC994" class="line" lang="c"> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">)</span><span class="n" style="color: #333;">rand_ii</span><span class="p">,</span></span>
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995
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<pre style="margin: 0;">+<span id="LC995" class="line" lang="c"> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">j</span><span class="p">);</span></span>
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996
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<pre style="margin: 0;">+<span id="LC996" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//gzputc(fpo, 'A');</span></span>
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997
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<pre style="margin: 0;">+<span id="LC997" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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998
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<pre style="margin: 0;">+<span id="LC998" class="line" lang="c"> <span class="n" style="color: #333;">gzputc</span><span class="p">(</span><span class="n" style="color: #333;">fpo</span><span class="p">,</span> <span class="s" style="color: #d14;">"ACGTN"</span><span class="p">[(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">tmp_seq</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">]]);</span></span>
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999
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<pre style="margin: 0;">+<span id="LC999" class="line" lang="c"> <span class="n" style="color: #333;">gzprintf</span><span class="p">(</span><span class="n" style="color: #333;">fpo</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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1000
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<pre style="margin: 0;">+<span id="LC1000" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="1001" 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">
1001
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<pre style="margin: 0;">+<span id="LC1001" class="line" lang="c"> <span class="n" style="color: #333;">gzputc</span><span class="p">(</span><span class="n" style="color: #333;">fpo</span><span class="p">,</span> <span class="n" style="color: #333;">qstr</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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1002
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<pre style="margin: 0;">+<span id="LC1002" class="line" lang="c"> <span class="n" style="color: #333;">gzprintf</span><span class="p">(</span><span class="n" style="color: #333;">fpo</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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1003
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<pre style="margin: 0;">+<span id="LC1003" class="line" lang="c"> <span class="p">}</span></span>
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976
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1004
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<pre style="margin: 0;"> <span id="LC1004" class="line" lang="c"> <span class="p">}</span></span>
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977
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<td class="new_line diff-line-num old" data-linenumber="1005" 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="LC977" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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978
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<td class="new_line diff-line-num old" data-linenumber="1005" 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="LC978" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Note: BWA ignores the adapter and the first color, so this is a misrepresentation </span></span>
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979
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<td class="new_line diff-line-num old" data-linenumber="1005" 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="LC979" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// in samtools. We must first skip the first color. Basically, a 50 color read is a </span></span>
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980
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<pre style="margin: 0;">-<span id="LC980" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// 49 color read for BWA.</span></span>
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981
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<pre style="margin: 0;">-<span id="LC981" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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982
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<pre style="margin: 0;">-<span id="LC982" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Note: BWA outputs F3 to read1, annotated as read "2", and outputs R3 to read2,</span></span>
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983
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<pre style="margin: 0;">-<span id="LC983" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// annotated as read "1".</span></span>
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984
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<pre style="margin: 0;">-<span id="LC984" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fpo</span><span class="p">,</span> <span class="s" style="color: #d14;">"@%s%s%s_%u_%u_%1u_%1u_%1u_%1u_%d:%d:%d_%d:%d:%d_%llx/%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> </span>
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1005
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<pre style="margin: 0;">+<span id="LC1005" class="line" lang="c"></span>
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1006
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<pre style="margin: 0;">+<span id="LC1006" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// BFAST output</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1007" 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">
1007
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<pre style="margin: 0;">+<span id="LC1007" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bfast</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="985" 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="new_line diff-line-num new" data-linenumber="1008" 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">
1008
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<pre style="margin: 0;">+<span id="LC1008" class="line" lang="c"> <span class="n" style="color: #333;">gzprintf</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bfast</span><span class="p">,</span> <span class="s" style="color: #d14;">"@%s%s%s_%u_%u_%1u_%1u_%1u_%1u_%d:%d:%d_%d:%d:%d_%llx</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> </span>
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<td class="old_line diff-line-num" data-linenumber="985" 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">
985
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<td class="new_line diff-line-num" data-linenumber="1009" 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">
1009
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<pre style="margin: 0;"> <span id="LC1009" class="line" lang="c"> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_prefix</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_prefix</span><span class="p">,</span></span>
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<td class="old_line diff-line-num" data-linenumber="986" 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">
986
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<td class="new_line diff-line-num" data-linenumber="1010" 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">
1010
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<pre style="margin: 0;"> <span id="LC1010" class="line" lang="c"> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_prefix</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"_"</span><span class="p">,</span></span>
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<td class="old_line diff-line-num" data-linenumber="987" 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">
987
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<td class="new_line diff-line-num" data-linenumber="1011" 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">
1011
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<pre style="margin: 0;"> <span id="LC1011" class="line" lang="c"> <span class="s" style="color: #d14;">"rand"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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<td class="old_line diff-line-num" data-linenumber="988" 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">
988
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<td class="new_line diff-line-num" data-linenumber="1012" 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">
1012
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<pre style="margin: 0;"> <span id="LC1012" class="line" lang="c"> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="989" 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">
989
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<td class="new_line diff-line-num old" data-linenumber="1013" 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="LC989" class="line" lang="c"> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">)</span><span class="n" style="color: #333;">rand_ii</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="990" 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">
990
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<td class="new_line diff-line-num old" data-linenumber="1013" 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="LC990" class="line" lang="c"> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">j</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="991" 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">
991
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<td class="new_line diff-line-num old" data-linenumber="1013" 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="LC991" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//fputc('A', fpo);</span></span>
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992
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<pre style="margin: 0;">-<span id="LC992" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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993
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<pre style="margin: 0;">-<span id="LC993" class="line" lang="c"> <span class="n" style="color: #333;">fputc</span><span class="p">(</span><span class="s" style="color: #d14;">"ACGTN"</span><span class="p">[(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">tmp_seq</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">]],</span> <span class="n" style="color: #333;">fpo</span><span class="p">);</span></span>
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994
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<pre style="margin: 0;">-<span id="LC994" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fpo</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="995" 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">
995
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<td class="new_line diff-line-num old" data-linenumber="1013" 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="LC995" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> </span>
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<td class="old_line diff-line-num old" data-linenumber="996" 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">
996
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<td class="new_line diff-line-num old" data-linenumber="1013" 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="LC996" class="line" lang="c"> <span class="n" style="color: #333;">fputc</span><span class="p">(</span><span class="n" style="color: #333;">qstr</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">fpo</span><span class="p">);</span></span>
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997
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<pre style="margin: 0;">-<span id="LC997" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fpo</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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998
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<pre style="margin: 0;">-<span id="LC998" class="line" lang="c"> <span class="p">}</span></span>
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999
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<td class="new_line diff-line-num old" data-linenumber="1013" 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="LC999" class="line" lang="c"></span>
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1000
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<pre style="margin: 0;">-<span id="LC1000" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// BFAST output</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1001" 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">
1001
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<pre style="margin: 0;">-<span id="LC1001" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bfast</span><span class="p">,</span> <span class="s" style="color: #d14;">"@%s%s%s_%u_%u_%1u_%1u_%1u_%1u_%d:%d:%d_%d:%d:%d_%llx</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> </span>
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1002
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<pre style="margin: 0;">-<span id="LC1002" class="line" lang="c"> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_prefix</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_prefix</span><span class="p">,</span></span>
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1003
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<td class="new_line diff-line-num old" data-linenumber="1013" 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="LC1003" class="line" lang="c"> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_prefix</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"_"</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1004" 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">
1004
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<pre style="margin: 0;">-<span id="LC1004" class="line" lang="c"> <span class="s" style="color: #d14;">"rand"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1005" 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">
1005
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<td class="new_line diff-line-num old" data-linenumber="1013" 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="LC1005" class="line" lang="c"> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1006" 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">
1006
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<td class="new_line diff-line-num old" data-linenumber="1013" 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="LC1006" class="line" lang="c"> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">)</span><span class="n" style="color: #333;">rand_ii</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1007" 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">
1007
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<td class="new_line diff-line-num old" data-linenumber="1013" 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="LC1007" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">ILLUMINA</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data_type</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">IONTORRENT</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data_type</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1008" 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">
1008
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<td class="new_line diff-line-num old" data-linenumber="1013" 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="LC1008" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1009" 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">
1009
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<td class="new_line diff-line-num old" data-linenumber="1013" 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="LC1009" class="line" lang="c"> <span class="n" style="color: #333;">fputc</span><span class="p">(</span><span class="s" style="color: #d14;">"ACGTN"</span><span class="p">[(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">tmp_seq</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">]],</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bfast</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1010" 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">
1010
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<td class="new_line diff-line-num old" data-linenumber="1013" 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="LC1010" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bfast</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">qstr</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1011" 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">
1011
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<td class="new_line diff-line-num old" data-linenumber="1013" 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="LC1011" class="line" lang="c"> <span class="p">}</span></span>
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1012
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<td class="new_line diff-line-num old" data-linenumber="1013" 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="LC1012" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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1013
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<td class="new_line diff-line-num old" data-linenumber="1013" 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="LC1013" class="line" lang="c"> <span class="n" style="color: #333;">fputc</span><span class="p">(</span><span class="sc" style="color: #d14;">'A'</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bfast</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1014" 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">
1014
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<td class="new_line diff-line-num old" data-linenumber="1013" 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="LC1014" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1015" 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">
1015
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<td class="new_line diff-line-num old" data-linenumber="1013" 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="LC1015" class="line" lang="c"> <span class="n" style="color: #333;">fputc</span><span class="p">(</span><span class="s" style="color: #d14;">"01234"</span><span class="p">[(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">tmp_seq</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">]],</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bfast</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1016" 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">
1016
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<td class="new_line diff-line-num old" data-linenumber="1013" 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="LC1016" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bfast</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1017" 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">
1017
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<td class="new_line diff-line-num old" data-linenumber="1013" 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="LC1017" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> </span>
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<td class="old_line diff-line-num old" data-linenumber="1018" 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">
1018
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<td class="new_line diff-line-num old" data-linenumber="1013" 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="LC1018" class="line" lang="c"> <span class="n" style="color: #333;">fputc</span><span class="p">(</span><span class="n" style="color: #333;">qstr</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bfast</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1019" 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">
1019
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<pre style="margin: 0;">-<span id="LC1019" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bfast</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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1013
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<pre style="margin: 0;">+<span id="LC1013" class="line" lang="c"> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">)</span><span class="n" style="color: #333;">rand_ii</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1014" 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">
1014
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<pre style="margin: 0;">+<span id="LC1014" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">ILLUMINA</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data_type</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">IONTORRENT</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data_type</span><span class="p">)</span> <span class="p">{</span></span>
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1015
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<pre style="margin: 0;">+<span id="LC1015" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1016" 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">
1016
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<pre style="margin: 0;">+<span id="LC1016" class="line" lang="c"> <span class="n" style="color: #333;">gzputc</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bfast</span><span class="p">,</span> <span class="s" style="color: #d14;">"ACGTN"</span><span class="p">[(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">tmp_seq</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">]]);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1017" 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">
1017
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<pre style="margin: 0;">+<span id="LC1017" class="line" lang="c"> <span class="n" style="color: #333;">gzprintf</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bfast</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">qstr</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1018" 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">
1018
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<pre style="margin: 0;">+<span id="LC1018" class="line" lang="c"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1019" 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">
1019
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<pre style="margin: 0;">+<span id="LC1019" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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1020
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<pre style="margin: 0;">+<span id="LC1020" class="line" lang="c"> <span class="n" style="color: #333;">gzputc</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bfast</span><span class="p">,</span> <span class="sc" style="color: #d14;">'A'</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1021" 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">
1021
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<pre style="margin: 0;">+<span id="LC1021" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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1022
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<pre style="margin: 0;">+<span id="LC1022" class="line" lang="c"> <span class="n" style="color: #333;">gzputc</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bfast</span><span class="p">,</span> <span class="s" style="color: #d14;">"01234"</span><span class="p">[(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">tmp_seq</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">]]);</span></span>
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1023
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<pre style="margin: 0;">+<span id="LC1023" class="line" lang="c"> <span class="n" style="color: #333;">gzprintf</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bfast</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">+</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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1024
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<pre style="margin: 0;">+<span id="LC1024" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> </span>
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1025
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<pre style="margin: 0;">+<span id="LC1025" class="line" lang="c"> <span class="n" style="color: #333;">gzputc</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bfast</span><span class="p">,</span> <span class="n" style="color: #333;">qstr</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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1026
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<pre style="margin: 0;">+<span id="LC1026" class="line" lang="c"> <span class="n" style="color: #333;">gzprintf</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bfast</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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1027
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<pre style="margin: 0;">+<span id="LC1027" class="line" lang="c"> <span class="p">}</span></span>
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1020
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1028
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<pre style="margin: 0;"> <span id="LC1028" class="line" lang="c"> <span class="p">}</span></span>
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1021
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1029
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<pre style="margin: 0;"> <span id="LC1029" class="line" lang="c"> <span class="p">}</span></span>
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1022
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1030
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<pre style="margin: 0;"> <span id="LC1030" class="line" lang="c"> <span class="n" style="color: #333;">rand_ii</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1063" 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="1071" 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">@@ -1063,7 +1071,7 @@ int main(int argc, char *argv[])</td>
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1063
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<td class="new_line diff-line-num" data-linenumber="1071" 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">
1071
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<pre style="margin: 0;"> <span id="LC1071" class="line" lang="c"> <span class="p">}</span></span>
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1064
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1072
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<pre style="margin: 0;"> <span id="LC1072" class="line" lang="c"></span>
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1065
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<td class="new_line diff-line-num" data-linenumber="1073" 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">
1073
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<pre style="margin: 0;"> <span id="LC1073" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Open files</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1066" 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">
1066
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<td class="new_line diff-line-num old" data-linenumber="1074" 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="LC1066" class="line" lang="c"> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_fa</span> <span class="o" style="font-weight: 600;">=</span><span class="idiff left right"> </span><span class="n" style="color: #333;">xopen</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">optind</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="s" style="color: #d14;">"r"</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1067" 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="new_line diff-line-num new" data-linenumber="1074" 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">
1074
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<pre style="margin: 0;">+<span id="LC1074" class="line" lang="c"> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_fa</span> <span class="o" style="font-weight: 600;">=</span><span class="idiff left right"> </span><span class="n" style="color: #333;">xopen</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">optind</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="s" style="color: #d14;">"r"</span><span class="p">);</span></span>
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1067
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<td class="new_line diff-line-num" data-linenumber="1075" 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">
1075
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<pre style="margin: 0;"> <span id="LC1075" class="line" lang="c"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">fn_fai</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">optind</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">0</span><span class="p">]);</span> <span class="n" style="color: #333;">strcat</span><span class="p">(</span><span class="n" style="color: #333;">fn_fai</span><span class="p">,</span> <span class="s" style="color: #d14;">".fai"</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1068" 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">
1068
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<td class="new_line diff-line-num" data-linenumber="1076" 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">
1076
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<pre style="margin: 0;"> <span id="LC1076" class="line" lang="c"> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_fai</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fopen</span><span class="p">(</span><span class="n" style="color: #333;">fn_fai</span><span class="p">,</span> <span class="s" style="color: #d14;">"r"</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// NB: depends on returning NULL;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1069" 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">
1069
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<td class="new_line diff-line-num" data-linenumber="1077" 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">
1077
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<pre style="margin: 0;"> <span id="LC1077" class="line" lang="c"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">fn_tmp</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">optind</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span> <span class="n" style="color: #333;">strcat</span><span class="p">(</span><span class="n" style="color: #333;">fn_tmp</span><span class="p">,</span> <span class="s" style="color: #d14;">".mutations.txt"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1071" 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="1079" 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">@@ -1071,12 +1079,16 @@ int main(int argc, char *argv[])</td>
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1071
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<td class="new_line diff-line-num" data-linenumber="1079" 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">
1079
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<pre style="margin: 0;"> <span id="LC1079" class="line" lang="c"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">fn_tmp</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">optind</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span> <span class="n" style="color: #333;">strcat</span><span class="p">(</span><span class="n" style="color: #333;">fn_tmp</span><span class="p">,</span> <span class="s" style="color: #d14;">".mutations.vcf"</span><span class="p">);</span></span>
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1072
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<td class="new_line diff-line-num" data-linenumber="1080" 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">
1080
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<pre style="margin: 0;"> <span id="LC1080" class="line" lang="c"> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_vcf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xopen</span><span class="p">(</span><span class="n" style="color: #333;">fn_tmp</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">);</span></span>
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1073
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<td class="new_line diff-line-num" data-linenumber="1081" 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">
1081
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<pre style="margin: 0;"> <span id="LC1081" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">muts_only</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1074" 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">
1074
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<td class="new_line diff-line-num old" data-linenumber="1082" 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="LC1074" class="line" lang="c"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">fn_tmp</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">optind</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span> <span class="n" style="color: #333;">strcat</span><span class="p">(</span><span class="n" style="color: #333;">fn_tmp</span><span class="p">,</span> <span class="s" style="color: #d14;">".bfast.fastq"</span><span class="p">);</span></span>
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1075
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<td class="new_line diff-line-num old" data-linenumber="1082" 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="LC1075" class="line" lang="c"> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bfast</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xopen</span><span class="p">(</span><span class="n" style="color: #333;">fn_tmp</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1076" 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">
1076
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<td class="new_line diff-line-num old" data-linenumber="1082" 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="LC1076" class="line" lang="c"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">fn_tmp</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">optind</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span> <span class="n" style="color: #333;">strcat</span><span class="p">(</span><span class="n" style="color: #333;">fn_tmp</span><span class="p">,</span> <span class="s" style="color: #d14;">".bwa.read1.fastq"</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1077" 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">
1077
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<td class="new_line diff-line-num old" data-linenumber="1082" 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="LC1077" class="line" lang="c"> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bwa1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xopen</span><span class="p">(</span><span class="n" style="color: #333;">fn_tmp</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1078" 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">
1078
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<td class="new_line diff-line-num old" data-linenumber="1082" 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="LC1078" class="line" lang="c"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">fn_tmp</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">optind</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span> <span class="n" style="color: #333;">strcat</span><span class="p">(</span><span class="n" style="color: #333;">fn_tmp</span><span class="p">,</span> <span class="s" style="color: #d14;">".bwa.read2.fastq"</span><span class="p">);</span></span>
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1079
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<pre style="margin: 0;">-<span id="LC1079" class="line" lang="c"> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bwa2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xopen</span><span class="p">(</span><span class="n" style="color: #333;">fn_tmp</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">);</span></span>
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1082
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<pre style="margin: 0;">+<span id="LC1082" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">output_type</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">OUTPUT_TYPE_BWA</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1083" 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">
1083
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<pre style="margin: 0;">+<span id="LC1083" class="line" lang="c"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">fn_tmp</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">optind</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span> <span class="n" style="color: #333;">strcat</span><span class="p">(</span><span class="n" style="color: #333;">fn_tmp</span><span class="p">,</span> <span class="s" style="color: #d14;">".bfast.fastq.gz"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1084" 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">
1084
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<pre style="margin: 0;">+<span id="LC1084" class="line" lang="c"> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bfast</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gzopen</span><span class="p">(</span><span class="n" style="color: #333;">fn_tmp</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1085" 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">
1085
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<pre style="margin: 0;">+<span id="LC1085" class="line" lang="c"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1086" 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">
1086
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<pre style="margin: 0;">+<span id="LC1086" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">output_type</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">OUTPUT_TYPE_BFAST</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1087" 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">
1087
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<pre style="margin: 0;">+<span id="LC1087" class="line" lang="c"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">fn_tmp</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">optind</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span> <span class="n" style="color: #333;">strcat</span><span class="p">(</span><span class="n" style="color: #333;">fn_tmp</span><span class="p">,</span> <span class="s" style="color: #d14;">".bwa.read1.fastq.gz"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1088" 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">
1088
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<pre style="margin: 0;">+<span id="LC1088" class="line" lang="c"> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bwa1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gzopen</span><span class="p">(</span><span class="n" style="color: #333;">fn_tmp</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">);</span></span>
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1089
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<pre style="margin: 0;">+<span id="LC1089" class="line" lang="c"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">fn_tmp</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">optind</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span> <span class="n" style="color: #333;">strcat</span><span class="p">(</span><span class="n" style="color: #333;">fn_tmp</span><span class="p">,</span> <span class="s" style="color: #d14;">".bwa.read2.fastq.gz"</span><span class="p">);</span></span>
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1090
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<pre style="margin: 0;">+<span id="LC1090" class="line" lang="c"> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bwa2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gzopen</span><span class="p">(</span><span class="n" style="color: #333;">fn_tmp</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">);</span></span>
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1091
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<pre style="margin: 0;">+<span id="LC1091" class="line" lang="c"> <span class="p">}</span></span>
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1080
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1092
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<pre style="margin: 0;"> <span id="LC1092" class="line" lang="c"> <span class="p">}</span></span>
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1081
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1093
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<pre style="margin: 0;"> <span id="LC1093" class="line" lang="c"></span>
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1082
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1094
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<pre style="margin: 0;"> <span id="LC1094" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Run simulation</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1084" 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="1096" 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">@@ -1084,7 +1096,13 @@ int main(int argc, char *argv[])</td>
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1084
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1096
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<pre style="margin: 0;"> <span id="LC1096" class="line" lang="c"></span>
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1085
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1097
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<pre style="margin: 0;"> <span id="LC1097" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Close files</span></span>
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1086
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1098
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<pre style="margin: 0;"> <span id="LC1098" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">muts_only</span><span class="p">)</span> <span class="p">{</span></span>
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1087
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<td class="new_line diff-line-num old" data-linenumber="1099" 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="LC1087" class="line" lang="c"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_fa</span><span class="p">);</span> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bfast</span><span class="p">);</span> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bwa1</span><span class="p">);</span> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bwa2</span><span class="p">);</span> </span>
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1099
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<pre style="margin: 0;">+<span id="LC1099" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">output_type</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">OUTPUT_TYPE_BWA</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1100" 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">
1100
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<pre style="margin: 0;">+<span id="LC1100" class="line" lang="c"> <span class="n" style="color: #333;">gzclose</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bfast</span><span class="p">);</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="1101" 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">
1101
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<pre style="margin: 0;">+<span id="LC1101" class="line" lang="c"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1102" 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">
1102
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<pre style="margin: 0;">+<span id="LC1102" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">output_type</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">OUTPUT_TYPE_BFAST</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1103" 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">
1103
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<pre style="margin: 0;">+<span id="LC1103" class="line" lang="c"> <span class="n" style="color: #333;">gzclose</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bwa1</span><span class="p">);</span> <span class="n" style="color: #333;">gzclose</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bwa2</span><span class="p">);</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="1104" 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">
1104
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<pre style="margin: 0;">+<span id="LC1104" class="line" lang="c"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1105" 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">
1105
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<pre style="margin: 0;">+<span id="LC1105" class="line" lang="c"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_fa</span><span class="p">);</span> </span>
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1088
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1106
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<pre style="margin: 0;"> <span id="LC1106" class="line" lang="c"> <span class="p">}</span></span>
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1089
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<td class="new_line diff-line-num" data-linenumber="1107" 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">
1107
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<pre style="margin: 0;"> <span id="LC1107" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_fai</span><span class="p">)</span> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_fai</span><span class="p">);</span></span>
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1090
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1108
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<pre style="margin: 0;"> <span id="LC1108" class="line" lang="c"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_mut</span><span class="p">);</span></span>
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<li id="8b1a544f9bdc749248298113fcdb4d61b8852b21">
<a href="https://salsa.debian.org/med-team/dwgsim/-/compare/7dd19c7c56b00cbd3ecf5c57cd1fa13bd5ee8658...cc1268699bc3c40e6be51d57622451add0c4856e#8b1a544f9bdc749248298113fcdb4d61b8852b21"><strong>src/dwgsim_opt.c</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="32" 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="32" 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">@@ -32,6 +32,7 @@</td>
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32
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32
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stdint.h></span></span>
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33
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33
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <ctype.h></span></span>
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34
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34
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <string.h></span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <zlib.h></span></span>
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35
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36
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "mut.h"</span></span>
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36
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "dwgsim.h"</span></span>
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37
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38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "dwgsim_opt.h"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="56" 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">@@ -56,6 +57,7 @@ dwgsim_opt_t* dwgsim_opt_init()</td>
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56
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57
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="c"> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">rand_read</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mo" style="color: #099;">05</span><span class="p">;</span></span>
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57
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<td class="new_line diff-line-num" 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">
58
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="c"> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ILLUMINA</span><span class="p">;</span></span>
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58
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<td class="new_line diff-line-num" 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">
59
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="c"> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">strandedness</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="c"> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_one_strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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59
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61
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="c"> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max_n</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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60
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62
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="c"> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">flow_order</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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61
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63
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="c"> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">flow_order_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="67" 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="69" 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">@@ -67,7 +69,8 @@ dwgsim_opt_t* dwgsim_opt_init()</td>
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67
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="c"> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fn_muts_input</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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68
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="c"> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fn_muts_input_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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69
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="c"> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fn_regions_bed</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="c"> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_mut</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bfast</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bwa1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bwa2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="c"> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_mut</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" 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
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="c"> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bfast</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bwa1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_bwa2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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71
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="c"> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_fa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp_fai</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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72
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="c"> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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73
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="c"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="106" 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="109" 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">@@ -106,7 +109,7 @@ int dwgsim_opt_usage(dwgsim_opt_t *opt)</td>
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106
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" -r FLOAT rate of mutations [%.4f]</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mut_rate</span><span class="p">);</span></span>
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107
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" -F FLOAT frequency of given mutation to simulate low fequency somatic mutations [%.4f]</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mut_freq</span><span class="p">);</span></span>
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108
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" NB: freqeuncy F refers to the first strand of mutation, therefore mutations </span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span> </span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" on the second strand occ<span class="idiff left right">o</span>ur with a frequency of 1-F </span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" on the second strand occur with a frequency of 1-F </span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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110
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<td class="new_line diff-line-num" data-linenumber="113" 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">
113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" -R FLOAT fraction of mutations that are indels [%.2f]</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">indel_frac</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="111" 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">
111
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<td class="new_line diff-line-num" data-linenumber="114" 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">
114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" -X FLOAT probability an indel is extended [%.2f]</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">indel_extend</span><span class="p">);</span></span>
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112
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<td class="new_line diff-line-num" data-linenumber="115" 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">
115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" -I INT the minimum length indel [%d]</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">indel_min</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="116" 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="119" 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">@@ -116,10 +119,14 @@ int dwgsim_opt_usage(dwgsim_opt_t *opt)</td>
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<td class="old_line diff-line-num" data-linenumber="116" 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">
116
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<td class="new_line diff-line-num" data-linenumber="119" 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">
119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" 0: Illumina</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="117" 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">
117
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<td class="new_line diff-line-num" data-linenumber="120" 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">
120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" 1: SOLiD</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="118" 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">
118
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<td class="new_line diff-line-num" 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">
121
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" 2: Ion Torrent</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="119" 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">
119
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<td class="new_line diff-line-num old" data-linenumber="122" 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="LC119" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" -S INT generate <span class="idiff left right">reads</span> [%d]:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">strandedness</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="120" 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="new_line diff-line-num new" data-linenumber="122" 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">
122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" -S INT generate <span class="idiff left right">paired end reads with orientation</span> [%d]:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">strandedness</span><span class="p">);</span></span>
</pre>
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120
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<td class="new_line diff-line-num" 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="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" 0: default (opposite strand for Illumina, same strand for SOLiD/Ion Torrent)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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<td class="old_line diff-line-num" 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">
121
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<td class="new_line diff-line-num" data-linenumber="124" 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">
124
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" 1: same strand (mate pair)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="122" 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">
122
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<td class="new_line diff-line-num" data-linenumber="125" 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">
125
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" 2: opposite strand (paired end)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="123" 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="new_line diff-line-num new" data-linenumber="126" 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">
126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" -A INT generate paired end reads with read one [%d]:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_one_strand</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="123" 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="new_line diff-line-num new" data-linenumber="127" 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">
127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" 0: default (both, random)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="123" 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="new_line diff-line-num new" data-linenumber="128" 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">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" 1: forward genomic strand</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="123" 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="new_line diff-line-num new" data-linenumber="129" 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">
129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" 2: reverse genomic strand</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" data-linenumber="130" 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">
130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" -f STRING the flow order for Ion Torrent data [%s]</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">flow_order</span><span class="p">);</span></span>
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124
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<td class="new_line diff-line-num" data-linenumber="131" 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">
131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" -B use a per-base error rate for Ion Torrent data [%s]</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">__IS_TRUE</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">use_base_error</span><span class="p">));</span></span>
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125
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<td class="new_line diff-line-num" data-linenumber="132" 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">
132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" -H haploid mode [%s]</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">__IS_TRUE</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_hap</span><span class="p">));</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="133" 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="140" 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">@@ -133,6 +140,10 @@ int dwgsim_opt_usage(dwgsim_opt_t *opt)</td>
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<td class="old_line diff-line-num" data-linenumber="133" 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">
133
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" -q STRING a fixed base quality to apply (single character) [%s]</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fixed_quality</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"not using"</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fixed_quality</span><span class="p">);</span></span>
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134
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<td class="new_line diff-line-num" data-linenumber="141" 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">
141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" -Q FLOAT standard deviation of the base quality scores [%.2lf]</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fixed_quality</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">quality_std</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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135
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<td class="new_line diff-line-num" data-linenumber="142" 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">
142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" -s INT standard deviation of the distance for pairs [%.3f]</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">std_dev</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="143" 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">
143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" -o INT output type for the FASTQ files [%d]:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">output_type</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="144" 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">
144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" 0: interleaved (bfast) and per-read-end (bwa)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="136" 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="new_line diff-line-num new" data-linenumber="145" 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">
145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" 1: per-read-end (bwa) only</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="146" 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">
146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" 2: interleaved (bfast) only</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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136
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<td class="new_line diff-line-num" data-linenumber="147" 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">
147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" -h print this message</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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137
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<td class="new_line diff-line-num" data-linenumber="148" 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">
148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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138
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<td class="new_line diff-line-num" data-linenumber="149" 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">
149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Note: For SOLiD mate pair reads and BFAST, the first read is F3 and the second is R3. For SOLiD mate pair reads</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="192" 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="203" 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">@@ -192,7 +203,7 @@ dwgsim_opt_parse(dwgsim_opt_t *opt, int argc, char *argv[])</td>
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192
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">c</span><span class="p">;</span></span>
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193
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204
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">muts_input_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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194
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="c"> </span>
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<td class="old_line diff-line-num old" data-linenumber="195" 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">
195
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<td class="new_line diff-line-num old" data-linenumber="206" 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="LC195" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getopt</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="s" style="color: #d14;">"id:s:N:C:1:2:e:E:r:F:R:X:I:c:S:n:y:BHf:z:Mm:b:v:x:P:q:Q:h"</span><span class="p">))</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getopt</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="s" style="color: #d14;">"id:s:N:C:1:2:e:E:r:F:R:X:I:c:S:<span class="idiff left">A:</span>n:y:BHf:z:Mm:b:v:x:P:q:Q:<span class="idiff right">o:</span>h"</span><span class="p">))</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="196" 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">
196
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<td class="new_line diff-line-num" data-linenumber="207" 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">
207
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="c"> <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="197" 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">
197
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<td class="new_line diff-line-num" data-linenumber="208" 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">
208
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'i'</span><span class="p">:</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_inner</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="198" 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">
198
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<td class="new_line diff-line-num" data-linenumber="209" 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">
209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'d'</span><span class="p">:</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">dist</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dwgsim_atoi</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">,</span> <span class="sc" style="color: #d14;">'d'</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="210" 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="221" 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">@@ -210,6 +221,7 @@ dwgsim_opt_parse(dwgsim_opt_t *opt, int argc, char *argv[])</td>
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<td class="old_line diff-line-num" data-linenumber="210" 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">
210
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<td class="new_line diff-line-num" data-linenumber="221" 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">
221
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'I'</span><span class="p">:</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">indel_min</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dwgsim_atoi</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">,</span> <span class="sc" style="color: #d14;">'I'</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="211" 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">
211
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<td class="new_line diff-line-num" data-linenumber="222" 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">
222
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'c'</span><span class="p">:</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dwgsim_atoi</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">,</span> <span class="sc" style="color: #d14;">'c'</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="212" 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">
212
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<td class="new_line diff-line-num" data-linenumber="223" 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">
223
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'S'</span><span class="p">:</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">strandedness</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dwgsim_atoi</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">,</span> <span class="sc" style="color: #d14;">'S'</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="213" 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="new_line diff-line-num new" data-linenumber="224" 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">
224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'A'</span><span class="p">:</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_one_strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dwgsim_atoi</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">,</span> <span class="sc" style="color: #d14;">'A'</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="213" 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">
213
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<td class="new_line diff-line-num" data-linenumber="225" 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">
225
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'n'</span><span class="p">:</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max_n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dwgsim_atoi</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">,</span> <span class="sc" style="color: #d14;">'n'</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="214" 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">
214
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<td class="new_line diff-line-num" data-linenumber="226" 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">
226
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'y'</span><span class="p">:</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">rand_read</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">atof</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">);</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="215" 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">
215
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<td class="new_line diff-line-num" data-linenumber="227" 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">
227
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'f'</span><span class="p">:</span> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="228" 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="240" 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">@@ -228,6 +240,7 @@ dwgsim_opt_parse(dwgsim_opt_t *opt, int argc, char *argv[])</td>
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<td class="old_line diff-line-num" data-linenumber="228" 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">
228
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<td class="new_line diff-line-num" data-linenumber="240" 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">
240
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'P'</span><span class="p">:</span> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_prefix</span><span class="p">);</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strdup</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">);</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="229" 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">
229
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<td class="new_line diff-line-num" data-linenumber="241" 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">
241
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'q'</span><span class="p">:</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fixed_quality</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strdup</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">);</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="230" 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">
230
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<td class="new_line diff-line-num" data-linenumber="242" 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">
242
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'Q'</span><span class="p">:</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">quality_std</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">atof</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">);</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="231" 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">
</td>
<td class="new_line diff-line-num new" data-linenumber="243" 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">
243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'o'</span><span class="p">:</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">output_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">atoi</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">);</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="231" 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">
231
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244
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="c"> <span class="nl">default:</span> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Unrecognized option: -%c</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">);</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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232
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245
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="c"> <span class="p">}</span></span>
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233
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246
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="290" 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">@@ -277,6 +290,7 @@ dwgsim_opt_parse(dwgsim_opt_t *opt, int argc, char *argv[])</td>
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277
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<td class="new_line diff-line-num" data-linenumber="290" 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">
290
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="c"> <span class="n" style="color: #333;">__check_option</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">indel_min</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">INT32_MAX</span><span class="p">,</span> <span class="s" style="color: #d14;">"-I"</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" 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">
278
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<td class="new_line diff-line-num" data-linenumber="291" 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">
291
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="c"> <span class="n" style="color: #333;">__check_option</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data_type</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="s" style="color: #d14;">"-c"</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="279" 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">
279
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<td class="new_line diff-line-num" data-linenumber="292" 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">
292
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="c"> <span class="n" style="color: #333;">__check_option</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">strandedness</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="s" style="color: #d14;">"-S"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="293" 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">
293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="c"> <span class="n" style="color: #333;">__check_option</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_one_strand</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="s" style="color: #d14;">"-A"</span><span class="p">);</span></span>
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280
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<td class="new_line diff-line-num" data-linenumber="294" 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">
294
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="c"> <span class="n" style="color: #333;">__check_option</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max_n</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">INT32_MAX</span><span class="p">,</span> <span class="s" style="color: #d14;">"-n"</span><span class="p">);</span></span>
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281
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<td class="new_line diff-line-num" data-linenumber="295" 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">
295
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="c"> <span class="n" style="color: #333;">__check_option</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">rand_read</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">"-y"</span><span class="p">);</span></span>
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282
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<td class="new_line diff-line-num" data-linenumber="296" 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">
296
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">IONTORRENT</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data_type</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">flow_order</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="296" 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="310" 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">@@ -296,17 +310,7 @@ dwgsim_opt_parse(dwgsim_opt_t *opt, int argc, char *argv[])</td>
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296
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310
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Warning: remember to use the -P option with dwgsim_eval</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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297
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311
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="c"> <span class="p">}</span></span>
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298
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<td class="new_line diff-line-num" data-linenumber="312" 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">
312
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<pre style="margin: 0;"> <span id="LC312" class="line" lang="c"></span>
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<td class="old_line diff-line-num old" data-linenumber="299" 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">
299
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<td class="new_line diff-line-num old" data-linenumber="313" 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="LC299" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]){</span> <span class="c1" style="color: #998; font-style: italic;">//paired end / mate pair</span></span>
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<td class="old_line diff-line-num old" data-linenumber="300" 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">
300
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_inner</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="301" 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">
301
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<td class="new_line diff-line-num old" data-linenumber="313" 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="LC301" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">dist</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">std_dev</span><span class="p">;</span></span>
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302
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<pre style="margin: 0;">-<span id="LC302" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">6</span><span class="p">){</span></span>
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303
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<pre style="margin: 0;">-<span id="LC303" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Error: command line option -d is too small for the read length (%d)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">dist</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC304" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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305
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="c"> <span class="p">}</span></span>
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306
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">4</span><span class="p">){</span></span>
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307
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Warning: command line option -d is small for the read length (%d). Generation speed could be affected.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">dist</span><span class="p">);</span></span>
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308
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<pre style="margin: 0;">-<span id="LC308" class="line" lang="c"> <span class="p">}</span></span>
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309
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="c"> <span class="p">}</span></span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="c"> <span class="n" style="color: #333;">__check_option</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">output_type</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="s" style="color: #d14;">"-o"</span><span class="p">);</span></span>
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314
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="c"></span>
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315
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="c"> <span class="k" style="font-weight: 600;">switch</span><span class="p">(</span><span class="n" style="color: #333;">muts_input_type</span><span class="p">)</span> <span class="p">{</span></span>
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316
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="mh" style="color: #099;">0x0</span><span class="p">:</span></span>
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<a href="https://salsa.debian.org/med-team/dwgsim/-/compare/7dd19c7c56b00cbd3ecf5c57cd1fa13bd5ee8658...cc1268699bc3c40e6be51d57622451add0c4856e#39520621c459de4e7f9bbce08e8cb714f082ccb8"><strong>src/dwgsim_opt.h</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef DWGSIM_OPT_H</span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define DWGSIM_OPT_H</span></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "zlib.h"</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="c"></span>
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4
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define ERROR_RATE_NUM_RANDOM_READS 1000000</span></span>
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5
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="c"></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define OUTPUT_TYPE_ALL 0</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define OUTPUT_TYPE_BWA 1</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define OUTPUT_TYPE_BFAST 2</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="c"></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="c"></span>
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6
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="c"><span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">struct</span> <span class="p">{</span></span>
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7
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">by</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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8
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="c"><span class="p">}</span> <span class="n" style="color: #333;">error_t</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="31" 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">@@ -24,6 +31,7 @@ typedef struct {</td>
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24
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">max_n</span><span class="p">;</span></span>
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25
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32
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">data_type</span><span class="p">;</span></span>
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26
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33
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">strandedness</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="34" 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">
34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">read_one_strand</span><span class="p">;</span></span>
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27
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35
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int8_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flow_order</span><span class="p">;</span></span>
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28
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36
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">flow_order_len</span><span class="p">;</span></span>
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29
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">use_base_error</span><span class="p">;</span></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">@@ -37,12 +45,13 @@ typedef struct {</td>
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45
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fn_regions_bed</span><span class="p">;</span></span>
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46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_mut</span><span class="p">;</span></span>
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_vcf</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">FILE</span></span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_bfast</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">FILE</span></span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_bwa1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">FILE</span></span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_bwa2</span><span class="p">;</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left right">gzFile</span></span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_bfast</span><span class="p">;</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left right">gzFile</span></span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_bwa1</span><span class="p">;</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left right">gzFile</span></span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_bwa2</span><span class="p">;</span></span>
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43
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51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_fa</span><span class="p">;</span></span>
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44
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52
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp_fai</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">read_prefix</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">output_type</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="c"><span class="p">}</span> <span class="n" style="color: #333;">dwgsim_opt_t</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="c"><span class="n" style="color: #333;">dwgsim_opt_t</span><span class="o" style="font-weight: 600;">*</span> </span>
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<a href="https://salsa.debian.org/med-team/dwgsim/-/compare/7dd19c7c56b00cbd3ecf5c57cd1fa13bd5ee8658...cc1268699bc3c40e6be51d57622451add0c4856e#018f262518f189e45af7e9d496e0bc11d93d630d"><strong>src/mut_txt.c</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">@@ -58,7 +58,7 @@ muts_txt_t *muts_txt_init(FILE *fp, contigs_t *c)</td>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="c"> <span class="n" style="color: #333;">prev_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Error: contig not found [%s]</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Error: <span class="idiff left">mutation </span>contig not found <span class="idiff right">or out of order </span>[%s]</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">contigs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="p">{</span></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">@@ -15,14 +15,17 @@ popd</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir </span>tmp</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Generate the new test data</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="shell">./dwgsim <span class="nt" style="color: #000080;">-z</span> 13 <span class="nt" style="color: #000080;">-N</span> 10000 samtools/examples/ex1.fa ex1.test</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell">./dwgsim <span class="nt" style="color: #000080;">-z</span> 13 <span class="nt" style="color: #000080;">-N</span> 10000 samtools/examples/ex1.fa <span class="idiff left right">tmp/</span>ex1.test</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Test the differences</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>FILE <span class="k" style="font-weight: 600;">in</span> <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">ls</span> <span class="nt" style="color: #000080;">-1</span> ex1.test<span class="k" style="font-weight: 600;">*</span><span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span><span class="idiff left">GZ</span>FILE <span class="k" style="font-weight: 600;">in</span> <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">ls</span> <span class="nt" style="color: #000080;">-1</span> <span class="idiff">tmp/</span>ex1.test<span class="k" style="font-weight: 600;">*</span><span class="idiff right">gz</span><span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="shell"><span class="k" style="font-weight: 600;">do </span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>diff <span class="nt" style="color: #000080;">-q</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">FILE</span><span class="k" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">TESTDATADIR</span><span class="k" style="font-weight: 600;">}</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">FILE</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">gunzip</span> <span class="nv" style="color: #008080;">$GZFILE</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"> <span class="nv" style="color: #008080;">FILE</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="nv" style="color: #008080;">$GZFILE</span> .gz<span class="si" style="color: #d14;">)</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"> diff <span class="nt" style="color: #000080;">-q</span> tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">FILE</span><span class="k" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">TESTDATADIR</span><span class="k" style="font-weight: 600;">}</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">FILE</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Clean up the testdata</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="shell">find <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">TESTDATADIR</span><span class="k" style="font-weight: 600;">}</span> <span class="se" style="color: #d14;">\!</span> <span class="nt" style="color: #000080;">-name</span> <span class="s2" style="color: #d14;">"*gz"</span> <span class="nt" style="color: #000080;">-type</span> f | <span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: #000080;">-v</span> sh<span class="nv" style="color: #008080;">$ </span>| xargs <span class="nb" style="color: #0086b3;">rm</span><span class="p">;</span> </span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-r</span> tmp<span class="p">;</span></span></pre>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-r</span> tmp</span></pre>
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