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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/libssw">Debian Med / libssw</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/libssw/-/commit/c9c6106f955eac1ec9d8a40cc85495ccf3178810">c9c6106f</a></strong>
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<span>by Andreas Tille</span>
<i>at 2022-05-24T07:21:16+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.2.4</pre>
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<h4>26 changed files:</h4>
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README.md
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demo/pRead.fa
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src/.gitignore
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src/Makefile
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src/example.cpp
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src/kseq.h
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src/main.c
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src/pyssw.py
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src/ssw.c
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src/ssw.h
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src/ssw_cpp.cpp
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src/ssw_cpp.h
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src/ssw_lib.py
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<h4>Changes:</h4>
<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/libssw/-/commit/c9c6106f955eac1ec9d8a40cc85495ccf3178810#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<td class="new_line diff-line-num old" data-linenumber="1" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;">#SSW Library: An SIMD Smith-Waterman C/C++/Python/Java Library for Use in Genomic Applications</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># SSW Library</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown"></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## An SIMD Smith-Waterman C/C++/Python/Java/R Library for Use in Genomic Applications</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="LC4" class="line" lang="markdown"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown">License: MIT</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">@@ -10,21 +12,24 @@ The above copyright notice and this permission notice shall be included in all c</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC13" class="line" lang="markdown">THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC14" class="line" lang="markdown"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC13" class="line" lang="markdown">Author: </span>
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<td class="new_line diff-line-num old" data-linenumber="15" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC14" class="line" lang="markdown">C implementation: Mengyao Zhao </span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC15" class="line" lang="markdown">C++ wrapper: Wan-Ping Lee </span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC16" class="line" lang="markdown">Python wrapper: Yongan Zhao </span>
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<td class="old_line diff-line-num old" data-linenumber="17" 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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<td class="new_line diff-line-num old" data-linenumber="15" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC17" class="line" lang="markdown">Java wrapper: Daniel Cameron</span>
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<td class="old_line diff-line-num new" data-linenumber="18" 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="15" 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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown">Authors:</span>
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<td class="old_line diff-line-num new" data-linenumber="18" 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="16" 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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown"><span class="p">*</span> C implementation: Mengyao Zhao</span>
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<td class="old_line diff-line-num new" data-linenumber="18" 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="17" 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">
17
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"><span class="p">*</span> C++ wrapper: Wan-Ping Lee</span>
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18
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown"><span class="p">*</span> Python wrapper: Yongan Zhao</span>
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19
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown"><span class="p">*</span> Java wrapper: Daniel Cameron</span>
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20
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown"><span class="p">*</span> R package: Nan Xiao</span>
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21
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown"></span>
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22
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown">Contact:</span>
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<td class="new_line diff-line-num new" data-linenumber="23" 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">
23
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"><span class="p">*</span> Mengyao Zhao <span class="nv" style="color: #008080;"><zhaomengyao@gmail.com></span></span>
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<td class="new_line diff-line-num new" data-linenumber="24" 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">
24
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown"><span class="p">*</span> Wan-Ping Lee <span class="nv" style="color: #008080;"><wanping.lee@gmail.com></span></span>
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25
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown"><span class="p">*</span> Yongan Zhao <span class="nv" style="color: #008080;"><zhaoyanswill@gmail.com></span></span>
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<td class="new_line diff-line-num new" data-linenumber="26" 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">
26
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown"><span class="p">*</span> Daniel Cameron <span class="nv" style="color: #008080;"><cameron.d@wehi.edu.au></span></span>
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27
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown"><span class="p">*</span> Nan Xiao <span class="nv" style="color: #008080;"><me@nanx.me></span></span>
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18
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28
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC28" class="line" lang="markdown"></span>
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19
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<td class="new_line diff-line-num old" data-linenumber="29" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC19" class="line" lang="markdown">Contact: </span>
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20
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<td class="new_line diff-line-num old" data-linenumber="29" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC20" class="line" lang="markdown">Mengyao Zhao <span class="nv" style="color: #008080;"><zhaomengyao@gmail.com></span> </span>
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21
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<td class="new_line diff-line-num old" data-linenumber="29" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC21" class="line" lang="markdown">Wan-Ping Lee <span class="nv" style="color: #008080;"><wanping.lee@gmail.com></span> </span>
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<td class="old_line diff-line-num old" data-linenumber="22" 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">
22
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<td class="new_line diff-line-num old" data-linenumber="29" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC22" class="line" lang="markdown">Yongan Zhao <span class="nv" style="color: #008080;"><zhaoyanswill@gmail.com></span> </span>
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23
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<td class="new_line diff-line-num old" data-linenumber="29" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC23" class="line" lang="markdown">Daniel Cameron <span class="nv" style="color: #008080;"><cameron.d@wehi.edu.au></span> </span>
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29
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown">Last revision: 2022-May-20</span>
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24
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30
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC30" class="line" lang="markdown"></span>
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25
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<td class="new_line diff-line-num old" data-linenumber="31" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC25" class="line" lang="markdown"><span class="idiff left right deletion">Last revision: 06/29/2016</span></span>
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31
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC31" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;"><span class="idiff left right addition">## Overview</span></span></span>
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26
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC32" class="line" lang="markdown"></span>
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<td class="new_line diff-line-num old" data-linenumber="33" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC27" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">##Overview</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="LC33" class="line" lang="markdown">SSW is a fast implementation of the Smith-Waterman algorithm, which uses the Single-Instruction Multiple-Data (SIMD) instructions to parallelize the algorithm at the instruction level. SSW library provides an API that can be flexibly used by programs written in C, C++ and other languages. We also provide a software that can do protein and genome alignment directly. Current version of our implementation is ~50 times faster than an ordinary Smith-Waterman. It can return the Smith-Waterman score, alignment location and traceback path (cigar) of the optimal alignment accurately; and return the sub-optimal alignment score and location heuristically.</span>
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34
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC34" class="line" lang="markdown"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC35" class="line" lang="markdown">The Debian package of this library can be achieved here:</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">@@ -34,45 +39,49 @@ Note: When SSW open a gap, the gap open penalty alone is applied.</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC40" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## C/C++ interface</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="LC41" class="line" lang="markdown"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC37" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">###How to use the API</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC38" class="line" lang="markdown">The API files include ssw.h and ssw.c, which can be directly used by any C or C++ program. For the C++ users who are more comfortable to use a C++ style interface, an additional C++ wrapper is provided with the file ssw_cpp.cpp and ssw_cpp.h.</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC42" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### How to use the API</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC43" class="line" lang="markdown"></span>
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<td class="new_line diff-line-num new" data-linenumber="44" 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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC44" class="line" lang="markdown">The API files include <span class="sb" style="color: #d14;">`ssw.h`</span> and <span class="sb" style="color: #d14;">`ssw.c`</span>, which can be directly used by any C or C++ program. For the C++ users who are more comfortable to use a C++ style interface, an additional C++ wrapper is provided with the file <span class="sb" style="color: #d14;">`ssw_cpp.cpp`</span> and <span class="sb" style="color: #d14;">`ssw_cpp.h`</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="LC45" class="line" lang="markdown"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC46" class="line" lang="markdown">To use the C style API, please:</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC47" class="line" lang="markdown"></span>
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<td class="old_line diff-line-num old" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="48" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC42" class="line" lang="markdown"><span class="p">1.</span> Download ssw.h and ssw.c, and put them in the same folder of your own program files.</span>
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<td class="new_line diff-line-num old" data-linenumber="48" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC43" class="line" lang="markdown"><span class="p">2.</span> Write #include "ssw.h" into your file that will call the API functions.</span>
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<td class="new_line diff-line-num new" data-linenumber="48" 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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC48" class="line" lang="markdown"><span class="p">1.</span> Download <span class="sb" style="color: #d14;"><span class="idiff left addition">`</span>ssw.h<span class="idiff addition">`</span></span> and <span class="sb" style="color: #d14;"><span class="idiff addition">`</span>ssw.c<span class="idiff right addition">`</span></span>, and put them in the same folder of your own program files.</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC49" class="line" lang="markdown"><span class="p">2.</span> Write <span class="sb" style="color: #d14;"><span class="idiff left addition">`</span>#include "ssw.h"<span class="idiff right addition">`</span></span> into your file that will call the API functions.</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC50" class="line" lang="markdown"><span class="p">3.</span> The API files are ready to be compiled together with your own C/C++ files.</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC51" class="line" lang="markdown"></span>
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<td class="new_line diff-line-num old" data-linenumber="52" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC46" class="line" lang="markdown">The API function descriptions are in the file ssw.h. One simple example of the API usage is example.c. The Smith-Waterman penalties need to be integers. Small penalty numbers such as: match: 2, mismatch: -1, gap open (the total penalty when one gap is opened): -3, gap extension: -1 are recommended, which will lead to shorter running time.<span class="idiff left right deletion"> </span></span>
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<td class="new_line diff-line-num new" data-linenumber="52" 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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC52" class="line" lang="markdown">The API function descriptions are in the file <span class="sb" style="color: #d14;"><span class="idiff left addition">`</span>ssw.h<span class="idiff addition">`</span></span>. One simple example of the API usage is <span class="sb" style="color: #d14;"><span class="idiff addition">`</span>example.c<span class="idiff right addition">`</span></span>. The Smith-Waterman penalties need to be integers. Small penalty numbers such as: match: 2, mismatch: -1, gap open (the total penalty when one gap is opened): -3, gap extension: -1 are recommended, which will lead to shorter running time.</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC53" class="line" lang="markdown"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC54" class="line" lang="markdown">To use the C++ style API, please:</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC55" class="line" lang="markdown"></span>
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<td class="new_line diff-line-num old" data-linenumber="56" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC50" class="line" lang="markdown"><span class="p">1.</span> Download ssw.h, ssw.c, ssw_cpp.cpp and ssw_cpp.h<span class="idiff left right deletion"> and</span> put them in the same folder of your own program files.</span>
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<td class="new_line diff-line-num old" data-linenumber="56" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC51" class="line" lang="markdown"><span class="p">2.</span> Write #include "ssw_cpp.h" into your file that will call the API functions.</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC56" class="line" lang="markdown"><span class="p">1.</span> Download <span class="sb" style="color: #d14;"><span class="idiff left addition">`</span>ssw.h<span class="idiff addition">`</span></span>, <span class="sb" style="color: #d14;"><span class="idiff addition">`</span>ssw.c<span class="idiff addition">`</span></span>, <span class="sb" style="color: #d14;"><span class="idiff addition">`</span>ssw_cpp.cpp<span class="idiff addition">`</span></span> and <span class="sb" style="color: #d14;"><span class="idiff addition">`</span>ssw_cpp.h<span class="idiff addition">`</span></span><span class="idiff right addition">,</span> put them in the same folder of your own program files.</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC57" class="line" lang="markdown"><span class="p">2.</span> Write <span class="sb" style="color: #d14;"><span class="idiff left addition">`</span>#include "ssw_cpp.h"<span class="idiff right addition">`</span></span> into your file that will call the API functions.</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC58" class="line" lang="markdown"><span class="p">3.</span> The API files are ready to be compiled together with your own C/C++ files.</span>
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59
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC59" class="line" lang="markdown"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC54" class="line" lang="markdown">The API function descriptions are in the file ssw_cpp.h. A simple example of using the C++ API is example.cpp.</span>
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60
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC60" class="line" lang="markdown">The API function descriptions are in the file <span class="sb" style="color: #d14;">`ssw_cpp.h`</span>. A simple example of using the C++ API is <span class="sb" style="color: #d14;">`example.cpp`</span>.</span>
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61
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC61" class="line" lang="markdown"></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC62" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Speed and memory usage of the API</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="LC63" class="line" lang="markdown"></span>
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<td class="new_line diff-line-num old" data-linenumber="64" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC56" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;"><span class="idiff left right deletion">###Speed and memory usage of the API</span></span></span>
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<td class="new_line diff-line-num old" data-linenumber="64" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC57" class="line" lang="markdown"><span class="idiff left right deletion">Test data set: </span></span>
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58
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<td class="new_line diff-line-num old" data-linenumber="64" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC58" class="line" lang="markdown">Target sequence: reference genome of E. coli strain 536 (4,938,920 nucleotides) from NCBI</span>
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59
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<td class="new_line diff-line-num old" data-linenumber="64" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC59" class="line" lang="markdown">Query sequences: 1000 reads of Ion Torrent sequenced E. coli strain DH10B (C23-140, 318 PGM Run, 11/2011), read length: ~25-540 bp, most reads are ~200 bp</span>
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64
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC64" class="line" lang="markdown"><span class="idiff left right addition">Test data set:</span></span>
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65
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC65" class="line" lang="markdown"></span>
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66
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC66" class="line" lang="markdown"><span class="p"><span class="idiff left addition">*</span></span><span class="idiff addition"> </span>Target sequence: reference genome of <span class="idiff addition">_</span>E. coli<span class="idiff right addition">_</span> strain 536 (4,938,920 nucleotides) from NCBI</span>
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67
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC67" class="line" lang="markdown"><span class="p"><span class="idiff left addition">*</span></span><span class="idiff addition"> </span>Query sequences: 1000 reads of Ion Torrent sequenced <span class="idiff addition">_</span>E. coli<span class="idiff right addition">_</span> strain DH10B (C23-140, 318 PGM Run, 11/2011), read length: ~25-540 bp, most reads are ~200 bp</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC68" class="line" lang="markdown"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC69" class="line" lang="markdown">CPU time:</span>
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62
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70
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC70" class="line" lang="markdown"></span>
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63
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC71" class="line" lang="markdown"><span class="p">*</span> AMD CPU: default penalties: ~880 seconds; -m1 -x3 -o5 -e2: ~460 seconds</span>
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64
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<td class="new_line diff-line-num old" data-linenumber="72" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC64" class="line" lang="markdown"><span class="p">*</span> Intel CPU: default penalties: ~960 seconds; -m1 -x3 -o5 -e2: ~500 seconds<span class="idiff left right deletion"> </span></span>
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72
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC72" class="line" lang="markdown"><span class="p">*</span> Intel CPU: default penalties: ~960 seconds; -m1 -x3 -o5 -e2: ~500 seconds</span>
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65
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73
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC73" class="line" lang="markdown"></span>
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66
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC74" class="line" lang="markdown">Memory usage: ~40MB</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC68" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">###Install the software</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC76" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">###<span class="idiff left right addition"> </span>Install the software</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="LC77" class="line" lang="markdown"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC78" class="line" lang="markdown"><span class="p">1.</span> Download the software from https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library.</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC71" class="line" lang="markdown"><span class="p">2.</span> cd src</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC72" class="line" lang="markdown"><span class="p">3.</span> make</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC73" class="line" lang="markdown"><span class="p">4.</span> The executable file will be ssw_test.</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC79" class="line" lang="markdown"><span class="p">2.</span> <span class="sb" style="color: #d14;">`cd src`</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC80" class="line" lang="markdown"><span class="p">3.</span> <span class="sb" style="color: #d14;">`make`</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC81" class="line" lang="markdown"><span class="p">4.</span> The executable file will be <span class="sb" style="color: #d14;">`ssw_test`</span>.</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC83" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Run the software</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="LC84" class="line" lang="markdown"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC75" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">###Run the software</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="LC85" class="line" lang="markdown"><span class="p">```</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="LC86" class="line" lang="markdown">Usage: ssw_test [options] ... <target.fasta> <query.fasta>(or <query.fastq>)</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC87" class="line" lang="markdown">Options:</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">@@ -89,15 +98,18 @@ Options:</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC98" class="line" lang="markdown"> -h If -s is used, include header in SAM output.</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC99" class="line" lang="markdown"><span class="p">```</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="LC100" class="line" lang="markdown"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC92" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">###Software input</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC101" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Software input</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="LC103" class="line" lang="markdown">The input files can be in FASTA or FASTQ format. Both target and query files can contain multiple sequences. Each sequence in the query file will be aligned with all sequences in the target file. If your target file has N sequences and your query file has M sequences, the results will have M<span class="err" style="color: #a61717; background-color: #e3d2d2;">*</span>N alignments.</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC104" class="line" lang="markdown"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC95" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">###Software output</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC96" class="line" lang="markdown">The software can output SAM format or BLAST like format results. </span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC105" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Software output</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC107" class="line" lang="markdown">The software can output SAM format or BLAST like format results.</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC109" class="line" lang="markdown"><span class="p">1.</span> SAM format output:</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC110" class="line" lang="markdown"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC111" class="line" lang="markdown">Example:</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC113" class="line" lang="markdown"><span class="p">```</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="LC114" class="line" lang="markdown">@HD VN:1.4 SO:queryname</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC115" class="line" lang="markdown">@SQ SN:chr1 LN:1001</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -111,7 +123,9 @@ Y:26750420:R:-132;None;None/1 0 chr1 120 4 2M1I4M3D3M1I7M2I9M2D6M1I8M</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC123" class="line" lang="markdown"><span class="p">```</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="LC125" class="line" lang="markdown">What is the output?</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC114" class="line" lang="markdown">Please check the document "The SAM Format Specification" at: http://samtools.sourceforge.net/SAM1.pdf for the full description.</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC127" class="line" lang="markdown">Please check the document "The SAM Format Specification" at: http://samtools.github.io/hts-specs/SAMv1.pdf for the full description.</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC129" class="line" lang="markdown">The additional optional field "ZS" indicates the suboptimal alignment score. For example, the 1st record in the upper example means the optimal alignment score of the given sequence is 37; the suboptimal alignment score is 28; the mismatch and INDEL base count within the aligned fragment of the read is 11.</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC131" class="line" lang="markdown"><span class="p">2.</span> An example of the BLAST like output:</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">@@ -135,24 +149,33 @@ Query: 3 GA-AGAGTTAATTTAAGTCACTTCAAACAGATTAC-GTA-TCTTTT-TTTTCCCT 5</td>
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149
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC149" class="line" lang="markdown">...</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC150" class="line" lang="markdown"><span class="p">```</span></span>
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151
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC151" class="line" lang="markdown"></span>
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138
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC138" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">##Python interface</span></span>
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152
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC152" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Python interface</span></span>
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153
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC153" class="line" lang="markdown"></span>
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<td class="new_line diff-line-num new" data-linenumber="154" 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">
154
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC154" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### How to use the Python wrapper `ssw_lib.py`</span></span>
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139
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155
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC155" class="line" lang="markdown"></span>
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140
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<td class="new_line diff-line-num old" data-linenumber="156" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC140" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;"><span class="idiff left deletion">###How t</span>o use th<span class="idiff deletion">e p</span>ython <span class="idiff right deletion">wrapper ssw_lib.py</span></span></span>
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<td class="old_line diff-line-num new" data-linenumber="141" 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="156" 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">
156
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC156" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left addition">`ssw_lib.py`</span></span><span class="idiff addition"> is a Python wrapper that fully supports APIs of the C library. T</span>o use th<span class="idiff addition">is P</span>ython <span class="idiff right addition">library, C programming knowledge is not required.</span></span>
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141
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157
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC157" class="line" lang="markdown"></span>
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142
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<td class="new_line diff-line-num old" data-linenumber="158" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC142" class="line" lang="markdown"><span class="idiff left deletion">ssw_lib.py is a Python wrapper that fully supports APIs of the C library. </span>To use th<span class="idiff deletion">is</span> Python <span class="idiff right deletion">library, C programming knowledge is not required.</span></span>
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158
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC158" class="line" lang="markdown">To use th<span class="idiff left addition">e</span> Python <span class="idiff right addition">wrapper, please:</span></span>
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143
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159
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC159" class="line" lang="markdown"></span>
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144
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<td class="new_line diff-line-num old" data-linenumber="160" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC144" class="line" lang="markdown">To use the python wrapper, please:</span>
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160
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC160" class="line" lang="markdown"><span class="p">1.</span> Compile the <span class="sb" style="color: #d14;">`src`</span> folder by either using the <span class="sb" style="color: #d14;">`makefile`</span> or by compiling a dynamic shared library with <span class="sb" style="color: #d14;">`gcc`</span>:</span>
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161
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC161" class="line" lang="markdown"></span>
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162
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC162" class="line" lang="markdown"><span class="p">```</span></span>
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<td class="new_line diff-line-num new" data-linenumber="163" 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">
163
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC163" class="line" lang="markdown">gcc -Wall -O3 -pipe -fPIC -shared -rdynamic -o libssw.so ssw.c ssw.h</span>
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164
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC164" class="line" lang="markdown"><span class="p">```</span></span>
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165
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC165" class="line" lang="markdown"></span>
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<td class="new_line diff-line-num new" data-linenumber="166" 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">
166
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC166" class="line" lang="markdown"><span class="p">2.</span> Put <span class="sb" style="color: #d14;">`libssw.so`</span> and <span class="sb" style="color: #d14;">`ssw_lib.py`</span> in the same directory of your own program files or directories in sys.paths.</span>
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167
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC167" class="line" lang="markdown"></span>
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<td class="new_line diff-line-num new" data-linenumber="168" 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">
168
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC168" class="line" lang="markdown"><span class="p">3.</span> The <span class="sb" style="color: #d14;">`LD_LIBRARY_PATH`</span> environment variable may need to be modified to include the directory of the dynamic library <span class="sb" style="color: #d14;">`libssw.so`</span> by one of the two following mathods:</span>
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145
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169
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC169" class="line" lang="markdown"></span>
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146
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<td class="new_line diff-line-num old" data-linenumber="170" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC146" class="line" lang="markdown"><span class="p">1.</span> Compile the src folder by either using the makefile or by compiling a dynamic shared library with gcc </span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC147" class="line" lang="markdown"><span class="p">```</span><span class="nl">gcc -Wall -O3 -pipe -fPIC -shared -rdynamic -o libssw.so ssw.c ssw.h```</span></span>
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148
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC148" class="line" lang="markdown"><span class="sb" style="color: #d14;">2. Put libssw.so and ssw_lib.py in the same directory of your own program files or directories in sys.paths.</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC149" class="line" lang="markdown"><span class="sb" style="color: #d14;">3. The LD_LIBRARY_PATH environment variable may need to be modified to include the directory of the dynamic library libssw.so by one of the two following mathods:</span></span>
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150
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC170" class="line" lang="markdown"><span class="sb" style="color: #d14;"> * ```export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:path_of_libssw.so```</span></span>
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151
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC151" class="line" lang="markdown"><span class="sb" style="color: #d14;"> * For a definitive inclusion edit /etc/ld.so.conf and add the path of the libssw.so. Then, update the cache by ```/sbin/ldconfig```.</span></span>
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152
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC152" class="line" lang="markdown"><span class="sb" style="color: #d14;">4. In a python script or in a interactive interpreter, import the CSsw class by: ```from ssw_lib import CSsw``` or ```import ssw_lib``` and then call ```ssw_lib.CSsw```</span></span>
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153
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC153" class="line" lang="markdown"><span class="sb" style="color: #d14;">5. Call APIs with input parameters and parse the results (Please see pyssw.py as an example).</span></span>
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<td class="new_line diff-line-num new" data-linenumber="171" 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">
171
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC171" class="line" lang="markdown"><span class="sb" style="color: #d14;"> * For a definitive inclusion edit `/etc/ld.so.conf` and add the path of the `libssw.so`. Then, update the cache by `/sbin/ldconfig`.</span></span>
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172
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC172" class="line" lang="markdown"></span>
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173
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC173" class="line" lang="markdown"><span class="p">4.</span> In a Python script or in a interactive interpreter, import the CSsw class by: <span class="sb" style="color: #d14;">`from ssw_lib import CSsw`</span> or <span class="sb" style="color: #d14;">`import ssw_lib`</span> and then call <span class="sb" style="color: #d14;">`ssw_lib.CSsw`</span>.</span>
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174
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC174" class="line" lang="markdown"></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC175" class="line" lang="markdown"><span class="p">5.</span> Call APIs with input parameters and parse the results (Please see <span class="sb" style="color: #d14;">`pyssw.py`</span> as an example).</span>
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176
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC176" class="line" lang="markdown"></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC177" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Run pyssw standalone</span></span>
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154
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC178" class="line" lang="markdown"></span>
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155
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<td class="new_line diff-line-num old" data-linenumber="179" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC155" class="line" lang="markdown"><span class="sb" style="color: #d14;">###Run pyssw standalone </span></span>
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156
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC179" class="line" lang="markdown"><span class="p">```</span></span>
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157
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC180" class="line" lang="markdown">usage: pyssw.py [-h] [-l SLIBPATH] [-m NMATCH] [-x NMISMATCH] [-o NOPEN]</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC181" class="line" lang="markdown"> [-e NEXT] [-p] [-a SMATRIX] [-c] [-f NTHR] [-r] [-s] [-header]</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="193" 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="216" 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">@@ -193,38 +216,46 @@ optional arguments:</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC216" class="line" lang="markdown"> -header, --bHeader If -s is used, include header in SAM output.</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC217" class="line" lang="markdown"><span class="p">```</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="LC218" class="line" lang="markdown"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC196" class="line" lang="markdown">###pyssw output</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC219" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### pyssw output</span></span>
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220
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC220" class="line" lang="markdown"></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC221" class="line" lang="markdown">The software can output SAM format or BLAST like format results.</span>
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197
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC222" class="line" lang="markdown"></span>
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198
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC198" class="line" lang="markdown"><span class="idiff left right deletion">The software can output SAM format or BLAST like format results. </span></span>
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223
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC223" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;"><span class="idiff left right addition">### Speed and memory usage of pyssw</span></span></span>
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199
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224
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC224" class="line" lang="markdown"></span>
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200
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC200" class="line" lang="markdown"><span class="idiff left deletion">###S</span>peed and memory <span class="idiff deletion">u</span>sa<span class="idiff deletion">g</span>e <span class="idiff right deletion">of pyssw</span></span>
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225
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC225" class="line" lang="markdown"><span class="idiff left addition">The s</span>peed and memory <span class="idiff addition">are about the </span>sa<span class="idiff addition">m</span>e <span class="idiff right addition">as the C library.</span></span>
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201
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226
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC226" class="line" lang="markdown"></span>
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202
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC202" class="line" lang="markdown">The speed and memory are about the same as the c library.</span>
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203
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC203" class="line" lang="markdown"> </span>
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204
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC204" class="line" lang="markdown">##Java interface</span>
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227
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC227" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Java interface</span></span>
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205
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228
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC228" class="line" lang="markdown"></span>
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206
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<td class="new_line diff-line-num old" data-linenumber="229" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC206" class="line" lang="markdown">The <span class="idiff left right deletion">j</span>ava wrapper is a thin JNI (Java Native Interface) wrapper around the native C implementation.</span>
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<td class="new_line diff-line-num new" data-linenumber="229" 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">
229
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC229" class="line" lang="markdown">The <span class="idiff left right addition">J</span>ava wrapper is a thin JNI (Java Native Interface) wrapper around the native C implementation.</span>
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207
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230
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC230" class="line" lang="markdown"></span>
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208
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC208" class="line" lang="markdown">###Building</span>
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231
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC231" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">###<span class="idiff left right addition"> </span>Building</span></span>
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209
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232
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC232" class="line" lang="markdown"></span>
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210
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC210" class="line" lang="markdown">Only the C, C++ and C shared libraries are generated from the default make goal, and as such, the <span class="idiff left right deletion">j</span>ava interface must be built explicitly.</span>
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233
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC233" class="line" lang="markdown">Only the C, C++<span class="idiff left addition">,</span> and C shared libraries are generated from the default make goal, and as such, the <span class="idiff right addition">J</span>ava interface must be built explicitly.</span>
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211
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234
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC234" class="line" lang="markdown"></span>
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<td class="old_line diff-line-num old" data-linenumber="212" 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">
212
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<td class="new_line diff-line-num old" data-linenumber="235" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC212" class="line" lang="markdown">1. Ensure `javac` and `jar` are <span class="idiff left deletion">o</span>n <span class="idiff right deletion">path</span></span>
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<td class="old_line diff-line-num old" data-linenumber="213" 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">
213
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<td class="new_line diff-line-num old" data-linenumber="235" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC213" class="line" lang="markdown">2. Ensure JAVA_HOME is set to an installed JRE or JDK, or the JNI include directory is included in the C system library search path</span>
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<td class="old_line diff-line-num new" data-linenumber="214" 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="235" 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">
235
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC235" class="line" lang="markdown"><span class="p">1.</span> Ensure <span class="sb" style="color: #d14;">`javac`</span> and <span class="sb" style="color: #d14;">`jar`</span> are <span class="idiff left addition">i</span>n <span class="sb" style="color: #d14;"><span class="idiff addition">`PATH`</span></span><span class="idiff right addition">.</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC236" class="line" lang="markdown"><span class="p">2.</span> Ensure <span class="sb" style="color: #d14;"><span class="idiff left addition">`</span>JAVA_HOME<span class="idiff addition">`</span></span> is set to an installed JRE or JDK, or the JNI include directory is included in the C system library search path<span class="idiff right addition">.</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="LC237" class="line" lang="markdown"><span class="p">3.</span> <span class="sb" style="color: #d14;">`make java`</span> from the src directory.</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC215" class="line" lang="markdown">4. libsswjni.so and ssw.jar should be built.</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC238" class="line" lang="markdown"><span class="p">4.</span> <span class="sb" style="color: #d14;">`libsswjni.so`</span> and <span class="sb" style="color: #d14;">`ssw.jar`</span> should be built.</span>
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239
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC239" class="line" lang="markdown"></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC240" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### How to use the Java wrapper</span></span>
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241
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC241" class="line" lang="markdown"></span>
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<td class="new_line diff-line-num new" data-linenumber="242" 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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC242" class="line" lang="markdown">The Java wrapper consist of the following components:</span>
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243
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC243" class="line" lang="markdown"></span>
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<td class="new_line diff-line-num new" data-linenumber="244" 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">
244
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC244" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`libsswjni.so`</span>: native C library exposing the JNI entry points</span>
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<td class="new_line diff-line-num new" data-linenumber="245" 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">
245
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC245" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`ssw.jar`</span> is a Java library containing the Java interface to the native C library. This small wrapper library is composed of:</span>
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246
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC246" class="line" lang="markdown"></span>
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<td class="new_line diff-line-num new" data-linenumber="247" 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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC247" class="line" lang="markdown"><span class="sb" style="color: #d14;"> * `ssw.Aligner` Java class: a thread-safe static class that exposes two `align()` methods. The first exposes the SSW C library directly. No error checking is performed on arguments passed to this method and misuse is highly likely to crash the JVM. The second `align()` method is a more user-friendly entry point that exposes a simpler API and performs some basic error checking.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="248" 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">
248
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC248" class="line" lang="markdown"><span class="sb" style="color: #d14;"> * `ssw.Alignment` Java class: this class stores alignment results. Each each field has a direct correspondence and identical meaning to the C s_align struct.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="249" 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">
249
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC249" class="line" lang="markdown"><span class="sb" style="color: #d14;"> * `ssw.Example` Java class: Java version of the example_c sample code. Run `java -jar ssw.jar` to execute the sample.</span></span>
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250
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC250" class="line" lang="markdown"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC217" class="line" lang="markdown"><span class="idiff left right deletion">###How to use the java wrapper</span></span>
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<td class="new_line diff-line-num new" data-linenumber="251" 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">
251
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC251" class="line" lang="markdown"><span class="idiff left addition">To use the library, either reference the </span><span class="sb" style="color: #d14;"><span class="idiff addition">`ssw.jar`</span></span><span class="idiff addition"> or including the Aligner and Alignment classes directly. As for any JNI library, the native library must be loaded (using </span><span class="sb" style="color: #d14;"><span class="idiff addition">`System.loadLibrary("sswjni")`</span></span><span class="idiff addition"> or similar) before invokation of native methods. For the JVM to find the library, ensure that either the library is included in the </span><span class="sb" style="color: #d14;"><span class="idiff addition">`LD_LIBRARY_PATH`</span></span><span class="idiff addition"> environment variable, or </span><span class="sb" style="color: #d14;"><span class="idiff addition">`-Djava.library.path=<directory containing libsswjni.so>`</span></span><span class="idiff right addition"> is set on the Java command line.</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="LC252" class="line" lang="markdown"></span>
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<td class="new_line diff-line-num old" data-linenumber="253" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC219" class="line" lang="markdown"><span class="idiff left right deletion">The java wrapper consist of the following components:</span></span>
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253
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC253" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;"><span class="idiff left right addition">## R package</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="LC254" class="line" lang="markdown"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC221" class="line" lang="markdown">* libsswjni.so: native C library exposing the JNI entry points</span>
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<td class="new_line diff-line-num old" data-linenumber="255" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC222" class="line" lang="markdown">* ssw.jar is a java library containing the Java interface to the native C library. This small wrapper library is composed of:</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC223" class="line" lang="markdown"> * ssw.Aligner java class: a thread-safe static class that exposes two `align()` methods. The first exposes the SSW C library directly. No error checking is performed on arguments passed to this method and misuse is highly likely to crash the JVM. The second align() method is a more user-friendly entry point that exposes a simpler API and performs some basic error checking.</span>
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224
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC224" class="line" lang="markdown"> * ssw.Alignment java class: this class stores alignment results. Each each field has a direct correspondence and identical meaning to the C s_align struct.</span>
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225
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC225" class="line" lang="markdown"> * ssw.Example java class: java version of the example_c sample code. Run `java -jar ssw.jar` to execute the sample.</span>
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255
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC255" class="line" lang="markdown">Please check all the R package information here:</span>
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256
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC256" class="line" lang="markdown">https://github.com/nanxstats/ssw-r</span>
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226
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257
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC257" class="line" lang="markdown"></span>
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227
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC227" class="line" lang="markdown"><span class="idiff left right deletion">To use the library, either reference the ssw.jar or including the Aligner and Alignment classes directly. As for any JNI library, the native library must be loaded (using `System.loadLibrary("sswjni")` or similar) before invokation of native methods. For the JVM to find the library, ensure that either the library is included in the LD_LIBRARY_PATH environment variable, or `-Djava.library.path=<directory containing libsswjni.so>` is set on the java command line.</span></span>
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258
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC258" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;"><span class="idiff left right addition">## Citation</span></span></span>
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228
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259
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC259" class="line" lang="markdown"></span>
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229
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<td class="new_line diff-line-num old" data-linenumber="260" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC229" class="line" lang="markdown"><span class="idiff left right deletion">###</span>Please cite this paper, if you need:</span>
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230
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<td class="new_line diff-line-num old" data-linenumber="260" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC230" class="line" lang="markdown">http://d<span class="idiff left right deletion">x.plos</span>.org/10.1371/journal.pone.0082138</span></pre></td>
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<td class="new_line diff-line-num new" data-linenumber="260" 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">
260
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC260" class="line" lang="markdown">Please cite this paper, if you need:</span>
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261
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC261" class="line" lang="markdown">http<span class="idiff left addition">s</span>://d<span class="idiff right addition">oi</span>.org/10.1371/journal.pone.0082138</span></pre></td>
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<li id="55d5632a29e4dfe633b39497efa3554a26991f65">
<a href="https://salsa.debian.org/med-team/libssw/-/commit/c9c6106f955eac1ec9d8a40cc85495ccf3178810#55d5632a29e4dfe633b39497efa3554a26991f65"><strong>demo/blosum62.txt</strong></a>
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1
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># Matrix made by matblas from blosum62.iij</span>
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2
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"># * column uses minimum score</span>
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<td class="new_line diff-line-num new" data-linenumber="3" 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">
3
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"># BLOSUM Clustered Scoring Matrix in 1/2 Bit Units</span>
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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"># Blocks Database = /data/blocks_5.0/blocks.dat</span>
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<td class="new_line diff-line-num new" data-linenumber="5" 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">
5
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"># Cluster Percentage: >= 62</span>
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6
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"># Entropy = 0.6979, Expected = -0.5209</span>
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7
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> A R N D C Q E G H I L K M F P S T W Y V B Z X *</span>
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<td class="new_line diff-line-num new" data-linenumber="8" 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">
8
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 0 -4 </span>
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<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">R -1 5 0 -2 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -4 </span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="10" 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">
10
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">N -2 0 6 1 -3 0 0 0 1 -3 -3 0 -2 -3 -2 1 0 -4 -2 -3 3 0 -1 -4 </span>
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<td class="new_line diff-line-num new" data-linenumber="11" 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">
11
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">D -2 -2 1 6 -3 0 2 -1 -1 -3 -4 -1 -3 -3 -1 0 -1 -4 -3 -3 4 1 -1 -4 </span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="12" 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">
12
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">C 0 -3 -3 -3 9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2 -4 </span>
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13
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Q -1 1 0 0 -3 5 2 -2 0 -3 -2 1 0 -3 -1 0 -1 -2 -1 -2 0 3 -1 -4 </span>
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14
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">E -1 0 0 2 -4 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4 </span>
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15
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">G 0 -2 0 -1 -3 -2 -2 6 -2 -4 -4 -2 -3 -3 -2 0 -2 -2 -3 -3 -1 -2 -1 -4 </span>
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16
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">H -2 0 1 -1 -3 0 0 -2 8 -3 -3 -1 -2 -1 -2 -1 -2 -2 2 -3 0 0 -1 -4 </span>
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17
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">I -1 -3 -3 -3 -1 -3 -3 -4 -3 4 2 -3 1 0 -3 -2 -1 -3 -1 3 -3 -3 -1 -4 </span>
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18
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">L -1 -2 -3 -4 -1 -2 -3 -4 -3 2 4 -2 2 0 -3 -2 -1 -2 -1 1 -4 -3 -1 -4 </span>
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19
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">K -1 2 0 -1 -3 1 1 -2 -1 -3 -2 5 -1 -3 -1 0 -1 -3 -2 -2 0 1 -1 -4 </span>
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20
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">M -1 -1 -2 -3 -1 0 -2 -3 -2 1 2 -1 5 0 -2 -1 -1 -1 -1 1 -3 -1 -1 -4 </span>
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21
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">F -2 -3 -3 -3 -2 -3 -3 -3 -1 0 0 -3 0 6 -4 -2 -2 1 3 -1 -3 -3 -1 -4 </span>
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22
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7 -1 -1 -4 -3 -2 -2 -1 -2 -4 </span>
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23
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4 1 -3 -2 -2 0 0 0 -4 </span>
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24
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 -2 -2 0 -1 -1 0 -4 </span>
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25
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1 1 -4 -3 -2 11 2 -3 -4 -3 -2 -4 </span>
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26
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -1 -3 -2 -1 -4 </span>
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27
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">V 0 -3 -3 -3 -1 -2 -2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4 -3 -2 -1 -4 </span>
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28
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">B -2 -1 3 4 -3 0 1 -1 0 -3 -4 0 -3 -3 -2 0 -1 -4 -3 -3 4 1 -1 -4 </span>
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29
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">Z -1 0 0 1 -3 3 4 -2 0 -3 -3 1 -1 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4 </span>
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30
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 0 0 -2 -1 -1 -1 -1 -1 -4 </span>
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31
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">* -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 1</span></pre></td>
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<a href="https://salsa.debian.org/med-team/libssw/-/commit/c9c6106f955eac1ec9d8a40cc85495ccf3178810#7bbe96905d224e4ef9b6241676a0ee94932d3e19"><strong>demo/new.txt</strong></a>
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1
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">target_name: chr3</span>
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2
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">query_name: 6:163296599:F:198;None;None/1</span>
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3
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">optimal_alignment_score: 53 suboptimal_alignment_score: 52 strand: + target_end: 745864 query_end: 54</span>
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4
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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5
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">target_name: chr3</span>
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6
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">query_name: 3:153409880:F:224;None;3,153410143,G,A/1</span>
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7
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">optimal_alignment_score: 47 suboptimal_alignment_score: 45 strand: + target_end: 350986 query_end: 53</span>
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8
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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9
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">target_name: chr3</span>
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10
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">query_name: Y:26750420:R:-132;None;None/1</span>
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<td class="new_line diff-line-num new" data-linenumber="11" 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">
11
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">optimal_alignment_score: 50 suboptimal_alignment_score: 49 strand: + target_end: 319376 query_end: 52</span>
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12
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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13
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">target_name: chr3</span>
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14
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">query_name: 13:91170622:R:-276;None;None/1</span>
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15
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">optimal_alignment_score: 49 suboptimal_alignment_score: 48 strand: + target_end: 353946 query_end: 49</span>
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16
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
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17
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">target_name: chr3</span>
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18
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">query_name: 15:37079528:R:-240;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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19
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">optimal_alignment_score: 40 suboptimal_alignment_score: 39 strand: + target_end: 257705 query_end: 53</span>
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20
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"></span>
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21
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">target_name: chr3</span>
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22
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">query_name: 9:92308501:R:-176;None;None/1</span>
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23
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">optimal_alignment_score: 80 suboptimal_alignment_score: 70 strand: + target_end: 105983 query_end: 48</span>
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24
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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25
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">target_name: chr3</span>
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26
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">query_name: 3:109533106:R:-128;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="27" 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">
27
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">optimal_alignment_score: 42 suboptimal_alignment_score: 42 strand: + target_end: 198965 query_end: 47</span>
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28
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="29" 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">
29
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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30
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">query_name: 16:32366683:R:-158;16,32366730,G,A;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
31
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">optimal_alignment_score: 50 suboptimal_alignment_score: 46 strand: + target_end: 823370 query_end: 52</span>
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32
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"></span>
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33
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">target_name: chr3</span>
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34
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">query_name: 13:111809970:R:-237;None;None/1</span>
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35
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">optimal_alignment_score: 43 suboptimal_alignment_score: 40 strand: + target_end: 509164 query_end: 53</span>
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36
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"></span>
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37
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">target_name: chr3</span>
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38
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">query_name: 3:38871305:F:159;None;None/1</span>
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<td class="new_line diff-line-num new" data-linenumber="39" 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">
39
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">optimal_alignment_score: 39 suboptimal_alignment_score: 37 strand: + target_end: 841259 query_end: 54</span>
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40
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"></span>
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41
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">target_name: chr3</span>
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42
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">query_name: 19:8434785:F:295;None;None/1</span>
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<td class="new_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">optimal_alignment_score: 47 suboptimal_alignment_score: 43 strand: + target_end: 330617 query_end: 53</span>
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44
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"></span>
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45
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">target_name: chr3</span>
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46
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">query_name: 8:132563397:R:-144;None;None/1</span>
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47
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">optimal_alignment_score: 49 suboptimal_alignment_score: 40 strand: + target_end: 54827 query_end: 54</span>
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48
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"></span>
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49
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">target_name: chr3</span>
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50
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">query_name: 3:190507952:R:-57;3,190507958,G,A;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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51
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">optimal_alignment_score: 41 suboptimal_alignment_score: 41 strand: + target_end: 138110 query_end: 54</span>
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52
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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53
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">target_name: chr3</span>
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54
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">query_name: 10:59883855:R:-120;None;None/1</span>
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55
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">optimal_alignment_score: 43 suboptimal_alignment_score: 43 strand: + target_end: 244247 query_end: 53</span>
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56
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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57
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">target_name: chr3</span>
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<td class="new_line diff-line-num new" data-linenumber="58" 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">
58
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">query_name: 6:148630669:R:-271;None;None/1</span>
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<td class="new_line diff-line-num new" data-linenumber="59" 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">
59
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">optimal_alignment_score: 41 suboptimal_alignment_score: 39 strand: + target_end: 658593 query_end: 54</span>
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60
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
61
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">target_name: chr3</span>
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<td class="new_line diff-line-num new" data-linenumber="62" 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">
62
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">query_name: 3:64518566:R:-93;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="63" 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">
63
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">optimal_alignment_score: 46 suboptimal_alignment_score: 45 strand: + target_end: 881546 query_end: 44</span>
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64
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
65
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
66
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">query_name: 14:42514746:R:-187;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
67
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">optimal_alignment_score: 58 suboptimal_alignment_score: 58 strand: + target_end: 206906 query_end: 48</span>
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68
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
69
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
70
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">query_name: 7:126497810:R:-191;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
71
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">optimal_alignment_score: 45 suboptimal_alignment_score: 40 strand: + target_end: 232372 query_end: 54</span>
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72
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
74
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">query_name: 21:15123085:R:-140;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
75
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">optimal_alignment_score: 43 suboptimal_alignment_score: 43 strand: + target_end: 492310 query_end: 51</span>
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76
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
77
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
78
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">query_name: 2:217172401:R:-226;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
79
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">optimal_alignment_score: 42 suboptimal_alignment_score: 41 strand: + target_end: 261738 query_end: 54</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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80
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
81
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
82
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">query_name: 6:129456169:R:-167;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
83
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">optimal_alignment_score: 42 suboptimal_alignment_score: 39 strand: + target_end: 750865 query_end: 53</span>
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84
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext"></span>
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85
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">target_name: chr3</span>
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86
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">query_name: 4:160333309:R:-131;None;4,160333230,T,G/1</span>
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<td class="new_line diff-line-num new" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
87
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">optimal_alignment_score: 42 suboptimal_alignment_score: 41 strand: + target_end: 465814 query_end: 54</span>
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88
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
89
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">target_name: chr3</span>
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90
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">query_name: 3:37890126:R:-228;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="91" 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">
91
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">optimal_alignment_score: 40 suboptimal_alignment_score: 40 strand: + target_end: 661952 query_end: 53</span>
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92
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext"></span>
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93
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">target_name: chr3</span>
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94
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">query_name: 17:49899522:F:154;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="95" 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">
95
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">optimal_alignment_score: 47 suboptimal_alignment_score: 46 strand: + target_end: 94043 query_end: 51</span>
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96
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"></span>
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97
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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98
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">query_name: 8:138662818:R:-211;None;8,138662609,C,T/1</span>
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99
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">optimal_alignment_score: 43 suboptimal_alignment_score: 41 strand: + target_end: 175380 query_end: 50</span>
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100
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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101
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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102
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">query_name: 3:97260940:R:-254;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="103" 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">
103
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">optimal_alignment_score: 39 suboptimal_alignment_score: 38 strand: + target_end: 903012 query_end: 54</span>
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104
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="105" 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">
105
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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106
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">query_name: 7:14401638:F:350;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="107" 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">
107
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">optimal_alignment_score: 50 suboptimal_alignment_score: 47 strand: + target_end: 265434 query_end: 48</span>
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108
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="109" 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">
109
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext">target_name: chr3</span>
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110
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">query_name: 13:19068477:F:246;None;None/1</span>
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111
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext">optimal_alignment_score: 47 suboptimal_alignment_score: 45 strand: + target_end: 628991 query_end: 54</span>
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112
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext"></span>
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113
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext">target_name: chr3</span>
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114
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">query_name: 3:179655047:F:206;None;None/1</span>
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<td class="new_line diff-line-num new" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
115
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext">optimal_alignment_score: 45 suboptimal_alignment_score: 44 strand: + target_end: 476787 query_end: 51</span>
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116
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="117" 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">
117
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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118
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">query_name: 20:15001091:F:174;None;None/1</span>
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119
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext">optimal_alignment_score: 44 suboptimal_alignment_score: 43 strand: + target_end: 226051 query_end: 51</span>
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120
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext"></span>
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121
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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122
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext">query_name: 2:54967337:R:-153;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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123
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext">optimal_alignment_score: 43 suboptimal_alignment_score: 42 strand: + target_end: 689523 query_end: 54</span>
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124
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext"></span>
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125
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext">query_name: 18:39435195:F:202;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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127
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext">optimal_alignment_score: 51 suboptimal_alignment_score: 45 strand: + target_end: 998370 query_end: 53</span>
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128
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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130
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext">query_name: X:68133790:F:167;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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131
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext">optimal_alignment_score: 43 suboptimal_alignment_score: 40 strand: + target_end: 612440 query_end: 50</span>
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132
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="133" 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">
133
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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134
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext">query_name: 9:18241281:F:267;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="135" 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">
135
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext">optimal_alignment_score: 53 suboptimal_alignment_score: 49 strand: + target_end: 872860 query_end: 53</span>
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136
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="137" 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">
137
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext">target_name: chr3</span>
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<td class="new_line diff-line-num new" data-linenumber="138" 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">
138
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext">query_name: 7:141812631:F:239;None;None/1</span>
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<td class="new_line diff-line-num new" data-linenumber="139" 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">
139
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext">optimal_alignment_score: 40 suboptimal_alignment_score: 40 strand: + target_end: 510995 query_end: 44</span>
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140
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="141" 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">
141
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext">target_name: chr3</span>
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<td class="new_line diff-line-num new" data-linenumber="142" 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">
142
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext">query_name: 15:54133744:R:-269;None;None/1</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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext">optimal_alignment_score: 41 suboptimal_alignment_score: 40 strand: + target_end: 725603 query_end: 53</span>
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144
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext"></span>
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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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext">target_name: chr3</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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext">query_name: 4:66588719:R:-245;None;None/1</span>
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<td class="new_line diff-line-num new" data-linenumber="147" 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">
147
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext">optimal_alignment_score: 58 suboptimal_alignment_score: 58 strand: + target_end: 163129 query_end: 54</span>
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148
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext"></span>
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149
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext">target_name: chr3</span>
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150
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext">query_name: 1:217587184:F:229;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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151
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext">optimal_alignment_score: 46 suboptimal_alignment_score: 46 strand: + target_end: 196793 query_end: 52</span>
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152
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="153" 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">
153
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext">target_name: chr3</span>
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<td class="new_line diff-line-num new" data-linenumber="154" 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">
154
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext">query_name: 2:119213044:R:-184;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="155" 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">
155
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext">optimal_alignment_score: 49 suboptimal_alignment_score: 44 strand: + target_end: 552663 query_end: 50</span>
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156
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC156" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="157" 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">
157
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC157" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="158" 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">
158
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext">query_name: 2:36811349:F:265;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="159" 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">
159
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC159" class="line" lang="plaintext">optimal_alignment_score: 44 suboptimal_alignment_score: 43 strand: + target_end: 945971 query_end: 52</span>
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160
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC160" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="161" 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">
161
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext">target_name: chr3</span>
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<td class="new_line diff-line-num new" data-linenumber="162" 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">
162
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext">query_name: 1:68786835:F:349;None;None/1</span>
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<td class="new_line diff-line-num new" data-linenumber="163" 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">
163
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext">optimal_alignment_score: 45 suboptimal_alignment_score: 45 strand: + target_end: 528144 query_end: 52</span>
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164
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="165" 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">
165
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="166" 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">
166
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext">query_name: 4:126634771:F:185;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="167" 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">
167
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext">optimal_alignment_score: 45 suboptimal_alignment_score: 42 strand: + target_end: 745309 query_end: 50</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="168" 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">
168
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="169" 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">
169
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC169" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="170" 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">
170
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC170" class="line" lang="plaintext">query_name: 4:114171402:R:-296;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="171" 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">
171
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC171" class="line" lang="plaintext">optimal_alignment_score: 44 suboptimal_alignment_score: 42 strand: + target_end: 751541 query_end: 53</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="172" 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">
172
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC172" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="173" 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">
173
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC173" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="174" 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">
174
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext">query_name: 9:125206364:R:-140;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="175" 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">
175
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC175" class="line" lang="plaintext">optimal_alignment_score: 41 suboptimal_alignment_score: 39 strand: + target_end: 932480 query_end: 50</span>
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<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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176
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC176" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="177" 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">
177
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC177" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="178" 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">
178
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC178" class="line" lang="plaintext">query_name: X:25208394:F:245;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="179" 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">
179
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC179" class="line" lang="plaintext">optimal_alignment_score: 42 suboptimal_alignment_score: 41 strand: + target_end: 696734 query_end: 52</span>
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<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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180
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="181" 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">
181
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="182" 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">
182
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext">query_name: 2:222217158:F:227;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="183" 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">
183
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext">optimal_alignment_score: 41 suboptimal_alignment_score: 40 strand: + target_end: 704921 query_end: 53</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="184" 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">
184
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="185" 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">
185
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC185" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="186" 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">
186
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext">query_name: 1:196837088:F:230;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="187" 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">
187
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext">optimal_alignment_score: 46 suboptimal_alignment_score: 45 strand: + target_end: 563639 query_end: 53</span>
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188
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC188" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="189" 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">
189
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC189" class="line" lang="plaintext">target_name: chr3</span>
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<td class="new_line diff-line-num new" data-linenumber="190" 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">
190
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext">query_name: 7:24300836:R:-208;7,24300863,*,+1T;None/1</span>
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<td class="new_line diff-line-num new" data-linenumber="191" 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">
191
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext">optimal_alignment_score: 44 suboptimal_alignment_score: 42 strand: + target_end: 239063 query_end: 54</span>
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192
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC192" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="193" 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">
193
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext">target_name: chr3</span>
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<td class="new_line diff-line-num new" data-linenumber="194" 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">
194
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext">query_name: 1:76948473:F:230;None;None/1</span>
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<td class="new_line diff-line-num new" data-linenumber="195" 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">
195
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC195" class="line" lang="plaintext">optimal_alignment_score: 45 suboptimal_alignment_score: 45 strand: + target_end: 386767 query_end: 54</span>
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196
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC196" class="line" lang="plaintext"></span>
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197
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC197" class="line" lang="plaintext">target_name: chr3</span>
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<td class="new_line diff-line-num new" data-linenumber="198" 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">
198
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC198" class="line" lang="plaintext">query_name: 8:62727783:F:135;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="199" 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">
199
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC199" class="line" lang="plaintext">optimal_alignment_score: 47 suboptimal_alignment_score: 46 strand: + target_end: 406541 query_end: 54</span>
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200
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC200" class="line" lang="plaintext"></span>
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201
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC201" class="line" lang="plaintext">target_name: chr3</span>
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202
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC202" class="line" lang="plaintext">query_name: 7:94677617:R:-155;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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203
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC203" class="line" lang="plaintext">optimal_alignment_score: 46 suboptimal_alignment_score: 46 strand: + target_end: 345086 query_end: 54</span>
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204
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC204" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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205
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC205" class="line" lang="plaintext">target_name: chr3</span>
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206
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC206" class="line" lang="plaintext">query_name: 4:10707991:F:305;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="207" 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">
207
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC207" class="line" lang="plaintext">optimal_alignment_score: 94 suboptimal_alignment_score: 86 strand: + target_end: 198089 query_end: 53</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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208
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC208" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="209" 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">
209
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC209" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="210" 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">
210
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC210" class="line" lang="plaintext">query_name: 1:183203391:R:-141;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="211" 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">
211
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC211" class="line" lang="plaintext">optimal_alignment_score: 48 suboptimal_alignment_score: 45 strand: + target_end: 344874 query_end: 53</span>
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212
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC212" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_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">
213
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC213" class="line" lang="plaintext">target_name: chr3</span>
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<td class="new_line diff-line-num new" data-linenumber="214" 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">
214
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC214" class="line" lang="plaintext">query_name: 15:63526307:R:-83;None;None/1</span>
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<td class="new_line diff-line-num new" data-linenumber="215" 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">
215
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC215" class="line" lang="plaintext">optimal_alignment_score: 40 suboptimal_alignment_score: 40 strand: + target_end: 78739 query_end: 52</span>
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216
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC216" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="217" 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">
217
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC217" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="218" 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">
218
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC218" class="line" lang="plaintext">query_name: 8:79068236:F:137;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="219" 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">
219
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC219" class="line" lang="plaintext">optimal_alignment_score: 43 suboptimal_alignment_score: 42 strand: + target_end: 326507 query_end: 47</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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220
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC220" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="221" 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">
221
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC221" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="222" 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">
222
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC222" class="line" lang="plaintext">query_name: 9:1290219:R:-251;None;None/1</span>
</pre></td>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="223" 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">
223
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC223" class="line" lang="plaintext">optimal_alignment_score: 84 suboptimal_alignment_score: 80 strand: + target_end: 537411 query_end: 54</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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224
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC224" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="225" 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">
225
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC225" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="226" 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">
226
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC226" class="line" lang="plaintext">query_name: 5:122248402:R:-212;None;None/1</span>
</pre></td>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="227" 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">
227
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC227" class="line" lang="plaintext">optimal_alignment_score: 40 suboptimal_alignment_score: 39 strand: + target_end: 40834 query_end: 52</span>
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<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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228
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC228" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="229" 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">
229
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC229" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="230" 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">
230
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC230" class="line" lang="plaintext">query_name: X:153897575:R:-263;None;None/1</span>
</pre></td>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_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">
231
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC231" class="line" lang="plaintext">optimal_alignment_score: 75 suboptimal_alignment_score: 74 strand: + target_end: 223405 query_end: 49</span>
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<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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232
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC232" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="233" 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">
233
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC233" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="234" 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">
234
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC234" class="line" lang="plaintext">query_name: 6:95453360:F:204;None;None/1</span>
</pre></td>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="235" 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">
235
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC235" class="line" lang="plaintext">optimal_alignment_score: 45 suboptimal_alignment_score: 42 strand: + target_end: 182708 query_end: 52</span>
</pre></td>
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<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="236" 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">
236
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC236" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="237" 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">
237
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC237" class="line" lang="plaintext">target_name: chr3</span>
</pre></td>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="238" 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">
238
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC238" class="line" lang="plaintext">query_name: 10:6951101:R:-212;None;None/1</span>
</pre></td>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="239" 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">
239
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC239" class="line" lang="plaintext">optimal_alignment_score: 41 suboptimal_alignment_score: 38 strand: + target_end: 897043 query_end: 47</span>
</pre></td>
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240
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241
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC241" class="line" lang="plaintext">target_name: chr3</span>
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<td class="new_line diff-line-num new" data-linenumber="242" 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">
242
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC242" class="line" lang="plaintext">query_name: 13:59325230:F:98;None;None/1</span>
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<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC243" class="line" lang="plaintext">optimal_alignment_score: 39 suboptimal_alignment_score: 38 strand: + target_end: 773481 query_end: 54</span>
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244
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC244" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="245" 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">
245
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC245" class="line" lang="plaintext">target_name: chr3</span>
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<td class="new_line diff-line-num new" data-linenumber="246" 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">
246
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC246" class="line" lang="plaintext">query_name: 3:37059536:F:184;None;None/1</span>
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<td class="new_line diff-line-num new" data-linenumber="247" 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">
247
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC247" class="line" lang="plaintext">optimal_alignment_score: 49 suboptimal_alignment_score: 44 strand: + target_end: 899262 query_end: 54</span>
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248
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC248" class="line" lang="plaintext"></span>
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249
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC249" class="line" lang="plaintext">target_name: chr3</span>
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250
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC250" class="line" lang="plaintext">query_name: 9:91156368:F:149;None;None/1</span>
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<td class="new_line diff-line-num new" data-linenumber="251" 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">
251
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC251" class="line" lang="plaintext">optimal_alignment_score: 43 suboptimal_alignment_score: 42 strand: + target_end: 606747 query_end: 51</span>
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252
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC252" class="line" lang="plaintext"></span>
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253
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC253" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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254
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC254" class="line" lang="plaintext">query_name: 12:55970708:R:-246;12,55970762,C,T;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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255
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC255" class="line" lang="plaintext">optimal_alignment_score: 92 suboptimal_alignment_score: 88 strand: + target_end: 771042 query_end: 54</span>
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256
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC256" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="257" 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">
257
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC257" class="line" lang="plaintext">target_name: chr3</span>
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258
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC258" class="line" lang="plaintext">query_name: 3:120828442:F:203;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="259" 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">
259
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC259" class="line" lang="plaintext">optimal_alignment_score: 44 suboptimal_alignment_score: 41 strand: + target_end: 595794 query_end: 50</span>
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260
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC260" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="261" 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">
261
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC261" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="262" 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">
262
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC262" class="line" lang="plaintext">query_name: 19:60104965:R:-147;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="263" 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">
263
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC263" class="line" lang="plaintext">optimal_alignment_score: 65 suboptimal_alignment_score: 64 strand: + target_end: 866783 query_end: 52</span>
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264
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC264" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="265" 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">
265
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC265" class="line" lang="plaintext">target_name: chr3</span>
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<td class="new_line diff-line-num new" data-linenumber="266" 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">
266
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC266" class="line" lang="plaintext">query_name: 11:98782460:R:-46;None;None/1</span>
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<td class="new_line diff-line-num new" data-linenumber="267" 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">
267
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC267" class="line" lang="plaintext">optimal_alignment_score: 56 suboptimal_alignment_score: 42 strand: + target_end: 819223 query_end: 51</span>
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<td class="new_line diff-line-num new" data-linenumber="268" 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">
268
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC268" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="269" 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">
269
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC269" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="270" 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">
270
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC270" class="line" lang="plaintext">query_name: 12:91111930:F:209;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="271" 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">
271
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC271" class="line" lang="plaintext">optimal_alignment_score: 43 suboptimal_alignment_score: 42 strand: + target_end: 679515 query_end: 51</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="272" 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">
272
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC272" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="273" 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">
273
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC273" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="274" 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">
274
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC274" class="line" lang="plaintext">query_name: 3:192601514:F:196;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="275" 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">
275
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC275" class="line" lang="plaintext">optimal_alignment_score: 42 suboptimal_alignment_score: 40 strand: + target_end: 392672 query_end: 40</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="276" 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">
276
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC276" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="277" 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">
277
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC277" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="278" 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">
278
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC278" class="line" lang="plaintext">query_name: X:47989386:R:-46;None;None/1</span>
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<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="279" 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">
279
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC279" class="line" lang="plaintext">optimal_alignment_score: 39 suboptimal_alignment_score: 36 strand: + target_end: 793950 query_end: 54</span>
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<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
280
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC280" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="281" 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">
281
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC281" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="282" 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">
282
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC282" class="line" lang="plaintext">query_name: 2:39824446:R:-127;None;None/1</span>
</pre></td>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="283" 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">
283
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC283" class="line" lang="plaintext">optimal_alignment_score: 72 suboptimal_alignment_score: 70 strand: + target_end: 972352 query_end: 54</span>
</pre></td>
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<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="284" 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">
284
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC284" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="285" 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">
285
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC285" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="286" 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">
286
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC286" class="line" lang="plaintext">query_name: 1:227528596:F:219;None;None/1</span>
</pre></td>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="287" 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">
287
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC287" class="line" lang="plaintext">optimal_alignment_score: 44 suboptimal_alignment_score: 42 strand: + target_end: 869543 query_end: 51</span>
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<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="288" 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">
288
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC288" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="289" 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">
289
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC289" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="290" 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">
290
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC290" class="line" lang="plaintext">query_name: X:4440324:R:-90;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="291" 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">
291
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC291" class="line" lang="plaintext">optimal_alignment_score: 42 suboptimal_alignment_score: 40 strand: + target_end: 100289 query_end: 52</span>
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292
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC292" class="line" lang="plaintext"></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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC293" class="line" lang="plaintext">target_name: chr3</span>
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<td class="new_line diff-line-num new" data-linenumber="294" 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">
294
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC294" class="line" lang="plaintext">query_name: X:73634281:F:88;None;None/1</span>
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<td class="new_line diff-line-num new" data-linenumber="295" 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">
295
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC295" class="line" lang="plaintext">optimal_alignment_score: 52 suboptimal_alignment_score: 41 strand: + target_end: 922600 query_end: 49</span>
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296
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC296" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="297" 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">
297
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC297" class="line" lang="plaintext">target_name: chr3</span>
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<td class="new_line diff-line-num new" data-linenumber="298" 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">
298
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC298" class="line" lang="plaintext">query_name: 3:53909823:F:239;None;3,53910104,T,C/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="299" 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">
299
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC299" class="line" lang="plaintext">optimal_alignment_score: 44 suboptimal_alignment_score: 44 strand: + target_end: 640897 query_end: 47</span>
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300
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC300" class="line" lang="plaintext"></span>
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301
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC301" class="line" lang="plaintext">target_name: chr3</span>
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<td class="new_line diff-line-num new" data-linenumber="302" 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">
302
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC302" class="line" lang="plaintext">query_name: 3:170059370:R:-173;None;3,170059212,G,C/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="303" 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">
303
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC303" class="line" lang="plaintext">optimal_alignment_score: 44 suboptimal_alignment_score: 43 strand: + target_end: 483764 query_end: 54</span>
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304
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC304" class="line" lang="plaintext"></span>
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305
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC305" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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306
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC306" class="line" lang="plaintext">query_name: 20:8823533:F:251;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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307
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC307" class="line" lang="plaintext">optimal_alignment_score: 39 suboptimal_alignment_score: 38 strand: + target_end: 887639 query_end: 49</span>
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308
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC308" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="309" 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">
309
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC309" class="line" lang="plaintext">target_name: chr3</span>
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310
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC310" class="line" lang="plaintext">query_name: 5:106802036:F:200;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="311" 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">
311
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC311" class="line" lang="plaintext">optimal_alignment_score: 44 suboptimal_alignment_score: 42 strand: + target_end: 137797 query_end: 53</span>
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312
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC312" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="313" 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">
313
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC313" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="314" 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">
314
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC314" class="line" lang="plaintext">query_name: 5:74632980:R:-252;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="315" 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">
315
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC315" class="line" lang="plaintext">optimal_alignment_score: 44 suboptimal_alignment_score: 43 strand: + target_end: 297976 query_end: 54</span>
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316
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC316" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="317" 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">
317
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC317" class="line" lang="plaintext">target_name: chr3</span>
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<td class="new_line diff-line-num new" data-linenumber="318" 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">
318
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC318" class="line" lang="plaintext">query_name: 12:84751900:F:268;None;None/1</span>
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<td class="new_line diff-line-num new" data-linenumber="319" 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">
319
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC319" class="line" lang="plaintext">optimal_alignment_score: 42 suboptimal_alignment_score: 42 strand: + target_end: 183485 query_end: 48</span>
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320
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC320" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="321" 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">
321
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC321" class="line" lang="plaintext">target_name: chr3</span>
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<td class="new_line diff-line-num new" data-linenumber="322" 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">
322
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC322" class="line" lang="plaintext">query_name: X:135811790:R:-164;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="323" 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">
323
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC323" class="line" lang="plaintext">optimal_alignment_score: 48 suboptimal_alignment_score: 44 strand: + target_end: 178654 query_end: 54</span>
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324
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC324" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="325" 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">
325
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC325" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="326" 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">
326
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC326" class="line" lang="plaintext">query_name: 10:53108829:R:-138;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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327
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC327" class="line" lang="plaintext">optimal_alignment_score: 45 suboptimal_alignment_score: 42 strand: + target_end: 625392 query_end: 50</span>
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328
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC328" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="329" 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">
329
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC329" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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330
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC330" class="line" lang="plaintext">query_name: 11:83660431:R:-245;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="331" 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">
331
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC331" class="line" lang="plaintext">optimal_alignment_score: 47 suboptimal_alignment_score: 44 strand: + target_end: 226749 query_end: 54</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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332
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC332" class="line" lang="plaintext"></span>
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333
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC333" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="334" 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">
334
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC334" class="line" lang="plaintext">query_name: 10:119650756:F:207;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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335
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC335" class="line" lang="plaintext">optimal_alignment_score: 44 suboptimal_alignment_score: 42 strand: + target_end: 529549 query_end: 41</span>
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336
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC336" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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337
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC337" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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338
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC338" class="line" lang="plaintext">query_name: 2:154848222:R:-185;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="339" 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">
339
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC339" class="line" lang="plaintext">optimal_alignment_score: 45 suboptimal_alignment_score: 43 strand: + target_end: 585761 query_end: 54</span>
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340
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC340" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="341" 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">
341
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC341" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="342" 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">
342
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC342" class="line" lang="plaintext">query_name: 3:63918850:F:276;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="343" 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">
343
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC343" class="line" lang="plaintext">optimal_alignment_score: 42 suboptimal_alignment_score: 41 strand: + target_end: 345340 query_end: 50</span>
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344
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345
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC345" class="line" lang="plaintext">target_name: chr3</span>
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346
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC346" class="line" lang="plaintext">query_name: 10:11447534:F:239;None;None/1</span>
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347
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC347" class="line" lang="plaintext">optimal_alignment_score: 38 suboptimal_alignment_score: 38 strand: + target_end: 114931 query_end: 52</span>
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348
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349
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC349" class="line" lang="plaintext">target_name: chr3</span>
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350
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC350" class="line" lang="plaintext">query_name: 1:57651555:R:-316;None;None/1</span>
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351
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC351" class="line" lang="plaintext">optimal_alignment_score: 46 suboptimal_alignment_score: 44 strand: + target_end: 104219 query_end: 54</span>
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352
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353
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC353" class="line" lang="plaintext">target_name: chr3</span>
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354
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC354" class="line" lang="plaintext">query_name: X:91671697:R:-206;None;X,91671506,G,A/1</span>
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355
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC355" class="line" lang="plaintext">optimal_alignment_score: 48 suboptimal_alignment_score: 47 strand: + target_end: 771479 query_end: 49</span>
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356
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357
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC357" class="line" lang="plaintext">target_name: chr3</span>
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358
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC358" class="line" lang="plaintext">query_name: 12:101622421:R:-187;None;None/1</span>
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359
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC359" class="line" lang="plaintext">optimal_alignment_score: 45 suboptimal_alignment_score: 44 strand: + target_end: 361502 query_end: 49</span>
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360
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361
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC361" class="line" lang="plaintext">target_name: chr3</span>
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362
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC362" class="line" lang="plaintext">query_name: 13:43163355:R:-200;None;None/1</span>
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363
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC363" class="line" lang="plaintext">optimal_alignment_score: 42 suboptimal_alignment_score: 42 strand: + target_end: 167308 query_end: 53</span>
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364
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365
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC365" class="line" lang="plaintext">target_name: chr3</span>
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366
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC366" class="line" lang="plaintext">query_name: 19:37349825:R:-160;None;None/1</span>
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367
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC367" class="line" lang="plaintext">optimal_alignment_score: 70 suboptimal_alignment_score: 68 strand: + target_end: 261459 query_end: 54</span>
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368
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369
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC369" class="line" lang="plaintext">target_name: chr3</span>
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<td class="new_line diff-line-num new" data-linenumber="370" 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">
370
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC370" class="line" lang="plaintext">query_name: 8:41173199:R:-175;None;8,41173056,T,C/1</span>
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<td class="new_line diff-line-num new" data-linenumber="371" 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">
371
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC371" class="line" lang="plaintext">optimal_alignment_score: 44 suboptimal_alignment_score: 43 strand: + target_end: 644612 query_end: 47</span>
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372
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC372" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="373" 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">
373
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC373" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="374" 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">
374
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC374" class="line" lang="plaintext">query_name: 16:29068055:R:-232;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="375" 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">
375
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC375" class="line" lang="plaintext">optimal_alignment_score: 44 suboptimal_alignment_score: 40 strand: + target_end: 934198 query_end: 53</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="376" 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">
376
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC376" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="377" 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">
377
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC377" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="378" 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">
378
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC378" class="line" lang="plaintext">query_name: 1:4694340:F:179;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="379" 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">
379
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC379" class="line" lang="plaintext">optimal_alignment_score: 48 suboptimal_alignment_score: 45 strand: + target_end: 140768 query_end: 54</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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380
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC380" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="381" 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">
381
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC381" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="382" 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">
382
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC382" class="line" lang="plaintext">query_name: 17:76451446:F:221;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="383" 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">
383
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC383" class="line" lang="plaintext">optimal_alignment_score: 42 suboptimal_alignment_score: 40 strand: + target_end: 561765 query_end: 54</span>
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<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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384
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC384" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="385" 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">
385
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC385" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="386" 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">
386
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC386" class="line" lang="plaintext">query_name: 1:242817485:F:158;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="387" 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">
387
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC387" class="line" lang="plaintext">optimal_alignment_score: 52 suboptimal_alignment_score: 46 strand: + target_end: 396383 query_end: 50</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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388
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC388" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="389" 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">
389
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC389" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="390" 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">
390
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC390" class="line" lang="plaintext">query_name: 18:29611708:R:-146;None;18,29611585,G,A/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="391" 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">
391
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC391" class="line" lang="plaintext">optimal_alignment_score: 45 suboptimal_alignment_score: 40 strand: + target_end: 157255 query_end: 47</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="392" 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">
392
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC392" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="393" 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">
393
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC393" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="394" 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">
394
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC394" class="line" lang="plaintext">query_name: 9:36493018:F:206;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="395" 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">
395
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC395" class="line" lang="plaintext">optimal_alignment_score: 82 suboptimal_alignment_score: 80 strand: + target_end: 872774 query_end: 54</span>
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396
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC396" class="line" lang="plaintext"></span>
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397
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC397" class="line" lang="plaintext">target_name: chr3</span>
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<td class="new_line diff-line-num new" data-linenumber="398" 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">
398
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC398" class="line" lang="plaintext">query_name: 9:16274705:F:129;9,16274709,C,A:9,16274719,C,G:9,16274741,A,T;9,16274862,A,G/1</span>
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<td class="new_line diff-line-num new" data-linenumber="399" 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">
399
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC399" class="line" lang="plaintext">optimal_alignment_score: 72 suboptimal_alignment_score: 64 strand: + target_end: 524699 query_end: 54</span>
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400
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC400" class="line" lang="plaintext"></span></pre></td>
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<li id="df0e4caa90dc2ac431eb6ba5305faf8a0e284b6e">
<a href="https://salsa.debian.org/med-team/libssw/-/commit/c9c6106f955eac1ec9d8a40cc85495ccf3178810#df0e4caa90dc2ac431eb6ba5305faf8a0e284b6e"><strong>demo/old.txt</strong></a>
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1
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">target_name: chr3</span>
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2
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">query_name: 6:163296599:F:198;None;None/1</span>
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<td class="new_line diff-line-num new" data-linenumber="3" 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">
3
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">optimal_alignment_score: 53 suboptimal_alignment_score: 52 strand: + target_end: 745864 query_end: 54</span>
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4
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="5" 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">
5
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">query_name: 3:153409880:F:224;None;3,153410143,G,A/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">optimal_alignment_score: 47 suboptimal_alignment_score: 45 strand: + target_end: 350986 query_end: 53</span>
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8
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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9
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">target_name: chr3</span>
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10
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">query_name: Y:26750420:R:-132;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="11" 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">
11
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">optimal_alignment_score: 50 suboptimal_alignment_score: 49 strand: + target_end: 319376 query_end: 52</span>
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12
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">target_name: chr3</span>
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14
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">query_name: 13:91170622:R:-276;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="15" 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">
15
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">optimal_alignment_score: 49 suboptimal_alignment_score: 48 strand: + target_end: 353946 query_end: 49</span>
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16
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="17" 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">
17
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">target_name: chr3</span>
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18
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">query_name: 15:37079528:R:-240;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="19" 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">
19
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">optimal_alignment_score: 40 suboptimal_alignment_score: 39 strand: + target_end: 257705 query_end: 53</span>
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20
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"></span>
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21
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">target_name: chr3</span>
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22
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">query_name: 9:92308501:R:-176;None;None/1</span>
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<td class="new_line diff-line-num new" data-linenumber="23" 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">
23
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">optimal_alignment_score: 80 suboptimal_alignment_score: 70 strand: + target_end: 105983 query_end: 48</span>
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24
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"></span>
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25
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">target_name: chr3</span>
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26
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">query_name: 3:109533106:R:-128;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="27" 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">
27
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">optimal_alignment_score: 42 suboptimal_alignment_score: 42 strand: + target_end: 198965 query_end: 47</span>
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28
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="29" 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">
29
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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30
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">query_name: 16:32366683:R:-158;16,32366730,G,A;None/1</span>
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<td class="new_line diff-line-num new" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
31
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">optimal_alignment_score: 50 suboptimal_alignment_score: 46 strand: + target_end: 823370 query_end: 52</span>
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32
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"></span>
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33
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">target_name: chr3</span>
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34
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">query_name: 13:111809970:R:-237;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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35
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">optimal_alignment_score: 43 suboptimal_alignment_score: 40 strand: + target_end: 509164 query_end: 53</span>
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36
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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37
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">target_name: chr3</span>
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38
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">query_name: 3:38871305:F:159;None;None/1</span>
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<td class="new_line diff-line-num new" data-linenumber="39" 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">
39
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">optimal_alignment_score: 39 suboptimal_alignment_score: 37 strand: + target_end: 841259 query_end: 54</span>
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40
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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41
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">target_name: chr3</span>
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42
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">query_name: 19:8434785:F:295;None;None/1</span>
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<td class="new_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">optimal_alignment_score: 47 suboptimal_alignment_score: 43 strand: + target_end: 330617 query_end: 53</span>
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44
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"></span>
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45
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">target_name: chr3</span>
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46
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">query_name: 8:132563397:R:-144;None;None/1</span>
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<td class="new_line diff-line-num new" data-linenumber="47" 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">
47
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">optimal_alignment_score: 49 suboptimal_alignment_score: 40 strand: + target_end: 54827 query_end: 54</span>
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48
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="49" 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">
49
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">target_name: chr3</span>
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<td class="new_line diff-line-num new" data-linenumber="50" 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">
50
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">query_name: 3:190507952:R:-57;3,190507958,G,A;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="51" 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">
51
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">optimal_alignment_score: 41 suboptimal_alignment_score: 41 strand: + target_end: 138110 query_end: 54</span>
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52
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="53" 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">
53
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="54" 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">
54
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">query_name: 10:59883855:R:-120;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="55" 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">
55
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">optimal_alignment_score: 43 suboptimal_alignment_score: 43 strand: + target_end: 244247 query_end: 53</span>
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56
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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57
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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58
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">query_name: 6:148630669:R:-271;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="59" 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">
59
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">optimal_alignment_score: 41 suboptimal_alignment_score: 39 strand: + target_end: 658593 query_end: 54</span>
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60
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
61
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">target_name: chr3</span>
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62
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">query_name: 3:64518566:R:-93;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="63" 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">
63
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">optimal_alignment_score: 46 suboptimal_alignment_score: 45 strand: + target_end: 881546 query_end: 44</span>
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64
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
65
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
66
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">query_name: 14:42514746:R:-187;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
67
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">optimal_alignment_score: 58 suboptimal_alignment_score: 58 strand: + target_end: 206906 query_end: 48</span>
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68
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
69
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
70
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">query_name: 7:126497810:R:-191;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
71
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">optimal_alignment_score: 45 suboptimal_alignment_score: 40 strand: + target_end: 232372 query_end: 54</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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72
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"></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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">target_name: chr3</span>
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<td class="new_line diff-line-num new" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
74
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">query_name: 21:15123085:R:-140;None;None/1</span>
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<td class="new_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
75
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">optimal_alignment_score: 43 suboptimal_alignment_score: 43 strand: + target_end: 492310 query_end: 51</span>
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76
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
77
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
78
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">query_name: 2:217172401:R:-226;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
79
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">optimal_alignment_score: 42 suboptimal_alignment_score: 41 strand: + target_end: 261738 query_end: 54</span>
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80
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
81
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
82
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">query_name: 6:129456169:R:-167;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
83
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">optimal_alignment_score: 42 suboptimal_alignment_score: 39 strand: + target_end: 750865 query_end: 53</span>
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84
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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85
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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86
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">query_name: 4:160333309:R:-131;None;4,160333230,T,G/1</span>
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87
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">optimal_alignment_score: 42 suboptimal_alignment_score: 41 strand: + target_end: 465814 query_end: 54</span>
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88
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
89
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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90
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">query_name: 3:37890126:R:-228;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="91" 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">
91
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">optimal_alignment_score: 40 suboptimal_alignment_score: 40 strand: + target_end: 661952 query_end: 53</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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92
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="93" 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">
93
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="94" 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">
94
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">query_name: 17:49899522:F:154;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="95" 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">
95
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">optimal_alignment_score: 47 suboptimal_alignment_score: 46 strand: + target_end: 94043 query_end: 51</span>
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96
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="97" 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">
97
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="98" 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">
98
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">query_name: 8:138662818:R:-211;None;8,138662609,C,T/1</span>
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99
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">optimal_alignment_score: 43 suboptimal_alignment_score: 41 strand: + target_end: 175380 query_end: 50</span>
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100
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="101" 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">
101
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">target_name: chr3</span>
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<td class="new_line diff-line-num new" data-linenumber="102" 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">
102
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">query_name: 3:97260940:R:-254;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="103" 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">
103
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">optimal_alignment_score: 39 suboptimal_alignment_score: 38 strand: + target_end: 903012 query_end: 54</span>
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104
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="105" 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">
105
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="106" 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">
106
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">query_name: 7:14401638:F:350;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="107" 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">
107
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">optimal_alignment_score: 50 suboptimal_alignment_score: 47 strand: + target_end: 265434 query_end: 48</span>
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108
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="109" 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">
109
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="110" 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">
110
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">query_name: 13:19068477:F:246;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="111" 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">
111
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext">optimal_alignment_score: 47 suboptimal_alignment_score: 45 strand: + target_end: 628991 query_end: 54</span>
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112
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext"></span>
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113
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext">target_name: chr3</span>
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114
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">query_name: 3:179655047:F:206;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
115
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext">optimal_alignment_score: 45 suboptimal_alignment_score: 44 strand: + target_end: 476787 query_end: 51</span>
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116
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="117" 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">
117
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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118
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">query_name: 20:15001091:F:174;None;None/1</span>
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119
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext">optimal_alignment_score: 44 suboptimal_alignment_score: 43 strand: + target_end: 226051 query_end: 51</span>
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120
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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121
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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122
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext">query_name: 2:54967337:R:-153;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_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">
123
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext">optimal_alignment_score: 43 suboptimal_alignment_score: 42 strand: + target_end: 689523 query_end: 54</span>
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124
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="125" 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">
125
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext">target_name: chr3</span>
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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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext">query_name: 18:39435195:F:202;None;None/1</span>
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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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext">optimal_alignment_score: 51 suboptimal_alignment_score: 45 strand: + target_end: 998370 query_end: 53</span>
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128
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext"></span>
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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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="130" 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">
130
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext">query_name: X:68133790:F:167;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="131" 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">
131
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext">optimal_alignment_score: 43 suboptimal_alignment_score: 40 strand: + target_end: 612440 query_end: 50</span>
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132
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="133" 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">
133
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="134" 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">
134
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext">query_name: 9:18241281:F:267;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="135" 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">
135
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext">optimal_alignment_score: 53 suboptimal_alignment_score: 49 strand: + target_end: 872860 query_end: 53</span>
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136
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="137" 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">
137
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="138" 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">
138
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext">query_name: 7:141812631:F:239;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="139" 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">
139
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext">optimal_alignment_score: 40 suboptimal_alignment_score: 40 strand: + target_end: 510995 query_end: 44</span>
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140
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="141" 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">
141
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="142" 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">
142
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext">query_name: 15:54133744:R:-269;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext">optimal_alignment_score: 41 suboptimal_alignment_score: 40 strand: + target_end: 725603 query_end: 53</span>
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144
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext">query_name: 4:66588719:R:-245;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="147" 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">
147
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext">optimal_alignment_score: 58 suboptimal_alignment_score: 58 strand: + target_end: 163129 query_end: 54</span>
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148
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="149" 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">
149
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="150" 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">
150
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext">query_name: 1:217587184:F:229;None;None/1</span>
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<td class="new_line diff-line-num new" data-linenumber="151" 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">
151
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext">optimal_alignment_score: 46 suboptimal_alignment_score: 46 strand: + target_end: 196793 query_end: 52</span>
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152
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="153" 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">
153
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext">target_name: chr3</span>
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<td class="new_line diff-line-num new" data-linenumber="154" 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">
154
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext">query_name: 2:119213044:R:-184;None;None/1</span>
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<td class="new_line diff-line-num new" data-linenumber="155" 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">
155
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext">optimal_alignment_score: 49 suboptimal_alignment_score: 44 strand: + target_end: 552663 query_end: 50</span>
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156
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC156" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="157" 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">
157
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC157" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="158" 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">
158
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext">query_name: 2:36811349:F:265;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="159" 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">
159
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC159" class="line" lang="plaintext">optimal_alignment_score: 44 suboptimal_alignment_score: 43 strand: + target_end: 945971 query_end: 52</span>
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160
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC160" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="161" 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">
161
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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162
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext">query_name: 1:68786835:F:349;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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163
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext">optimal_alignment_score: 45 suboptimal_alignment_score: 45 strand: + target_end: 528144 query_end: 52</span>
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164
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext"></span>
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165
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext">target_name: chr3</span>
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166
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext">query_name: 4:126634771:F:185;None;None/1</span>
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167
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext">optimal_alignment_score: 45 suboptimal_alignment_score: 42 strand: + target_end: 745309 query_end: 50</span>
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168
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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169
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC169" class="line" lang="plaintext">target_name: chr3</span>
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<td class="new_line diff-line-num new" data-linenumber="170" 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">
170
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC170" class="line" lang="plaintext">query_name: 4:114171402:R:-296;None;None/1</span>
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171
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC171" class="line" lang="plaintext">optimal_alignment_score: 44 suboptimal_alignment_score: 42 strand: + target_end: 751541 query_end: 53</span>
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172
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC172" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="173" 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">
173
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC173" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="174" 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">
174
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext">query_name: 9:125206364:R:-140;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="175" 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">
175
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC175" class="line" lang="plaintext">optimal_alignment_score: 41 suboptimal_alignment_score: 39 strand: + target_end: 932480 query_end: 50</span>
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176
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC176" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="177" 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">
177
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC177" class="line" lang="plaintext">target_name: chr3</span>
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<td class="new_line diff-line-num new" data-linenumber="178" 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">
178
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC178" class="line" lang="plaintext">query_name: X:25208394:F:245;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="179" 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">
179
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC179" class="line" lang="plaintext">optimal_alignment_score: 42 suboptimal_alignment_score: 41 strand: + target_end: 696734 query_end: 52</span>
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180
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="181" 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">
181
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="182" 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">
182
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext">query_name: 2:222217158:F:227;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="183" 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">
183
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext">optimal_alignment_score: 41 suboptimal_alignment_score: 40 strand: + target_end: 704921 query_end: 53</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="184" 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">
184
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="185" 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">
185
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC185" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="186" 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">
186
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext">query_name: 1:196837088:F:230;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="187" 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">
187
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext">optimal_alignment_score: 46 suboptimal_alignment_score: 45 strand: + target_end: 563639 query_end: 53</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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188
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC188" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="189" 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">
189
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC189" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="190" 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">
190
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext">query_name: 7:24300836:R:-208;7,24300863,*,+1T;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="191" 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">
191
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext">optimal_alignment_score: 44 suboptimal_alignment_score: 42 strand: + target_end: 239063 query_end: 54</span>
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192
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC192" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="193" 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">
193
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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194
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext">query_name: 1:76948473:F:230;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="195" 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">
195
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC195" class="line" lang="plaintext">optimal_alignment_score: 45 suboptimal_alignment_score: 45 strand: + target_end: 386767 query_end: 54</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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196
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC196" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="197" 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">
197
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC197" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="198" 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">
198
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC198" class="line" lang="plaintext">query_name: 8:62727783:F:135;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="199" 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">
199
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC199" class="line" lang="plaintext">optimal_alignment_score: 47 suboptimal_alignment_score: 46 strand: + target_end: 406541 query_end: 54</span>
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200
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC200" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="201" 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">
201
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC201" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="202" 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">
202
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC202" class="line" lang="plaintext">query_name: 7:94677617:R:-155;None;None/1</span>
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<td class="new_line diff-line-num new" data-linenumber="203" 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">
203
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC203" class="line" lang="plaintext">optimal_alignment_score: 46 suboptimal_alignment_score: 46 strand: + target_end: 345086 query_end: 54</span>
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<td class="new_line diff-line-num new" data-linenumber="204" 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">
204
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC204" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="205" 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">
205
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC205" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="206" 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">
206
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC206" class="line" lang="plaintext">query_name: 4:10707991:F:305;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="207" 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">
207
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC207" class="line" lang="plaintext">optimal_alignment_score: 94 suboptimal_alignment_score: 86 strand: + target_end: 198089 query_end: 53</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="208" 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">
208
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC208" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="209" 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">
209
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC209" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="210" 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">
210
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC210" class="line" lang="plaintext">query_name: 1:183203391:R:-141;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="211" 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">
211
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC211" class="line" lang="plaintext">optimal_alignment_score: 48 suboptimal_alignment_score: 45 strand: + target_end: 344874 query_end: 53</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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212
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC212" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_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">
213
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC213" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="214" 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">
214
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC214" class="line" lang="plaintext">query_name: 15:63526307:R:-83;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="215" 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">
215
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC215" class="line" lang="plaintext">optimal_alignment_score: 40 suboptimal_alignment_score: 40 strand: + target_end: 78739 query_end: 52</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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216
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC216" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="217" 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">
217
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC217" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="218" 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">
218
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC218" class="line" lang="plaintext">query_name: 8:79068236:F:137;None;None/1</span>
</pre></td>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="219" 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">
219
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC219" class="line" lang="plaintext">optimal_alignment_score: 43 suboptimal_alignment_score: 42 strand: + target_end: 326507 query_end: 47</span>
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<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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220
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC220" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="221" 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">
221
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC221" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="222" 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">
222
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC222" class="line" lang="plaintext">query_name: 9:1290219:R:-251;None;None/1</span>
</pre></td>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="223" 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">
223
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC223" class="line" lang="plaintext">optimal_alignment_score: 84 suboptimal_alignment_score: 80 strand: + target_end: 537411 query_end: 54</span>
</pre></td>
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<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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224
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC224" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="225" 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">
225
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC225" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="226" 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">
226
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC226" class="line" lang="plaintext">query_name: 5:122248402:R:-212;None;None/1</span>
</pre></td>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="227" 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">
227
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC227" class="line" lang="plaintext">optimal_alignment_score: 40 suboptimal_alignment_score: 39 strand: + target_end: 40834 query_end: 52</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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228
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC228" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="229" 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">
229
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC229" class="line" lang="plaintext">target_name: chr3</span>
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<td class="new_line diff-line-num new" data-linenumber="230" 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">
230
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC230" class="line" lang="plaintext">query_name: X:153897575:R:-263;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_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">
231
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC231" class="line" lang="plaintext">optimal_alignment_score: 75 suboptimal_alignment_score: 74 strand: + target_end: 223405 query_end: 49</span>
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232
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC232" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="233" 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">
233
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC233" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="234" 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">
234
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC234" class="line" lang="plaintext">query_name: 6:95453360:F:204;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="235" 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">
235
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC235" class="line" lang="plaintext">optimal_alignment_score: 45 suboptimal_alignment_score: 42 strand: + target_end: 182708 query_end: 52</span>
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236
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC236" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="237" 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">
237
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC237" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="238" 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">
238
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC238" class="line" lang="plaintext">query_name: 10:6951101:R:-212;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="239" 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">
239
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC239" class="line" lang="plaintext">optimal_alignment_score: 41 suboptimal_alignment_score: 38 strand: + target_end: 897043 query_end: 47</span>
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240
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC240" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="241" 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">
241
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC241" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="242" 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">
242
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC242" class="line" lang="plaintext">query_name: 13:59325230:F:98;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC243" class="line" lang="plaintext">optimal_alignment_score: 39 suboptimal_alignment_score: 38 strand: + target_end: 773481 query_end: 54</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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244
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC244" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="245" 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">
245
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC245" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="246" 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">
246
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC246" class="line" lang="plaintext">query_name: 3:37059536:F:184;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="247" 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">
247
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC247" class="line" lang="plaintext">optimal_alignment_score: 49 suboptimal_alignment_score: 44 strand: + target_end: 899262 query_end: 54</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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248
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC248" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="249" 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">
249
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC249" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="250" 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">
250
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC250" class="line" lang="plaintext">query_name: 9:91156368:F:149;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="251" 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">
251
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC251" class="line" lang="plaintext">optimal_alignment_score: 43 suboptimal_alignment_score: 42 strand: + target_end: 606747 query_end: 51</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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252
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC252" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="253" 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">
253
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC253" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="254" 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">
254
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC254" class="line" lang="plaintext">query_name: 12:55970708:R:-246;12,55970762,C,T;None/1</span>
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<td class="new_line diff-line-num new" data-linenumber="255" 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">
255
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC255" class="line" lang="plaintext">optimal_alignment_score: 92 suboptimal_alignment_score: 88 strand: + target_end: 771042 query_end: 54</span>
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256
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC256" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="257" 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">
257
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC257" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="258" 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">
258
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC258" class="line" lang="plaintext">query_name: 3:120828442:F:203;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="259" 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">
259
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC259" class="line" lang="plaintext">optimal_alignment_score: 44 suboptimal_alignment_score: 41 strand: + target_end: 595794 query_end: 50</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="260" 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">
260
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC260" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="261" 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">
261
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC261" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="262" 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">
262
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC262" class="line" lang="plaintext">query_name: 19:60104965:R:-147;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="263" 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">
263
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC263" class="line" lang="plaintext">optimal_alignment_score: 65 suboptimal_alignment_score: 64 strand: + target_end: 866783 query_end: 52</span>
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264
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC264" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="265" 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">
265
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC265" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="266" 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">
266
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC266" class="line" lang="plaintext">query_name: 11:98782460:R:-46;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="267" 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">
267
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC267" class="line" lang="plaintext">optimal_alignment_score: 56 suboptimal_alignment_score: 42 strand: + target_end: 819223 query_end: 51</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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268
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC268" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="269" 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">
269
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC269" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="270" 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">
270
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC270" class="line" lang="plaintext">query_name: 12:91111930:F:209;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="271" 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">
271
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC271" class="line" lang="plaintext">optimal_alignment_score: 43 suboptimal_alignment_score: 42 strand: + target_end: 679515 query_end: 51</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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272
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC272" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="273" 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">
273
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC273" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="274" 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">
274
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC274" class="line" lang="plaintext">query_name: 3:192601514:F:196;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="275" 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">
275
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC275" class="line" lang="plaintext">optimal_alignment_score: 42 suboptimal_alignment_score: 40 strand: + target_end: 392672 query_end: 40</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="276" 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">
276
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC276" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="277" 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">
277
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC277" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="278" 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">
278
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC278" class="line" lang="plaintext">query_name: X:47989386:R:-46;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="279" 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">
279
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC279" class="line" lang="plaintext">optimal_alignment_score: 39 suboptimal_alignment_score: 36 strand: + target_end: 793950 query_end: 54</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
280
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC280" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="281" 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">
281
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC281" class="line" lang="plaintext">target_name: chr3</span>
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<td class="new_line diff-line-num new" data-linenumber="282" 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">
282
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC282" class="line" lang="plaintext">query_name: 2:39824446:R:-127;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="283" 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">
283
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC283" class="line" lang="plaintext">optimal_alignment_score: 72 suboptimal_alignment_score: 70 strand: + target_end: 972352 query_end: 54</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="284" 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">
284
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC284" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="285" 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">
285
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC285" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="286" 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">
286
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC286" class="line" lang="plaintext">query_name: 1:227528596:F:219;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="287" 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">
287
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC287" class="line" lang="plaintext">optimal_alignment_score: 44 suboptimal_alignment_score: 42 strand: + target_end: 869543 query_end: 51</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="288" 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">
288
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC288" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="289" 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">
289
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC289" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="290" 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">
290
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC290" class="line" lang="plaintext">query_name: X:4440324:R:-90;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="291" 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">
291
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC291" class="line" lang="plaintext">optimal_alignment_score: 42 suboptimal_alignment_score: 40 strand: + target_end: 100289 query_end: 52</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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292
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC292" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC293" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="294" 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">
294
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC294" class="line" lang="plaintext">query_name: X:73634281:F:88;None;None/1</span>
</pre></td>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="295" 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">
295
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC295" class="line" lang="plaintext">optimal_alignment_score: 52 suboptimal_alignment_score: 41 strand: + target_end: 922600 query_end: 49</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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296
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC296" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="297" 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">
297
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC297" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="298" 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">
298
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC298" class="line" lang="plaintext">query_name: 3:53909823:F:239;None;3,53910104,T,C/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="299" 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">
299
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC299" class="line" lang="plaintext">optimal_alignment_score: 44 suboptimal_alignment_score: 44 strand: + target_end: 640897 query_end: 47</span>
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<tr class="line_holder new" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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300
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC300" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="301" 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">
301
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC301" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="302" 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">
302
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC302" class="line" lang="plaintext">query_name: 3:170059370:R:-173;None;3,170059212,G,C/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="303" 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">
303
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC303" class="line" lang="plaintext">optimal_alignment_score: 44 suboptimal_alignment_score: 43 strand: + target_end: 483764 query_end: 54</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="304" 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">
304
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC304" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="305" 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">
305
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC305" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="306" 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">
306
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC306" class="line" lang="plaintext">query_name: 20:8823533:F:251;None;None/1</span>
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<td class="new_line diff-line-num new" data-linenumber="307" 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">
307
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC307" class="line" lang="plaintext">optimal_alignment_score: 39 suboptimal_alignment_score: 38 strand: + target_end: 887639 query_end: 49</span>
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<td class="new_line diff-line-num new" data-linenumber="308" 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">
308
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC308" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="309" 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">
309
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC309" class="line" lang="plaintext">target_name: chr3</span>
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<td class="new_line diff-line-num new" data-linenumber="310" 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">
310
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC310" class="line" lang="plaintext">query_name: 5:106802036:F:200;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="311" 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">
311
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC311" class="line" lang="plaintext">optimal_alignment_score: 44 suboptimal_alignment_score: 42 strand: + target_end: 137797 query_end: 53</span>
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312
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC312" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="313" 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">
313
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC313" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="314" 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">
314
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC314" class="line" lang="plaintext">query_name: 5:74632980:R:-252;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="315" 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">
315
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC315" class="line" lang="plaintext">optimal_alignment_score: 44 suboptimal_alignment_score: 43 strand: + target_end: 297976 query_end: 54</span>
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316
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC316" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="317" 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">
317
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC317" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="318" 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">
318
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC318" class="line" lang="plaintext">query_name: 12:84751900:F:268;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="319" 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">
319
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC319" class="line" lang="plaintext">optimal_alignment_score: 42 suboptimal_alignment_score: 42 strand: + target_end: 183485 query_end: 48</span>
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320
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC320" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="321" 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">
321
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC321" class="line" lang="plaintext">target_name: chr3</span>
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322
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC322" class="line" lang="plaintext">query_name: X:135811790:R:-164;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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323
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC323" class="line" lang="plaintext">optimal_alignment_score: 48 suboptimal_alignment_score: 44 strand: + target_end: 178654 query_end: 54</span>
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324
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC324" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="325" 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">
325
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC325" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="326" 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">
326
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC326" class="line" lang="plaintext">query_name: 10:53108829:R:-138;None;None/1</span>
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<td class="new_line diff-line-num new" data-linenumber="327" 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">
327
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC327" class="line" lang="plaintext">optimal_alignment_score: 45 suboptimal_alignment_score: 42 strand: + target_end: 625392 query_end: 50</span>
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328
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC328" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="329" 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">
329
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC329" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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330
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC330" class="line" lang="plaintext">query_name: 11:83660431:R:-245;None;None/1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="331" 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">
331
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC331" class="line" lang="plaintext">optimal_alignment_score: 47 suboptimal_alignment_score: 44 strand: + target_end: 226749 query_end: 54</span>
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332
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC332" class="line" lang="plaintext"></span>
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333
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC333" class="line" lang="plaintext">target_name: chr3</span>
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<td class="new_line diff-line-num new" data-linenumber="334" 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">
334
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC334" class="line" lang="plaintext">query_name: 10:119650756:F:207;None;None/1</span>
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335
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC335" class="line" lang="plaintext">optimal_alignment_score: 44 suboptimal_alignment_score: 42 strand: + target_end: 529549 query_end: 41</span>
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336
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC336" class="line" lang="plaintext"></span>
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337
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC337" class="line" lang="plaintext">target_name: chr3</span>
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338
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC338" class="line" lang="plaintext">query_name: 2:154848222:R:-185;None;None/1</span>
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<td class="new_line diff-line-num new" data-linenumber="339" 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">
339
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC339" class="line" lang="plaintext">optimal_alignment_score: 45 suboptimal_alignment_score: 43 strand: + target_end: 585761 query_end: 54</span>
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340
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC340" class="line" lang="plaintext"></span>
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341
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC341" class="line" lang="plaintext">target_name: chr3</span>
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342
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC342" class="line" lang="plaintext">query_name: 3:63918850:F:276;None;None/1</span>
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343
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC343" class="line" lang="plaintext">optimal_alignment_score: 42 suboptimal_alignment_score: 41 strand: + target_end: 345340 query_end: 50</span>
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344
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC344" class="line" lang="plaintext"></span>
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345
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC345" class="line" lang="plaintext">target_name: chr3</span>
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346
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC346" class="line" lang="plaintext">query_name: 10:11447534:F:239;None;None/1</span>
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347
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC347" class="line" lang="plaintext">optimal_alignment_score: 38 suboptimal_alignment_score: 38 strand: + target_end: 114931 query_end: 52</span>
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348
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC348" class="line" lang="plaintext"></span>
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349
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC349" class="line" lang="plaintext">target_name: chr3</span>
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350
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC350" class="line" lang="plaintext">query_name: 1:57651555:R:-316;None;None/1</span>
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<td class="new_line diff-line-num new" data-linenumber="351" 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">
351
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC351" class="line" lang="plaintext">optimal_alignment_score: 46 suboptimal_alignment_score: 44 strand: + target_end: 104219 query_end: 54</span>
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352
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC352" class="line" lang="plaintext"></span>
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353
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC353" class="line" lang="plaintext">target_name: chr3</span>
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354
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC354" class="line" lang="plaintext">query_name: X:91671697:R:-206;None;X,91671506,G,A/1</span>
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<td class="new_line diff-line-num new" data-linenumber="355" 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">
355
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC355" class="line" lang="plaintext">optimal_alignment_score: 48 suboptimal_alignment_score: 47 strand: + target_end: 771479 query_end: 49</span>
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356
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC356" class="line" lang="plaintext"></span>
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357
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC357" class="line" lang="plaintext">target_name: chr3</span>
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358
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC358" class="line" lang="plaintext">query_name: 12:101622421:R:-187;None;None/1</span>
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<td class="new_line diff-line-num new" data-linenumber="359" 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">
359
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC359" class="line" lang="plaintext">optimal_alignment_score: 45 suboptimal_alignment_score: 44 strand: + target_end: 361502 query_end: 49</span>
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360
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC360" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="361" 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">
361
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC361" class="line" lang="plaintext">target_name: chr3</span>
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<td class="new_line diff-line-num new" data-linenumber="362" 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">
362
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC362" class="line" lang="plaintext">query_name: 13:43163355:R:-200;None;None/1</span>
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363
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC363" class="line" lang="plaintext">optimal_alignment_score: 42 suboptimal_alignment_score: 42 strand: + target_end: 167308 query_end: 53</span>
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364
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC364" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="365" 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">
365
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC365" class="line" lang="plaintext">target_name: chr3</span>
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<td class="new_line diff-line-num new" data-linenumber="366" 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">
366
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC366" class="line" lang="plaintext">query_name: 19:37349825:R:-160;None;None/1</span>
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367
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC367" class="line" lang="plaintext">optimal_alignment_score: 70 suboptimal_alignment_score: 68 strand: + target_end: 261459 query_end: 54</span>
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368
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC368" class="line" lang="plaintext"></span>
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369
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC369" class="line" lang="plaintext">target_name: chr3</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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370
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC370" class="line" lang="plaintext">query_name: 8:41173199:R:-175;None;8,41173056,T,C/1</span>
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371
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC371" class="line" lang="plaintext">optimal_alignment_score: 44 suboptimal_alignment_score: 43 strand: + target_end: 644612 query_end: 47</span>
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372
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC372" class="line" lang="plaintext"></span>
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373
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC373" class="line" lang="plaintext">target_name: chr3</span>
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374
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC374" class="line" lang="plaintext">query_name: 16:29068055:R:-232;None;None/1</span>
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375
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC375" class="line" lang="plaintext">optimal_alignment_score: 44 suboptimal_alignment_score: 40 strand: + target_end: 934198 query_end: 53</span>
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376
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC376" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="377" 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">
377
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC377" class="line" lang="plaintext">target_name: chr3</span>
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378
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC378" class="line" lang="plaintext">query_name: 1:4694340:F:179;None;None/1</span>
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379
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC379" class="line" lang="plaintext">optimal_alignment_score: 48 suboptimal_alignment_score: 45 strand: + target_end: 140768 query_end: 54</span>
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380
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC380" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="381" 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">
381
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC381" class="line" lang="plaintext">target_name: chr3</span>
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<td class="new_line diff-line-num new" data-linenumber="382" 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">
382
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC382" class="line" lang="plaintext">query_name: 17:76451446:F:221;None;None/1</span>
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<td class="new_line diff-line-num new" data-linenumber="383" 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">
383
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC383" class="line" lang="plaintext">optimal_alignment_score: 42 suboptimal_alignment_score: 40 strand: + target_end: 561765 query_end: 54</span>
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384
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC384" class="line" lang="plaintext"></span>
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385
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC385" class="line" lang="plaintext">target_name: chr3</span>
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<td class="new_line diff-line-num new" data-linenumber="386" 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">
386
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC386" class="line" lang="plaintext">query_name: 1:242817485:F:158;None;None/1</span>
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<td class="new_line diff-line-num new" data-linenumber="387" 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">
387
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC387" class="line" lang="plaintext">optimal_alignment_score: 52 suboptimal_alignment_score: 46 strand: + target_end: 396383 query_end: 50</span>
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388
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC388" class="line" lang="plaintext"></span>
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389
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC389" class="line" lang="plaintext">target_name: chr3</span>
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<td class="new_line diff-line-num new" data-linenumber="390" 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">
390
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC390" class="line" lang="plaintext">query_name: 18:29611708:R:-146;None;18,29611585,G,A/1</span>
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<td class="new_line diff-line-num new" data-linenumber="391" 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">
391
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC391" class="line" lang="plaintext">optimal_alignment_score: 45 suboptimal_alignment_score: 40 strand: + target_end: 157255 query_end: 47</span>
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392
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC392" class="line" lang="plaintext"></span>
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393
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC393" class="line" lang="plaintext">target_name: chr3</span>
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394
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC394" class="line" lang="plaintext">query_name: 9:36493018:F:206;None;None/1</span>
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<td class="new_line diff-line-num new" data-linenumber="395" 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">
395
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC395" class="line" lang="plaintext">optimal_alignment_score: 82 suboptimal_alignment_score: 80 strand: + target_end: 872774 query_end: 54</span>
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396
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC396" class="line" lang="plaintext"></span>
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397
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC397" class="line" lang="plaintext">target_name: chr3</span>
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398
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC398" class="line" lang="plaintext">query_name: 9:16274705:F:129;9,16274709,C,A:9,16274719,C,G:9,16274741,A,T;9,16274862,A,G/1</span>
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<td class="new_line diff-line-num new" data-linenumber="399" 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">
399
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC399" class="line" lang="plaintext">optimal_alignment_score: 72 suboptimal_alignment_score: 64 strand: + target_end: 524699 query_end: 54</span>
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400
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC400" class="line" lang="plaintext"></span></pre></td>
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<li id="953dea787ebfc7ec6cfb16e329ac3fad36e24098">
<a href="https://salsa.debian.org/med-team/libssw/-/commit/c9c6106f955eac1ec9d8a40cc85495ccf3178810#953dea787ebfc7ec6cfb16e329ac3fad36e24098"><strong>demo/pRead.fa</strong></a>
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1
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">>read</span>
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2
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">AGGTAGGTAGGTAGGTAGGTAGGTAGGTAGGTAGGTAGGT</span>
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<td class="new_line diff-line-num new" data-linenumber="3" 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">
3
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"></span></pre></td>
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<li id="ca1adc883fa7cae318a7544025e73368f380e7c4">
<a href="https://salsa.debian.org/med-team/libssw/-/commit/c9c6106f955eac1ec9d8a40cc85495ccf3178810#ca1adc883fa7cae318a7544025e73368f380e7c4"><strong>demo/pRef.fa</strong></a>
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1
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">>ref</span>
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<td class="new_line diff-line-num new" data-linenumber="2" 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">
2
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">CCCAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCT</span>
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<td class="new_line diff-line-num new" data-linenumber="3" 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">
3
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"></span></pre></td>
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<li id="ba2b8a31dd4ce686bef5fd0c5ad5fa9447b881fb">
<a href="https://salsa.debian.org/med-team/libssw/-/commit/c9c6106f955eac1ec9d8a40cc85495ccf3178810#ba2b8a31dd4ce686bef5fd0c5ad5fa9447b881fb"><strong>demo/protein1.fa</strong></a>
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<td class="new_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">>random1</span>
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2
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">CLKQTQMRTDHAMCGDFWEESHHHFTLCIA</span></pre></td>
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<a href="https://salsa.debian.org/med-team/libssw/-/commit/c9c6106f955eac1ec9d8a40cc85495ccf3178810#f3425f7ff4e8df66ef0f8b0151caac9ab2789a71"><strong>demo/protein2.fa</strong></a>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">>random1</span>
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2
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">CLKQTQMRTDHARCGDFWEESHHHHHHFTLCIA</span></pre></td>
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<li id="5cf4a933540afe944c2154fc9fce269a512ab6f0">
<a href="https://salsa.debian.org/med-team/libssw/-/commit/c9c6106f955eac1ec9d8a40cc85495ccf3178810#5cf4a933540afe944c2154fc9fce269a512ab6f0"><strong>demo/query.fastq</strong></a>
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1
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">@6:163296599:F:198;None;None/1</span>
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2
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">GTGTGAGCCACCACGCCCAGCCCAAAATCTGTTTTAATGGTGGATTTGTGTTTC</span>
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3
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4
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">%/978679:99788::8888689788888888986637/%/*%--/11,%*/*%</span>
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5
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">@3:153409880:F:224;None;3,153410143,G,A/1</span>
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6
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">AGGAAGAGTTAATTTAAGTCACTTCAAACAGATTACGTATCTTTTTTTTCCCTC</span>
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7
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8
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">%-;;8;;9289.73697758:5,2984,54687/*8,'.001/550'+'.(9((</span></pre></td>
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<li id="ce18ac8d0dec073f5834ae743188f88690e89f99">
<a href="https://salsa.debian.org/med-team/libssw/-/commit/c9c6106f955eac1ec9d8a40cc85495ccf3178810#ce18ac8d0dec073f5834ae743188f88690e89f99"><strong>demo/query2.fa</strong></a>
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1
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">>query2</span>
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2
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">CTTTCCTCCCCCTTGCCCTCTAGCAGGGGCCACCGGAGGAGGAGGGAGGGCAAACGAAGGATGGGGGAAGATGTG</span>
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3
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<a href="https://salsa.debian.org/med-team/libssw/-/commit/c9c6106f955eac1ec9d8a40cc85495ccf3178810#8211e4b2b9cd3dd81013e035545a6a836b70fef3"><strong>demo/r1.fa</strong></a>
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1
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">>HLA-B*08:01:01_2 AC:HLA00146.1 CR:AJ295294.1,AL669854.0,D84394.0,DQ249172.0,DQ249174.0,HG794374.0,L76093.1,LN624507.0,LN877354.0,LT220237.0,M24036.1,M28204.1,M59841.1</span>
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2
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">gctcccactccatgaggtatttcgacaccgccatgtcccggcccggccgcggggagccccgcttcatctcagtgggctacgtggacgacacgcagttcgtgaggttcgacagcgacgccgcgagtccgagagaggagccgcgggcgccgtggatagagcaggaggggccggagtattgggaccggaacacacagatcttcaagaccaacacacagactgaccgagagagcctgcggaacctgcgcggctactacaaccagagcgaggccg</span></pre></td>
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<a href="https://salsa.debian.org/med-team/libssw/-/commit/c9c6106f955eac1ec9d8a40cc85495ccf3178810#4900f4a91e22398bcbab45dea413b71c6fe68d14"><strong>demo/r1_query.fq</strong></a>
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1
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">@ST-E00185:49:H5LVWCCXX:5:1101:18001:19276 1:N:0:0</span>
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2
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">GGATCCCAGACCCGGAGACTCGGGAGTACCCGGGGCGTCCGTGGGGCATGGAGGTGGGGGGTCGTGATCTGCGCCCTGGGCCGGGGTTACTCACTGGCCTCGCTCTGGTTGTAGTAGCCGCGCAGGGTCTGCAGGTTCATTCTGTCAGTC</span>
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3
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4
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">AAFFFKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKFKKFKKKKKKKKKKKKKKKKKKKKAKKKKKKKKKKKKKKKKFKAAKAKKKKKKKKKKKKKKKKKKFKKKKKKKAFFKKKKAK<FFA<K</span></pre></td>
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<li id="177d21c38101fb4e45d3dc053245b33595d131c9">
<a href="https://salsa.debian.org/med-team/libssw/-/commit/c9c6106f955eac1ec9d8a40cc85495ccf3178810#177d21c38101fb4e45d3dc053245b33595d131c9"><strong>demo/target.fastq</strong></a>
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1
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">@20:8823533:F:251;None;None/1</span>
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2
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">GTGGTGGATGTCTCAGCAGAGGCCTGCATAGAAAGACGACATTGAGGATCAGTG</span>
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3
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">+</span>
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<a href="https://salsa.debian.org/med-team/libssw/-/commit/c9c6106f955eac1ec9d8a40cc85495ccf3178810#38e1c3f1ba1ea7a40337ac0d08f28678a3444a6b"><strong>demo/target2.fa</strong></a>
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<a href="https://salsa.debian.org/med-team/libssw/-/commit/c9c6106f955eac1ec9d8a40cc85495ccf3178810#09a8e11089bd7b184c2ba7778565c1350e1c7e3a"><strong>src/Makefile</strong></a>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1" class="line" lang="make"><span class="nv" style="color: #008080;">CC</span> <span class="o" style="font-weight: 600;">=</span> gcc</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;">CXX</span> <span class="o" style="font-weight: 600;">=</span> g++</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><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;">-Wall</span> <span class="nt" style="color: #000080;">-pipe</span> <span class="nt" style="color: #000080;">-O2</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="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;">-Wall</span> <span class="nt" style="color: #000080;">-pipe</span> <span class="nt" style="color: #000080;">-O2</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC4" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#CFLAGS += -Wall -pipe -g -fsanitize=address # for debug</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="LC5" class="line" lang="make"><span class="nv" style="color: #008080;">CXXFLAGS</span> <span class="o" style="font-weight: 600;">:=</span> <span class="nv" style="color: #008080;">$(CFLAGS)</span></span>
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6
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC6" class="line" lang="make"><span class="nv" style="color: #008080;">LOBJS</span> <span class="o" style="font-weight: 600;">=</span> ssw.o</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC7" class="line" lang="make"><span class="nv" style="color: #008080;">LCPPOBJS</span> <span class="o" style="font-weight: 600;">=</span> ssw_cpp.o</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,17 +11,16 @@ EXAMPLE = example_c</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC11" class="line" lang="make"><span class="nv" style="color: #008080;">EXAMPLE_CPP</span> <span class="o" style="font-weight: 600;">=</span> example_cpp</span>
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11
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<td class="new_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
12
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC12" class="line" lang="make"><span class="nv" style="color: #008080;">JAVA_JAR</span> <span class="o" style="font-weight: 600;">=</span> ssw.jar</span>
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12
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<td class="new_line diff-line-num" data-linenumber="13" 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">
13
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC13" class="line" lang="make"><span class="nv" style="color: #008080;">JAVA_LIB</span> <span class="o" style="font-weight: 600;">=</span> libsswjni.so</span>
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13
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<td class="new_line diff-line-num old" data-linenumber="14" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC13" class="line" lang="make"><span class="nv" style="color: #008080;">JAVA_INLCUDES</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-I</span><span class="s2" style="color: #d14;"><span class="idiff left deletion">"</span></span><span class="nv" style="color: #008080;">$(JAVA_HOME)</span><span class="s2" style="color: #d14;">/include<span class="idiff deletion">"</span></span> <span class="nt" style="color: #000080;">-I</span><span class="s2" style="color: #d14;"><span class="idiff deletion">"</span></span><span class="nv" style="color: #008080;">$(JAVA_HOME)</span><span class="s2" style="color: #d14;">/include/linux<span class="idiff right deletion">"</span></span></span>
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14
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC14" class="line" lang="make"><span class="nv" style="color: #008080;">JAVA_INLCUDES</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-I</span><span class="nv" style="color: #008080;">$(JAVA_HOME)</span>/include <span class="nt" style="color: #000080;">-I</span><span class="nv" style="color: #008080;">$(JAVA_HOME)</span>/include/linux</span>
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14
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<td class="new_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC15" class="line" lang="make"><span class="nv" style="color: #008080;">JAVA_OBJ</span> <span class="o" style="font-weight: 600;">=</span> ssw/Aligner.class ssw/Alignment.class ssw/Example.class</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC16" class="line" lang="make"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC17" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">all default java clean</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="LC18" class="line" lang="make"></span>
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18
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC19" class="line" lang="make"><span class="nl">default</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(PROG) $(EXAMPLE) $(EXAMPLE_CPP) $(LIB) </span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC20" class="line" lang="make"><span class="nl">core</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(PROG)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="21" 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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC21" class="line" lang="make"><span class="nl">java</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">java_home $(JAVA_JAR) $(JAVA_LIB)</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC22" class="line" lang="make"><span class="nl">all</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">default java</span></span>
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23
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC23" class="line" lang="make"></span>
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<td class="new_line diff-line-num old" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC22" class="line" lang="make"><span class="nl">java</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(JAVA_JAR) $(JAVA_LIB)</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC24" class="line" lang="make"><span class="nl">$(LIB)</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">ssw.c ssw.h</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="LC25" class="line" lang="make"> <span class="nv" style="color: #008080;">$(CC)</span> <span class="nv" style="color: #008080;">$(CFLAGS)</span> <span class="nt" style="color: #000080;">-fPIC</span> <span class="nt" style="color: #000080;">-shared</span> <span class="nt" style="color: #000080;">-rdynamic</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$<</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="LC26" class="line" lang="make"></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">@@ -28,11 +28,16 @@ $(PROG): main.c kseq.h</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC28" class="line" lang="make"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC29" class="line" lang="make"><span class="nl">$(EXAMPLE)</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">example.c</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="LC30" class="line" lang="make"></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC31" class="line" lang="make"><span class="k" style="font-weight: 600;">ifdef</span> <span class="nv" style="color: #008080;">__arm__ </span><span class="c" style="color: #998; font-style: italic;"># (M1)</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC32" class="line" lang="make"><span class="nl">$(PROG) $(EXAMPLE)</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(LOBJS)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="33" 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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC33" class="line" lang="make"> <span class="nv" style="color: #008080;">$(CC)</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">filter-out</span> %.h,<span class="nv" style="color: #008080;">$^</span><span class="nf" style="color: #900; font-weight: 600;">)</span> <span class="nv" style="color: #008080;">$(CFLAGS)</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nt" style="color: #000080;">-lm</span> <span class="nt" style="color: #000080;">-lz</span> <span class="nt" style="color: #000080;">-march</span><span class="o" style="font-weight: 600;">=</span>armv8-a+fp+simd+crypto+crc</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">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC34" class="line" lang="make"><span class="k" style="font-weight: 600;">else</span> <span class="c" style="color: #998; font-style: italic;"># x86(Intel)</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="LC35" class="line" lang="make"><span class="nl">$(PROG) $(EXAMPLE)</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(LOBJS)</span></span>
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<td class="new_line diff-line-num old" data-linenumber="36" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC32" class="line" lang="make"> <span class="nv" style="color: #008080;">$(CC)</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">filter-out</span> %.h,<span class="nv" style="color: #008080;">$^</span><span class="nf" style="color: #900; font-weight: 600;">)</span> <span class="nv" style="color: #008080;">$(CFLAGS)</span> <span class="nt" style="color: #000080;">-lm</span> <span class="nt" style="color: #000080;">-lz</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC36" class="line" lang="make"> <span class="nv" style="color: #008080;">$(CC)</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">filter-out</span> %.h,<span class="nv" style="color: #008080;">$^</span><span class="nf" style="color: #900; font-weight: 600;">)</span> <span class="nv" style="color: #008080;">$(CFLAGS)</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nt" style="color: #000080;">-lm</span> <span class="nt" style="color: #000080;">-lz</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC37" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC38" class="line" lang="make"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC39" class="line" lang="make"><span class="nl">$(EXAMPLE_CPP)</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">example.cpp $(LOBJS) $(LCPPOBJS)</span></span>
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<td class="new_line diff-line-num old" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC35" class="line" lang="make"> <span class="nv" style="color: #008080;">$(CXX)</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$^</span> <span class="nv" style="color: #008080;">$(CXXFLAGS)</span> <span class="nt" style="color: #000080;">-lm</span> <span class="nt" style="color: #000080;">-lz</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC40" class="line" lang="make"> <span class="nv" style="color: #008080;">$(CXX)</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$^</span> <span class="nv" style="color: #008080;">$(CXXFLAGS)</span> <span class="nv" style="color: #008080;"><span class="idiff left addition">$(LDFLAGS)</span></span><span class="idiff right addition"> </span><span class="nt" style="color: #000080;">-lm</span> <span class="nt" style="color: #000080;">-lz</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="LC41" class="line" lang="make"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC42" class="line" lang="make"><span class="nl">$(JAVA_LIB)</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">sswjni.c ssw.c ssw.h</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC43" class="line" lang="make"> <span class="nv" style="color: #008080;">$(CC)</span> <span class="nv" style="color: #008080;">$(CFLAGS)</span> <span class="nv" style="color: #008080;">$(JAVA_INLCUDES)</span> <span class="nt" style="color: #000080;">-fPIC</span> <span class="nt" style="color: #000080;">-shared</span> <span class="nt" style="color: #000080;">-rdynamic</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$<</span> ssw.c </span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="47" 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">@@ -42,7 +47,13 @@ $(JAVA_JAR): $(JAVA_OBJ)</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC47" class="line" lang="make"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC48" class="line" lang="make"><span class="nl">%.class</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">%.java</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC49" class="line" lang="make"> javac <span class="nt" style="color: #000080;">-cp</span> ./ <span class="nv" style="color: #008080;">$<</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC51" class="line" lang="make"><span class="nl">java_home</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC52" class="line" lang="make"><span class="k" style="font-weight: 600;">ifndef</span> <span class="nv" style="color: #008080;">JAVA_HOME</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC53" class="line" lang="make"> <span class="p">@</span><span class="nv" style="color: #008080;">$(ECHO)</span> <span class="s2" style="color: #d14;">"ERROR: Your JAVA_HOME environment variable is not set."</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC54" class="line" lang="make"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC57" class="line" lang="make"><span class="nl">ssw.o</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">ssw.c ssw.h</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC58" class="line" lang="make"> <span class="nv" style="color: #008080;">$(CC)</span> <span class="nt" style="color: #000080;">-c</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$<</span> <span class="nv" style="color: #008080;">$(CFLAGS)</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="LC59" class="line" lang="make"></span>
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<a href="https://salsa.debian.org/med-team/libssw/-/commit/c9c6106f955eac1ec9d8a40cc85495ccf3178810#35fb435cf9b530ce411f4095badbb793a4e1cd78"><strong>src/example.cpp</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">@@ -5,10 +5,11 @@</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// 1) g++ -Wall ssw_cpp.cpp ssw.c example.cpp</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="LC6" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// 2) ./a.out</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="LC7" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Created by Wan-Ping Lee on 09/04/12.</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC8" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Last revision by Mengyao Zhao on 2017-06-05</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="LC9" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// ==========================</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="LC10" class="line" lang="cpp"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC11" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <iostream></span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC11" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <string></span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC12" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <string<span class="idiff left right addition">.h</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="LC13" class="line" lang="cpp"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC14" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "ssw_cpp.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">@@ -21,6 +22,8 @@ static void PrintAlignment(const StripedSmithWaterman::Alignment& alignment);</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">()</span> <span class="p">{</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="LC23" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"CAGCCTTTCTGACCCGGAAATCAAAATAGGCACAACAAA"</span><span class="p">;</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="LC24" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">query</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"CTGAGCCGGTAAATC"</span><span class="p">;</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">maskLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">query</span><span class="p">.</span><span class="n" style="color: #333;">c_str</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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp"> <span class="n" style="color: #333;">maskLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maskLen</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">15</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">15</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">maskLen</span><span class="p">;</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="LC27" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//const string ref = "CCGTTTATCGCA";</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="LC28" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//const string query = "CCTTTTATCGCA";</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="LC29" class="line" lang="cpp"></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">@@ -31,7 +34,7 @@ int main() {</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Declares an alignment that stores the result</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="LC35" class="line" lang="cpp"> <span class="n" style="color: #333;">StripedSmithWaterman</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Alignment</span> <span class="n" style="color: #333;">alignment</span><span class="p">;</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="LC36" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Aligns the query to the ref</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC34" class="line" lang="cpp"> <span class="n" style="color: #333;">aligner</span><span class="p">.</span><span class="n" style="color: #333;">Align</span><span class="p">(</span><span class="n" style="color: #333;">query</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">ref</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">ref</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="n" style="color: #333;">filter</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">alignment</span><span class="p">);</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp"> <span class="n" style="color: #333;">aligner</span><span class="p">.</span><span class="n" style="color: #333;">Align</span><span class="p">(</span><span class="n" style="color: #333;">query</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">ref</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">ref</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="n" style="color: #333;">filter</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">alignment</span><span class="p"><span class="idiff left addition">,</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff right addition">maskLen</span></span><span class="p">);</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="LC38" class="line" lang="cpp"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC39" class="line" lang="cpp"> <span class="n" style="color: #333;">PrintAlignment</span><span class="p">(</span><span class="n" style="color: #333;">alignment</span><span class="p">);</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="LC40" class="line" lang="cpp"></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">@@ -25,7 +25,7 @@</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC26" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* Contact: Heng Li <lh3@sanger.ac.uk> */</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC28" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* Last Modified<span class="idiff left right deletion">: 12APR2009</span> */</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC28" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* Last Modified<span class="idiff left right addition"> by Mengyao: 2022Mar28</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="LC29" class="line" lang="c"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC30" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef AC_KSEQ_H</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="LC31" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define AC_KSEQ_H</span></span>
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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" 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">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -149,11 +149,11 @@ typedef struct __kstring_t {</td>
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149
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149
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC149" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> s->f = ks_init(fd); \</span></span>
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150
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150
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC150" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> return s; \</span></span>
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151
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151
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC151" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> } \</span></span>
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152
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC152" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> static inline void kseq_rewind(kseq_t *ks) \</span></span>
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152
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC152" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right addition">/*</span> static inline void kseq_rewind(kseq_t *ks) \</span></span>
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153
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153
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC153" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> { \</span></span>
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154
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154
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC154" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> ks->last_char = 0; \</span></span>
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155
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155
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC155" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> ks->f->is_eof = ks->f->begin = ks->f->end = 0; \</span></span>
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156
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC156" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> } \</span></span>
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156
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC156" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> } <span class="idiff left right addition">*/</span></span><span class="cp" style="color: #999; font-weight: 600;"> \</span></span>
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157
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157
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC157" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> static inline void kseq_destroy(kseq_t *ks) \</span></span>
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158
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158
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC158" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> { \</span></span>
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159
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159
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC159" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if (!ks) return; \</span></span>
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<a href="https://salsa.debian.org/med-team/libssw/-/commit/c9c6106f955eac1ec9d8a40cc85495ccf3178810#3a576e09615c0e19842e5f3ac31e858c9ae7fe41"><strong>src/main.c</strong></a>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* main.c</span></span>
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2
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2
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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="c"><span class="cm" style="color: #998; font-style: italic;"> * Created by Mengyao Zhao on 06/23/11.</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC3" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Version 1.<span class="idiff left right deletion">0</span></span></span>
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<td class="new_line diff-line-num old" data-linenumber="3" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC4" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Last revision by Mengyao Zhao on <span class="idiff left right deletion">07/19/16</span>.</span></span>
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3
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Version 1.<span class="idiff left right addition">2.2</span></span></span>
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4
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC4" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Last revision by Mengyao Zhao on <span class="idiff left right addition">2022-May-21</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="LC5" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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6
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC6" class="line" lang="c"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC7" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stdlib.h></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="LC8" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stdint.h></span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC9" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <emmintrin.h></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="LC9" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <zlib.h></span></span>
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10
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC10" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stdio.h></span></span>
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11
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC11" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <time.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">@@ -16,6 +15,13 @@</td>
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15
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC15" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "ssw.h"</span></span>
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16
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC16" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "kseq.h"</span></span>
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18
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17
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC17" class="line" lang="c"></span>
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18
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC18" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __ARM_NEON // (M1)</span></span>
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19
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC19" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "sse2neon.h"</span></span>
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20
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC20" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else // x86 (Intel)</span></span>
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21
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC21" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <emmintrin.h></span></span>
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22
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC22" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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23
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC25" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __GNUC__</span></span>
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26
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC26" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define LIKELY(x) __builtin_expect((x),1)</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="LC27" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define UNLIKELY(x) __builtin_expect((x),0)</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">@@ -60,6 +66,8 @@ static void ssw_write (s_align* a,</td>
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66
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC66" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">kseq_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ref_seq</span><span class="p">,</span></span>
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67
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC67" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">kseq_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">read</span><span class="p">,</span></span>
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68
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC68" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</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;">read_seq</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// strand == 0: original read; strand == 1: reverse complement read</span></span>
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69
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC69" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <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;">ref_num</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
70
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC70" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <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;">read_num</span><span class="p">,</span></span>
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63
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<td class="new_line diff-line-num" data-linenumber="71" 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">
71
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC71" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <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;">table</span><span class="p">,</span></span>
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64
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<td class="new_line diff-line-num" data-linenumber="72" 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">
72
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC72" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int8_t</span> <span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// 0: forward aligned ; 1: reverse complement aligned</span></span>
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65
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<td class="new_line diff-line-num" 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">
73
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC73" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int8_t</span> <span class="n" style="color: #333;">sam</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// 0: Blast like output; 1: Sam format output</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="163" 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">@@ -155,56 +163,28 @@ end:</td>
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155
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163
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC163" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">name</span><span class="p">.</span><span class="n" style="color: #333;">s</span><span class="p">);</span></span>
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156
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<td class="new_line diff-line-num" data-linenumber="164" 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">
164
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC164" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">score1</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;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"4</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">*</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">0</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">255</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">*</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">*</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">0</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">0</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">*</span><span class="se" style="color: #d14;">\t</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" data-linenumber="157" 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">
157
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<td class="new_line diff-line-num" data-linenumber="165" 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">
165
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC165" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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158
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<td class="new_line diff-line-num old" data-linenumber="166" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC158" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left deletion">l</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">=</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">a</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">-></span></span><span class="n" style="color: #333;"><span class="idiff deletion">read_end1</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">-</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">a</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">-></span></span><span class="n" style="color: #333;"><span class="idiff deletion">read_begin1</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">+</span></span><span class="idiff deletion"> </span><span class="mi" style="color: #099;"><span class="idiff deletion">1</span></span><span class="p"><span class="idiff deletion">,</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">qb</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">=</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">a</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">-></span></span><span class="n" style="color: #333;"><span class="idiff deletion">ref_begin1</span></span><span class="p"><span class="idiff deletion">,</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">pb</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">=</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">a</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">-></span></span><span class="n" style="color: #333;"><span class="idiff deletion">read_begin1</span></span><span class="p"><span class="idiff deletion">,</span></span><span class="idiff right deletion"> </span><span class="n" style="color: #333;">p</span><span class="p">;</span></span>
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<td class="old_line diff-line-num new" data-linenumber="159" 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="166" 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">
166
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC166" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="159" 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">
159
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<td class="new_line diff-line-num" data-linenumber="167" 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">
167
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC167" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">mapq</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">.</span><span class="mi" style="color: #099;">343</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">log</span><span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">score1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">score2</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">score1</span><span class="p">);</span></span>
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160
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<td class="new_line diff-line-num" data-linenumber="168" 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">
168
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC168" class="line" lang="c"> <span class="n" style="color: #333;">mapq</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">mapq</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">4</span><span class="p">.</span><span class="mi" style="color: #099;">99</span><span class="p">);</span></span>
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161
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<td class="new_line diff-line-num" data-linenumber="169" 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">
169
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC169" class="line" lang="c"> <span class="n" style="color: #333;">mapq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mapq</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">254</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">mapq</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">254</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="162" 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">
162
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<td class="new_line diff-line-num" data-linenumber="170" 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">
170
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC170" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strand</span><span class="p">)</span> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"16</span><span class="se" style="color: #d14;">\t</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="163" 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">
163
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<td class="new_line diff-line-num" data-linenumber="171" 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">
171
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC171" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"0</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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164
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172
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC172" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">ref_seq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">name</span><span class="p">.</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ref_begin1</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;">mapq</span><span class="p">);</span></span>
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165
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<td class="new_line diff-line-num old" data-linenumber="173" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC165" class="line" lang="c"> <span class="n" style="color: #333;">mismatch</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mark_mismatch</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ref_begin1</span><span class="p">,</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_begin1</span><span class="p">,</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_end1</span><span class="p">,</span> <span class="n" style="color: #333;">ref_<span class="idiff left deletion">seq</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">-></span></span><span class="n" style="color: #333;"><span class="idiff deletion">seq</span></span><span class="p"><span class="idiff deletion">.</span></span><span class="n" style="color: #333;"><span class="idiff deletion">s</span></span><span class="p">,</span> <span class="n" style="color: #333;">read_<span class="idiff right deletion">seq</span></span><span class="p">,</span> <span class="n" style="color: #333;">read</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;">l</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cigar</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cigarLen</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="173" 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">
173
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC173" class="line" lang="c"> <span class="n" style="color: #333;">mismatch</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mark_mismatch</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ref_begin1</span><span class="p">,</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_begin1</span><span class="p">,</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_end1</span><span class="p">,</span> <span class="n" style="color: #333;">ref_<span class="idiff left addition">num</span></span><span class="p">,</span> <span class="n" style="color: #333;">read_<span class="idiff right addition">num</span></span><span class="p">,</span> <span class="n" style="color: #333;">read</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;">l</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cigar</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cigarLen</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="166" 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">
166
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<td class="new_line diff-line-num" data-linenumber="174" 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">
174
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC174" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</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="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cigarLen</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">c</span><span class="p">)</span> <span class="p">{</span></span>
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167
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<td class="new_line diff-line-num" data-linenumber="175" 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">
175
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC175" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">letter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cigar_int_to_op</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cigar</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]);</span></span>
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<td class="old_line diff-line-num" data-linenumber="168" 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">
168
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<td class="new_line diff-line-num" data-linenumber="176" 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">
176
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC176" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cigar_int_to_len</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cigar</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]);</span></span>
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<td class="old_line diff-line-num" data-linenumber="169" 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">
169
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<td class="new_line diff-line-num" data-linenumber="177" 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">
177
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC177" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"%lu%c"</span><span class="p">,</span> <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="p">)</span><span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="n" style="color: #333;">letter</span><span class="p">);</span></span>
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170
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<td class="new_line diff-line-num" data-linenumber="178" 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">
178
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC178" class="line" lang="c"> <span class="p">}</span></span>
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171
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<td class="new_line diff-line-num old" data-linenumber="179" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC171" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// fprintf(stderr, "%s\tmismatch: %d\n", read->name.s, mismatch);</span></span>
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172
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179
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC179" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">*</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">0</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">0</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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173
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<td class="new_line diff-line-num old" data-linenumber="180" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC173" class="line" lang="c"> <span class="k" style="font-weight: 600;"><span class="idiff left deletion">for</span></span><span class="idiff deletion"> </span><span class="p"><span class="idiff deletion">(</span></span><span class="n" style="color: #333;"><span class="idiff deletion">c</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">=</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">a</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">-></span></span><span class="n" style="color: #333;"><span class="idiff deletion">read_begin1</span></span><span class="p"><span class="idiff deletion">;</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">c</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion"><=</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">a</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">-></span></span><span class="n" style="color: #333;"><span class="idiff deletion">read_end1</span></span><span class="p"><span class="idiff deletion">;</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">++</span></span><span class="n" style="color: #333;"><span class="idiff deletion">c</span></span><span class="p"><span class="idiff deletion">)</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"%<span class="idiff deletion">c</span>"</span><span class="p">,</span> <span class="n" style="color: #333;">read_seq</span><span class="p"><span class="idiff deletion">[</span></span><span class="n" style="color: #333;"><span class="idiff deletion">c</span></span><span class="p"><span class="idiff right deletion">]</span>);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="180" 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">
180
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC180" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"%<span class="idiff left right addition">s</span>"</span><span class="p">,</span> <span class="n" style="color: #333;">read_seq</span><span class="p">);</span></span>
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174
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<td class="new_line diff-line-num" data-linenumber="181" 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">
181
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC181" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</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="175" 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">
175
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<td class="new_line diff-line-num" data-linenumber="182" 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">
182
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC182" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qual</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;">strand</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="176" 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">
176
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<td class="new_line diff-line-num old" data-linenumber="183" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC176" class="line" lang="c"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_end1</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="177" 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">
177
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC177" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</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="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">l</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">c</span><span class="p">)</span> <span class="p">{</span></span>
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178
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><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;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"%c"</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qual</span><span class="p">.</span><span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">]);</span></span>
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179
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<td class="new_line diff-line-num old" data-linenumber="183" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC179" class="line" lang="c"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">p</span><span class="p">;</span></span>
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180
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<td class="new_line diff-line-num old" data-linenumber="183" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC180" class="line" lang="c"> <span class="p">}</span></span>
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181
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<td class="new_line diff-line-num old" data-linenumber="183" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC181" class="line" lang="c"> <span class="p">}</span><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;">read</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qual</span><span class="p">.</span><span class="n" style="color: #333;">s</span><span class="p">){</span></span>
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182
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<td class="new_line diff-line-num old" data-linenumber="183" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC182" class="line" lang="c"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_begin1</span><span class="p">;</span></span>
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183
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<td class="new_line diff-line-num old" data-linenumber="183" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC183" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</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="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">l</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">c</span><span class="p">)</span> <span class="p">{</span></span>
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184
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<td class="new_line diff-line-num old" data-linenumber="183" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC184" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"%c"</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qual</span><span class="p">.</span><span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">]);</span></span>
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185
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<td class="new_line diff-line-num old" data-linenumber="183" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC185" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">p</span><span class="p">;</span></span>
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186
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<td class="new_line diff-line-num old" data-linenumber="183" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC186" class="line" lang="c"> <span class="p">}</span></span>
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187
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<td class="new_line diff-line-num old" data-linenumber="183" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC187" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</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="188" 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="183" 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">
183
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC183" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qual</span><span class="p">.</span><span class="n" style="color: #333;">l</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;">p</span> <span class="o" style="font-weight: 600;">>=</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;">p</span><span class="p">)</span> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"%c"</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qual</span><span class="p">.</span><span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">]);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="188" 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="184" 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">
184
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC184" class="line" lang="c"> <span class="p">}</span><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;">read</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qual</span><span class="p">.</span><span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="n" style="color: #333;">fprintf</span> <span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qual</span><span class="p">.</span><span class="n" style="color: #333;">s</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="185" 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">
185
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC185" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"*"</span><span class="p">);</span></span>
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188
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<td class="new_line diff-line-num" data-linenumber="186" 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">
186
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC186" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">AS:i:%d"</span><span class="p">,</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">score1</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="189" 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">
189
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<td class="new_line diff-line-num old" data-linenumber="187" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC189" class="line" lang="c"> <span class="n" style="color: #333;">mapq</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// counter of difference</span></span>
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190
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<td class="new_line diff-line-num old" data-linenumber="187" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC190" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</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="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cigarLen</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">c</span><span class="p">)</span> <span class="p">{</span></span>
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191
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<td class="new_line diff-line-num old" data-linenumber="187" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC191" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">letter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cigar_int_to_op</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cigar</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]);</span></span>
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192
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<td class="new_line diff-line-num old" data-linenumber="187" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC192" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cigar_int_to_len</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cigar</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="193" 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">
193
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<td class="new_line diff-line-num old" data-linenumber="187" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC193" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">letter</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'M'</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="194" 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">
194
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<td class="new_line diff-line-num old" data-linenumber="187" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC194" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">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;">p</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">length</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">p</span><span class="p">){</span></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="187" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC195" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">table</span><span class="p">[(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">ref_seq</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;">s</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">qb</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">table</span><span class="p">[(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">read_seq</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">pb</span><span class="p">)])</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">mapq</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="196" 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">
196
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<td class="new_line diff-line-num old" data-linenumber="187" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC196" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">qb</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="197" 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">
197
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<td class="new_line diff-line-num old" data-linenumber="187" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC197" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">pb</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="198" 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">
198
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<td class="new_line diff-line-num old" data-linenumber="187" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC198" class="line" lang="c"> <span class="p">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="199" 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">
199
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<td class="new_line diff-line-num old" data-linenumber="187" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC199" class="line" lang="c"> <span class="p">}</span> <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;">letter</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'I'</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="200" 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">
200
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<td class="new_line diff-line-num old" data-linenumber="187" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC200" class="line" lang="c"> <span class="n" style="color: #333;">pb</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">length</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="201" 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">
201
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<td class="new_line diff-line-num old" data-linenumber="187" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC201" class="line" lang="c"> <span class="n" style="color: #333;">mapq</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">length</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="202" 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">
202
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<td class="new_line diff-line-num old" data-linenumber="187" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC202" class="line" lang="c"> <span class="p">}</span> <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="203" 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">
203
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<td class="new_line diff-line-num old" data-linenumber="187" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC203" class="line" lang="c"> <span class="n" style="color: #333;">qb</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">length</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="204" 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">
204
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<td class="new_line diff-line-num old" data-linenumber="187" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC204" class="line" lang="c"> <span class="n" style="color: #333;">mapq</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">length</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="205" 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">
205
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<td class="new_line diff-line-num old" data-linenumber="187" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC205" class="line" lang="c"> <span class="p">}</span></span>
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<td class="old_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">
206
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<td class="new_line diff-line-num old" data-linenumber="187" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC206" class="line" lang="c"> <span class="p">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="207" 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">
207
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<td class="new_line diff-line-num old" data-linenumber="187" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC207" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">NM:i:%d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">mapq</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="208" 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="187" 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">
187
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC187" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">NM:i:%d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">mismatch</span><span class="p">);</span></span>
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<td class="old_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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<td class="new_line diff-line-num" data-linenumber="188" 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">
188
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC188" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">score2</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;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"ZS:i:%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;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">score2</span><span class="p">);</span></span>
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<td class="old_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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<td class="new_line diff-line-num" data-linenumber="189" 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">
189
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC189" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</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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210
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<td class="new_line diff-line-num" data-linenumber="190" 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">
190
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC190" class="line" lang="c"> <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">@@ -217,13 +197,9 @@ int main (int argc, char * const argv[]) {</td>
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197
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC197" class="line" lang="c"> <span class="n" style="color: #333;">gzFile</span> <span class="n" style="color: #333;">read_fp</span><span class="p">,</span> <span class="n" style="color: #333;">ref_fp</span><span class="p">;</span></span>
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198
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC198" class="line" lang="c"> <span class="n" style="color: #333;">kseq_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">read_seq</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ref_seq</span><span class="p">;</span></span>
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219
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<td class="new_line diff-line-num" data-linenumber="199" 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">
199
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC199" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">mismatch</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">gap_open</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="n" style="color: #333;">gap_extension</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;">path</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;">reverse</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;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="n" style="color: #333;">sam</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;">protein</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;">header</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;">s1</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">67108864</span><span class="p">,</span> <span class="n" style="color: #333;">s2</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">128</span><span class="p">,</span> <span class="n" style="color: #333;">filter</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 old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC220" 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;">mata</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int8_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">calloc</span><span class="p">(</span><span class="mi" style="color: #099;">25</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int8_t</span><span class="p">));</span></span>
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221
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC221" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <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;">mat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mata</span><span class="p">;</span></span>
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222
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC222" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">mat_name</span><span class="p">[</span><span class="mi" style="color: #099;">16</span><span class="p">];</span></span>
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223
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC223" class="line" lang="c"> <span class="n" style="color: #333;">mat_name</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="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>
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224
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<td class="new_line diff-line-num old" data-linenumber="200" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC224" 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;">ref_num</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int8_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">s1</span><span class="p">);</span></span>
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225
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<td class="new_line diff-line-num old" data-linenumber="200" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC225" 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;">num</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int8_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">s2</span><span class="p">),</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">num_rc</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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226
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<td class="new_line diff-line-num old" data-linenumber="200" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC226" 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_rc</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="old_line diff-line-num new" data-linenumber="227" 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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200
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC200" 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;">mata</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ref_num</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">num</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">num_rc</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="new_line diff-line-num new" data-linenumber="201" 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">
201
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC201" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <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;">mat</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="202" 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">
202
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC202" 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_rc</span> <span class="o" style="font-weight: 600;">=</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;">mat_name</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" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC203" class="line" lang="c"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC204" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int8_t</span> <span class="n" style="color: #333;">mat50</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</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="LC205" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// A R N D C Q E G H I L K M F P S T W Y V B Z X *</span></span>
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<td class="diff-line-num unfold js-unfold old_line" 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">...</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">@@ -279,22 +255,6 @@ int main (int argc, char * const argv[]) {</td>
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279
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255
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC255" class="line" lang="c"></span>
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280
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256
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC256" 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;">table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nt_table</span><span class="p">;</span></span>
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281
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257
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC257" class="line" lang="c"></span>
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282
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<td class="new_line diff-line-num old" data-linenumber="258" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC282" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Parse command line.</span></span>
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283
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<td class="new_line diff-line-num old" data-linenumber="258" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC283" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="n" style="color: #333;">l</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;">"m:x:o:e:a:f:pcrsh"</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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284
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<td class="new_line diff-line-num old" data-linenumber="258" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC284" class="line" lang="c"> <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">)</span> <span class="p">{</span></span>
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285
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<td class="new_line diff-line-num old" data-linenumber="258" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC285" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'m'</span><span class="p">:</span> <span class="n" style="color: #333;">match</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>
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286
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<td class="new_line diff-line-num old" data-linenumber="258" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC286" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'x'</span><span class="p">:</span> <span class="n" style="color: #333;">mismatch</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>
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287
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<td class="new_line diff-line-num old" data-linenumber="258" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC287" 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;">gap_open</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>
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288
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<td class="new_line diff-line-num old" data-linenumber="258" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC288" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'e'</span><span class="p">:</span> <span class="n" style="color: #333;">gap_extension</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>
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289
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<td class="new_line diff-line-num old" data-linenumber="258" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC289" 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;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">mat_name</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 old" data-linenumber="290" 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">
290
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<td class="new_line diff-line-num old" data-linenumber="258" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC290" 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 class="n" style="color: #333;">filter</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>
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<td class="old_line diff-line-num old" data-linenumber="291" 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">
291
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<td class="new_line diff-line-num old" data-linenumber="258" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC291" 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;">protein</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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292
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<td class="new_line diff-line-num old" data-linenumber="258" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC292" 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;">path</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 old" data-linenumber="293" 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">
293
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<td class="new_line diff-line-num old" data-linenumber="258" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC293" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'r'</span><span class="p">:</span> <span class="n" style="color: #333;">reverse</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 old" data-linenumber="294" 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">
294
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<td class="new_line diff-line-num old" data-linenumber="258" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC294" 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;">sam</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 old" data-linenumber="295" 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">
295
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<td class="new_line diff-line-num old" data-linenumber="258" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC295" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'h'</span><span class="p">:</span> <span class="n" style="color: #333;">header</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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296
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<td class="new_line diff-line-num old" data-linenumber="258" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC296" class="line" lang="c"> <span class="p">}</span></span>
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297
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC297" class="line" lang="c"> <span class="p">}</span></span>
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298
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC258" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">2</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">argc</span><span class="p">)</span> <span class="p">{</span></span>
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299
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259
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC259" 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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300
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260
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC260" 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;">"Usage: ssw_test [options] ... <target.fasta> <query.fasta>(or <query.fastq>)</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="313" 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="273" 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">@@ -313,21 +273,52 @@ int main (int argc, char * const argv[]) {</td>
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313
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<td class="new_line diff-line-num" data-linenumber="273" 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">
273
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC273" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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314
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<td class="new_line diff-line-num" data-linenumber="274" 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">
274
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC274" class="line" lang="c"> <span class="p">}</span></span>
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315
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275
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC275" class="line" lang="c"></span>
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<td class="new_line diff-line-num new" data-linenumber="276" 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">
276
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC276" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Parse command line.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="277" 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">
277
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC277" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="n" style="color: #333;">l</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;">"m:x:o:e:a:f:pcrsh"</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="new_line diff-line-num new" data-linenumber="278" 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">
278
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC278" class="line" lang="c"> <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="279" 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">
279
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC279" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'m'</span><span class="p">:</span> <span class="n" style="color: #333;">match</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>
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<td class="new_line diff-line-num new" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
280
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC280" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'x'</span><span class="p">:</span> <span class="n" style="color: #333;">mismatch</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>
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<td class="new_line diff-line-num new" data-linenumber="281" 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">
281
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC281" 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;">gap_open</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>
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<td class="new_line diff-line-num new" data-linenumber="282" 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">
282
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC282" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'e'</span><span class="p">:</span> <span class="n" style="color: #333;">gap_extension</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>
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<td class="new_line diff-line-num new" data-linenumber="283" 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">
283
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC283" class="line" lang="c"></span>
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<td class="new_line diff-line-num new" data-linenumber="284" 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">
284
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC284" 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>
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<td class="new_line diff-line-num new" data-linenumber="285" 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">
285
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC285" class="line" lang="c"> <span class="n" style="color: #333;">mat_name</span> <span class="o" style="font-weight: 600;">=</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;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">optarg</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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<td class="new_line diff-line-num new" data-linenumber="286" 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">
286
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC286" class="line" lang="c"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">mat_name</span><span class="p">,</span> <span class="n" style="color: #333;">optarg</span><span class="p">);</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="287" 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">
287
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC287" class="line" lang="c"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="288" 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">
288
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC288" class="line" lang="c"></span>
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<td class="new_line diff-line-num new" data-linenumber="289" 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">
289
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC289" 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 class="n" style="color: #333;">filter</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>
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<td class="new_line diff-line-num new" data-linenumber="290" 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">
290
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC290" 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;">protein</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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291
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC291" 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;">path</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="new_line diff-line-num new" data-linenumber="292" 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">
292
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC292" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'r'</span><span class="p">:</span> <span class="n" style="color: #333;">reverse</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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC293" 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;">sam</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="new_line diff-line-num new" data-linenumber="294" 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">
294
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC294" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'h'</span><span class="p">:</span> <span class="n" style="color: #333;">header</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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295
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC295" class="line" lang="c"> <span class="p">}</span></span>
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296
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC296" class="line" lang="c"> <span class="p">}</span></span>
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297
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC297" class="line" lang="c"></span>
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316
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<td class="new_line diff-line-num" data-linenumber="298" 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">
298
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC298" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// initialize scoring matrix for genome sequences</span></span>
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<td class="old_line diff-line-num new" data-linenumber="317" 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="299" 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">
299
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC299" class="line" lang="c"> <span class="n" style="color: #333;">mata</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int8_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">calloc</span><span class="p">(</span><span class="mi" style="color: #099;">25</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int8_t</span><span class="p">));</span></span>
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317
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300
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC300" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">k</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;">LIKELY</span><span class="p">(</span><span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">l</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="318" 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">
318
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<td class="new_line diff-line-num" data-linenumber="301" 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">
301
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC301" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">m</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;">LIKELY</span><span class="p">(</span><span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">m</span><span class="p">)</span> <span class="n" style="color: #333;">mata</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">match</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">mismatch</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* weight_match : -weight_mismatch */</span></span>
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<td class="old_line diff-line-num" data-linenumber="319" 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">
319
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<td class="new_line diff-line-num" data-linenumber="302" 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">
302
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC302" class="line" lang="c"> <span class="n" style="color: #333;">mata</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">++</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="c1" style="color: #998; font-style: italic;">// ambiguous base</span></span>
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320
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303
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC303" class="line" lang="c"> <span class="p">}</span></span>
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321
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<td class="new_line diff-line-num" data-linenumber="304" 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">
304
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC304" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">m</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;">LIKELY</span><span class="p">(</span><span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">5</span><span class="p">);</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">m</span><span class="p">)</span> <span class="n" style="color: #333;">mata</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">++</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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<td class="new_line diff-line-num new" data-linenumber="305" 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">
305
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC305" class="line" lang="c"> <span class="n" style="color: #333;">mat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mata</span><span class="p">;</span></span>
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322
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306
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC306" class="line" lang="c"></span>
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<td class="old_line diff-line-num old" data-linenumber="323" 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">
323
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<td class="new_line diff-line-num old" data-linenumber="307" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC323" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">protein</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="p"><span class="idiff left deletion">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff deletion">!</span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;"><span class="idiff deletion">strcmp</span></span><span class="p"><span class="idiff deletion">(</span></span><span class="n" style="color: #333;"><span class="idiff deletion">mat_name</span></span><span class="p"><span class="idiff deletion">,</span></span><span class="idiff deletion"> </span><span class="s" style="color: #d14;"><span class="idiff deletion">"</span></span><span class="se" style="color: #d14;"><span class="idiff deletion">\0</span></span><span class="s" style="color: #d14;"><span class="idiff deletion">"</span></span><span class="p"><span class="idiff right deletion">))</span>)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num new" data-linenumber="324" 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="307" 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">
307
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC307" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">protein</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;"><span class="idiff left addition">mat_name</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">==</span></span><span class="idiff addition"> </span><span class="mi" style="color: #099;"><span class="idiff right addition">0</span></span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="324" 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">
324
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<td class="new_line diff-line-num" data-linenumber="308" 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">
308
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC308" class="line" lang="c"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">24</span><span class="p">;</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="LC309" class="line" lang="c"> <span class="n" style="color: #333;">table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aa_table</span><span class="p">;</span></span>
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326
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310
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC310" class="line" lang="c"> <span class="n" style="color: #333;">mat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mat50</span><span class="p">;</span></span>
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327
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<td class="new_line diff-line-num old" data-linenumber="311" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC327" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p"><span class="idiff left deletion">(</span></span><span class="n" style="color: #333;"><span class="idiff deletion">strcmp</span></span><span class="p">(</span><span class="n" style="color: #333;">mat_name</span><span class="p"><span class="idiff deletion">,</span></span><span class="idiff deletion"> </span><span class="s" style="color: #d14;"><span class="idiff deletion">"</span></span><span class="se" style="color: #d14;"><span class="idiff deletion">\0</span></span><span class="s" style="color: #d14;"><span class="idiff deletion">"</span></span><span class="p"><span class="idiff right deletion">)</span>)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="311" 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">
311
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC311" class="line" lang="c"> <span class="p">}</span> <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;">mat_name</span><span class="idiff left addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">!=</span></span><span class="idiff addition"> </span><span class="mi" style="color: #099;"><span class="idiff right addition">0</span></span><span class="p">)</span> <span class="p">{</span></span>
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312
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC312" class="line" lang="c"></span>
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329
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313
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC313" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Parse score matrix.</span></span>
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330
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314
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC314" 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;">f_mat</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;">mat_name</span><span class="p">,</span> <span class="s" style="color: #d14;">"r"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="315" 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">
315
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC315" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">mat_name</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="316" 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">
316
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC316" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f_mat</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="317" 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">
317
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC317" 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;">"Failed to open the weight matrix file.</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="318" 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">
318
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC318" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">mata</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="319" 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">
319
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC319" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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320
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC320" class="line" lang="c"> <span class="p">}</span></span>
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321
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC321" class="line" lang="c"></span>
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331
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC322" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">128</span><span class="p">];</span></span>
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332
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323
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC323" class="line" lang="c"> <span class="n" style="color: #333;">mata</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int8_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">realloc</span><span class="p">(</span><span class="n" style="color: #333;">mata</span><span class="p">,</span> <span class="mi" style="color: #099;">1024</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int8_t</span><span class="p">));</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="LC324" class="line" lang="c"> <span class="n" style="color: #333;">k</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="359" 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="350" 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">@@ -359,6 +350,7 @@ int main (int argc, char * const argv[]) {</td>
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359
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC350" class="line" lang="c"> <span class="p">}</span></span>
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360
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351
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC351" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">k</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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361
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352
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC352" 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;">"Problem of reading the weight matrix file.</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="353" 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">
353
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC353" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">mata</span><span class="p">);</span></span>
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362
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354
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC354" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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363
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355
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC355" class="line" lang="c"> <span class="p">}</span></span>
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364
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356
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC356" class="line" lang="c"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">f_mat</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="367" 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="359" 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">@@ -367,7 +359,6 @@ int main (int argc, char * const argv[]) {</td>
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367
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359
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC359" class="line" lang="c"> <span class="n" style="color: #333;">mat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mata</span><span class="p">;</span></span>
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368
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360
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC360" class="line" lang="c"> <span class="p">}</span></span>
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369
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361
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC361" class="line" lang="c"></span>
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370
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<td class="new_line diff-line-num old" data-linenumber="362" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC370" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//fprintf(stderr, "query: %s\n", argv[optind + 1]);</span></span>
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371
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362
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC362" class="line" lang="c"> <span class="n" style="color: #333;">read_fp</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;">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="s" style="color: #d14;">"r"</span><span class="p">);</span></span>
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372
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363
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC363" class="line" lang="c"></span>
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373
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364
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC364" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span> <span class="n" style="color: #333;">read_fp</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="380" 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">@@ -389,6 +380,8 @@ int main (int argc, char * const argv[]) {</td>
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389
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380
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC380" class="line" lang="c"> <span class="p">}</span></span>
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390
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381
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC381" class="line" lang="c"></span>
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391
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382
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC382" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// alignment</span></span>
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<td class="new_line diff-line-num new" data-linenumber="383" 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">
383
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC383" class="line" lang="c"> <span class="n" style="color: #333;">ref_num</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int8_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">s1</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="384" 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">
384
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC384" class="line" lang="c"> <span class="n" style="color: #333;">num</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int8_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">s2</span><span class="p">);</span></span>
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392
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385
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC385" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">reverse</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;">n</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">5</span><span class="p">)</span> <span class="p">{</span></span>
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393
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<td class="new_line diff-line-num" data-linenumber="386" 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">
386
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC386" class="line" lang="c"> <span class="n" style="color: #333;">read_rc</span> <span class="o" style="font-weight: 600;">=</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;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">s2</span><span class="p">);</span></span>
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394
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387
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC387" class="line" lang="c"> <span class="n" style="color: #333;">num_rc</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int8_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">s2</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="416" 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="409" 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">@@ -416,7 +409,13 @@ int main (int argc, char * const argv[]) {</td>
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416
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409
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC409" class="line" lang="c"> <span class="n" style="color: #333;">p_rc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ssw_init</span><span class="p">(</span><span class="n" style="color: #333;">num_rc</span><span class="p">,</span> <span class="n" style="color: #333;">readLen</span><span class="p">,</span> <span class="n" style="color: #333;">mat</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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417
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410
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC410" class="line" lang="c"> <span class="p">}</span><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;">reverse</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;">n</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">24</span><span class="p">)</span> <span class="p">{</span></span>
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418
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411
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC411" 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;">"Reverse complement alignment is not available for protein sequences. </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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419
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<td class="new_line diff-line-num old" data-linenumber="412" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC419" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</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="412" 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">
412
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC412" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">num</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="413" 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">
413
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC413" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">ref_num</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="414" 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">
414
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC414" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">num_rc</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="415" 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">
415
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC415" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">num_rc</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="416" 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">
416
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC416" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">read_rc</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="417" 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">
417
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC417" class="line" lang="c"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="418" 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">
418
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC418" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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419
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC419" class="line" lang="c"> <span class="p">}</span></span>
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420
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC420" class="line" lang="c"></span>
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421
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC421" class="line" lang="c"> <span class="n" style="color: #333;">ref_fp</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;">argv</span><span class="p">[</span><span class="n" style="color: #333;">optind</span><span class="p">],</span> <span class="s" style="color: #d14;">"r"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="436" 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="435" 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">@@ -436,12 +435,17 @@ int main (int argc, char * const argv[]) {</td>
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436
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435
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC435" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">reverse</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;">protein</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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437
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436
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC436" class="line" lang="c"> <span class="n" style="color: #333;">result_rc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ssw_align</span><span class="p">(</span><span class="n" style="color: #333;">p_rc</span><span class="p">,</span> <span class="n" style="color: #333;">ref_num</span><span class="p">,</span> <span class="n" style="color: #333;">refLen</span><span class="p">,</span> <span class="n" style="color: #333;">gap_open</span><span class="p">,</span> <span class="n" style="color: #333;">gap_extension</span><span class="p">,</span> <span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="n" style="color: #333;">filter</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">maskLen</span><span class="p">);</span></span>
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438
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<td class="new_line diff-line-num" data-linenumber="437" 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">
437
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC437" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">result_rc</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">result_rc</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">score1</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">score1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">result_rc</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">score1</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">filter</span><span class="p">)</span> <span class="p">{</span></span>
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439
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<td class="new_line diff-line-num old" data-linenumber="438" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC439" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sam</span><span class="p">)</span> <span class="n" style="color: #333;">ssw_write</span> <span class="p">(</span><span class="n" style="color: #333;">result_rc</span><span class="p">,</span> <span class="n" style="color: #333;">ref_seq</span><span class="p">,</span> <span class="n" style="color: #333;">read_seq</span><span class="p">,</span> <span class="n" style="color: #333;">read_rc</span><span class="p">,</span> <span class="n" style="color: #333;">table</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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440
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<td class="new_line diff-line-num old" data-linenumber="438" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC440" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">ssw_write</span> <span class="p">(</span><span class="n" style="color: #333;">result_rc</span><span class="p">,</span> <span class="n" style="color: #333;">ref_seq</span><span class="p">,</span> <span class="n" style="color: #333;">read_seq</span><span class="p">,</span> <span class="n" style="color: #333;">read_rc</span><span class="p">,</span> <span class="n" style="color: #333;">table</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>
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438
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC438" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">result_rc</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">)</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;">"Warning: The reverse compliment alignment of the following sequences may miss a small part.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">ref_seq: %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">read_seq: %s</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">ref_seq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">name</span><span class="p">.</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">read_seq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">name</span><span class="p">.</span><span class="n" style="color: #333;">s</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="439" 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">
439
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC439" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sam</span><span class="p">)</span> <span class="n" style="color: #333;">ssw_write</span> <span class="p">(</span><span class="n" style="color: #333;">result_rc</span><span class="p">,</span> <span class="n" style="color: #333;">ref_seq</span><span class="p">,</span> <span class="n" style="color: #333;">read_seq</span><span class="p">,</span> <span class="n" style="color: #333;">read_rc</span><span class="p">,</span> <span class="n" style="color: #333;">ref_num</span><span class="p">,</span> <span class="n" style="color: #333;">num_rc</span><span class="p">,</span> <span class="n" style="color: #333;">table</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="440" 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">
440
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC440" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">ssw_write</span> <span class="p">(</span><span class="n" style="color: #333;">result_rc</span><span class="p">,</span> <span class="n" style="color: #333;">ref_seq</span><span class="p">,</span> <span class="n" style="color: #333;">read_seq</span><span class="p">,</span> <span class="n" style="color: #333;">read_rc</span><span class="p">,</span> <span class="n" style="color: #333;">ref_num</span><span class="p">,</span> <span class="n" style="color: #333;">num_rc</span><span class="p">,</span> <span class="n" style="color: #333;">table</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>
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441
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<td class="new_line diff-line-num" data-linenumber="441" 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">
441
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC441" class="line" lang="c"> <span class="p">}</span><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;">result</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">score1</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">filter</span><span class="p">){</span></span>
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442
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<td class="new_line diff-line-num old" data-linenumber="442" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC442" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sam</span><span class="p">)</span> <span class="n" style="color: #333;">ssw_write</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">,</span> <span class="n" style="color: #333;">ref_seq</span><span class="p">,</span> <span class="n" style="color: #333;">read_seq</span><span class="p">,</span> <span class="n" style="color: #333;">read_seq</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;">s</span><span class="p">,</span> <span class="n" style="color: #333;">table</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>
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443
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<td class="new_line diff-line-num old" data-linenumber="442" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC443" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">ssw_write</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">,</span> <span class="n" style="color: #333;">ref_seq</span><span class="p">,</span> <span class="n" style="color: #333;">read_seq</span><span class="p">,</span> <span class="n" style="color: #333;">read_seq</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;">s</span><span class="p">,</span> <span class="n" style="color: #333;">table</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="444" 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">
444
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<td class="new_line diff-line-num old" data-linenumber="442" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC444" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span> <span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</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 new" data-linenumber="445" 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="442" 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">
442
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC442" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">)</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;">"Warning: The alignment of the following sequences may miss a small part.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">ref_seq: %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">read_seq: %s</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">ref_seq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">name</span><span class="p">.</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">read_seq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">name</span><span class="p">.</span><span class="n" style="color: #333;">s</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="443" 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">
443
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC443" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sam</span><span class="p">)</span> <span class="n" style="color: #333;">ssw_write</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">,</span> <span class="n" style="color: #333;">ref_seq</span><span class="p">,</span> <span class="n" style="color: #333;">read_seq</span><span class="p">,</span> <span class="n" style="color: #333;">read_seq</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;">s</span><span class="p">,</span> <span class="n" style="color: #333;">ref_num</span><span class="p">,</span> <span class="n" style="color: #333;">num</span><span class="p">,</span> <span class="n" style="color: #333;">table</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>
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<td class="new_line diff-line-num new" data-linenumber="444" 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">
444
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC444" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">ssw_write</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">,</span> <span class="n" style="color: #333;">ref_seq</span><span class="p">,</span> <span class="n" style="color: #333;">read_seq</span><span class="p">,</span> <span class="n" style="color: #333;">read_seq</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;">s</span><span class="p">,</span> <span class="n" style="color: #333;">ref_num</span><span class="p">,</span> <span class="n" style="color: #333;">num</span><span class="p">,</span> <span class="n" style="color: #333;">table</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="new_line diff-line-num new" data-linenumber="445" 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">
445
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC445" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span> <span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="446" 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">
446
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC446" 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: Alignment between the following sequences is failed.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">ref_seq: %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">read_seq: %s</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">ref_seq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">name</span><span class="p">.</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">read_seq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">name</span><span class="p">.</span><span class="n" style="color: #333;">s</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="447" 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">
447
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC447" class="line" lang="c"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="448" 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">
448
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC448" class="line" lang="c"> <span class="p">}</span></span>
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445
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<td class="new_line diff-line-num" data-linenumber="449" 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">
449
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC449" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">result_rc</span><span class="p">)</span> <span class="n" style="color: #333;">align_destroy</span><span class="p">(</span><span class="n" style="color: #333;">result_rc</span><span class="p">);</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="LC450" class="line" lang="c"> <span class="n" style="color: #333;">align_destroy</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">);</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="LC451" class="line" lang="c"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/libssw/-/commit/c9c6106f955eac1ec9d8a40cc85495ccf3178810#d2865ccf8daae26eb92ec69a4ec40f059f35ef86"><strong>src/pyssw.py</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">@@ -3,6 +3,7 @@</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="s" style="color: #d14;">Simple python wrapper for SSW library</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="LC4" class="line" lang="python"><span class="s" style="color: #d14;">Please put the path of libssw.so into LD_LIBRARY_PATH or pass it explicitly as a parameter</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="LC5" class="line" lang="python"><span class="s" style="color: #d14;">By Yongan Zhao (March 2016)</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="s" style="color: #d14;">Revised by Mengyao Zhao on 2022-May-23</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="LC7" class="line" lang="python"><span class="s" style="color: #d14;">"""</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="LC8" class="line" lang="python"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</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">@@ -12,12 +13,9 @@ import ctypes as ct</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">timeit</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">ti</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="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">gzip</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="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">math</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="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">ssw_lib</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="LC17" class="line" lang="python"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC18" class="line" lang="python"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">read</span><span class="p">(</span><span class="n" style="color: #333;">sFile</span><span class="p">):</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="LC20" class="line" lang="python"> <span class="s" style="color: #d14;">"""</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="LC21" class="line" lang="python"><span class="s" style="color: #d14;"> read a sequence file</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">@@ -52,9 +50,9 @@ def read(sFile):</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">sQual</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">''</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="LC51" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">l</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">f</span><span class="p">:</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="LC52" class="line" lang="python"> <span class="n" style="color: #333;">sId</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">()[</span><span class="mi" style="color: #099;">1</span><span class="p">:].</span><span class="n" style="color: #333;">split</span><span class="p">()[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">sSeq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="nb" style="color: #0086b3;"><span class="idiff left right deletion">next</span></span><span class="p">()</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">s3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="nb" style="color: #0086b3;"><span class="idiff left right deletion">next</span></span><span class="p">()</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">sQual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="nb" style="color: #0086b3;"><span class="idiff left right deletion">next</span></span><span class="p">()</span></span>
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53
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">sSeq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left addition">readline</span></span><span class="p"><span class="idiff addition">().</span></span><span class="n" style="color: #333;"><span class="idiff right addition">strip</span></span><span class="p">()</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">s3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left addition">readline</span></span><span class="p"><span class="idiff addition">().</span></span><span class="n" style="color: #333;"><span class="idiff right addition">strip</span></span><span class="p">()</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">sQual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left addition">readline</span></span><span class="p"><span class="idiff addition">().</span></span><span class="n" style="color: #333;"><span class="idiff right addition">strip</span></span><span class="p">()</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="LC56" class="line" lang="python"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">sId</span><span class="p">,</span> <span class="n" style="color: #333;">sSeq</span><span class="p">,</span> <span class="n" style="color: #333;">sQual</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="LC58" class="line" lang="python"></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">@@ -63,23 +61,23 @@ def read(sFile):</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">ext</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">splitext</span><span class="p">(</span><span class="n" style="color: #333;">sFile</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 class="n" style="color: #333;">strip</span><span class="p">().</span><span class="n" style="color: #333;">lower</span><span class="p">()</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="LC62" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ext</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'gz'</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">ext</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'gzip'</span><span class="p">:</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="LC63" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">gzip</span><span class="p">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">sFile</span><span class="p">,</span> <span class="s" style="color: #d14;">'r'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="nb" style="color: #0086b3;">ne<span class="idiff left right deletion">xt</span></span><span class="p">()</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right addition">readli</span>ne</span><span class="p">()</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="LC65" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'>'</span><span class="p">):</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="LC66" class="line" lang="python"> <span class="n" style="color: #333;">bFasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</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="LC67" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'@'</span><span class="p">):</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="LC68" class="line" lang="python"> <span class="n" style="color: #333;">bFasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</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="LC69" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC72" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left deletion">print</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">>></span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p"><span class="idiff deletion">,</span></span><span class="idiff deletion"> </span><span class="s" style="color: #d14;">'file format cannot be recognized<span class="idiff right deletion">'</span></span></span>
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70
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p"><span class="idiff left addition">.</span></span><span class="n" style="color: #333;"><span class="idiff addition">write</span></span><span class="p"><span class="idiff addition">(</span></span><span class="s" style="color: #d14;">'file format cannot be recognized</span><span class="se" style="color: #d14;"><span class="idiff addition">\n</span></span><span class="s" style="color: #d14;"><span class="idiff addition">'</span></span><span class="p"><span class="idiff right addition">)</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="LC71" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">()</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="LC72" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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75
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73
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC73" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">sFile</span><span class="p">,</span> <span class="s" style="color: #d14;">'r'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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76
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="nb" style="color: #0086b3;">ne<span class="idiff left right deletion">xt</span></span><span class="p">()</span></span>
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74
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right addition">readli</span>ne</span><span class="p">()</span></span>
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77
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75
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC75" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'>'</span><span class="p">):</span></span>
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78
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">bFasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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79
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77
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC77" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'@'</span><span class="p">):</span></span>
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80
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">bFasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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81
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79
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC79" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC82" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left deletion">print</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">>></span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p"><span class="idiff deletion">,</span></span><span class="idiff deletion"> </span><span class="s" style="color: #d14;">'file format cannot be recognized<span class="idiff right deletion">'</span></span></span>
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80
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p"><span class="idiff left addition">.</span></span><span class="n" style="color: #333;"><span class="idiff addition">write</span></span><span class="p"><span class="idiff addition">(</span></span><span class="s" style="color: #d14;">'file format cannot be recognized</span><span class="se" style="color: #d14;"><span class="idiff addition">\n</span></span><span class="s" style="color: #d14;"><span class="idiff addition">'</span></span><span class="p"><span class="idiff right addition">)</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="LC81" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">()</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="LC82" class="line" lang="python"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC83" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># read</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="171" 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="169" 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">@@ -171,7 +169,7 @@ def buildPath(q, r, nQryBeg, nRefBeg, lCigar):</td>
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171
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169
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC169" class="line" lang="python"></span>
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172
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170
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC170" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'M'</span><span class="p">:</span></span>
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173
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171
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC171" class="line" lang="python"> <span class="n" style="color: #333;">sQ</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">q</span><span class="p">[</span><span class="n" style="color: #333;">nQOff</span> <span class="p">:</span> <span class="n" style="color: #333;">nQOff</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">n</span><span class="p">]</span></span>
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174
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC174" class="line" lang="python"> <span class="n" style="color: #333;">sA</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">''</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'|'</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">q</span><span class="p">[</span><span class="n" style="color: #333;">nQOff</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;">r</span><span class="p">[</span><span class="n" style="color: #333;">nROff</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">'*'</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">j</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;"><span class="idiff left right deletion">x</span>range</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">)])</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC172" class="line" lang="python"> <span class="n" style="color: #333;">sA</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">''</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'|'</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">q</span><span class="p">[</span><span class="n" style="color: #333;">nQOff</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;">r</span><span class="p">[</span><span class="n" style="color: #333;">nROff</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">'*'</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">j</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">)])</span></span>
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173
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC173" class="line" lang="python"> <span class="n" style="color: #333;">sR</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">r</span><span class="p">[</span><span class="n" style="color: #333;">nROff</span> <span class="p">:</span> <span class="n" style="color: #333;">nROff</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">n</span><span class="p">]</span></span>
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174
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC174" class="line" lang="python"> <span class="n" style="color: #333;">nQOff</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">n</span></span>
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175
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC175" class="line" lang="python"> <span class="n" style="color: #333;">nROff</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">n</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="185" 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="183" 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">@@ -185,36 +183,33 @@ def buildPath(q, r, nQryBeg, nRefBeg, lCigar):</td>
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185
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183
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC183" class="line" lang="python"> <span class="n" style="color: #333;">sA</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;">n</span></span>
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186
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184
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC184" class="line" lang="python"> <span class="n" style="color: #333;">sR</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">r</span><span class="p">[</span><span class="n" style="color: #333;">nROff</span> <span class="p">:</span> <span class="n" style="color: #333;">nROff</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">n</span><span class="p">]</span></span>
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187
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185
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC185" class="line" lang="python"> <span class="n" style="color: #333;">nROff</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">n</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC188" class="line" lang="python"></span>
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186
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC186" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sCigar</span><span class="p">,</span> <span class="n" style="color: #333;">sQ</span><span class="p">,</span> <span class="n" style="color: #333;">sA</span><span class="p">,</span> <span class="n" style="color: #333;">sR</span></span>
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190
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187
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC187" class="line" lang="python"></span>
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188
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC188" class="line" lang="python"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC193" class="line" lang="python"></span>
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189
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC189" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">):</span></span>
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190
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC190" class="line" lang="python"> <span class="n" style="color: #333;">lEle</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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191
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC191" class="line" lang="python"> <span class="n" style="color: #333;">dRc</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span> </span>
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197
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192
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC192" class="line" lang="python"> <span class="n" style="color: #333;">dEle2Int</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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193
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC193" class="line" lang="python"> <span class="n" style="color: #333;">dInt2Ele</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC199" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">False</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">bProt<span class="idiff left right deletion">i</span>en</span><span class="p">:</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC194" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">False</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">bProte<span class="idiff left right addition">i</span>n</span><span class="p">:</span></span>
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200
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195
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC195" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># init DNA score matrix</span></span>
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201
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196
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC196" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">sMatrix</span><span class="p">:</span></span>
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202
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197
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC197" class="line" lang="python"> <span class="n" style="color: #333;">lEle</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'G'</span><span class="p">,</span> <span class="s" style="color: #d14;">'T'</span><span class="p">,</span> <span class="s" style="color: #d14;">'N'</span><span class="p">]</span></span>
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203
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<td class="new_line diff-line-num old" data-linenumber="198" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC203" class="line" lang="python"> <span class="n" style="color: #333;">dRc</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'A'</span><span class="p">:</span><span class="s" style="color: #d14;">'<span class="idiff left deletion">C</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C'</span><span class="p">:</span><span class="s" style="color: #d14;">'G'</span><span class="p">,</span> <span class="s" style="color: #d14;">'G'</span><span class="p">:</span><span class="s" style="color: #d14;">'C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'T'</span><span class="p">:</span><span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'a'</span><span class="p">:</span><span class="s" style="color: #d14;">'<span class="idiff right deletion">C</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'c'</span><span class="p">:</span><span class="s" style="color: #d14;">'G'</span><span class="p">,</span> <span class="s" style="color: #d14;">'g'</span><span class="p">:</span><span class="s" style="color: #d14;">'C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'t'</span><span class="p">:</span><span class="s" style="color: #d14;">'A'</span><span class="p">}</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="198" 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">
198
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC198" class="line" lang="python"> <span class="n" style="color: #333;">dRc</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'A'</span><span class="p">:</span><span class="s" style="color: #d14;">'<span class="idiff left addition">T</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C'</span><span class="p">:</span><span class="s" style="color: #d14;">'G'</span><span class="p">,</span> <span class="s" style="color: #d14;">'G'</span><span class="p">:</span><span class="s" style="color: #d14;">'C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'T'</span><span class="p">:</span><span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'a'</span><span class="p">:</span><span class="s" style="color: #d14;">'<span class="idiff right addition">T</span>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'c'</span><span class="p">:</span><span class="s" style="color: #d14;">'G'</span><span class="p">,</span> <span class="s" style="color: #d14;">'g'</span><span class="p">:</span><span class="s" style="color: #d14;">'C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'t'</span><span class="p">:</span><span class="s" style="color: #d14;">'A'</span><span class="p">}</span> </span>
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204
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199
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC199" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span><span class="n" style="color: #333;">ele</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">lEle</span><span class="p">):</span></span>
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205
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200
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC200" class="line" lang="python"> <span class="n" style="color: #333;">dEle2Int</span><span class="p">[</span><span class="n" style="color: #333;">ele</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span></span>
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206
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201
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC201" class="line" lang="python"> <span class="n" style="color: #333;">dEle2Int</span><span class="p">[</span><span class="n" style="color: #333;">ele</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">()]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span></span>
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207
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202
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">dInt2Ele</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="n" style="color: #333;">ele</span></span>
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208
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203
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC203" class="line" lang="python"> <span class="n" style="color: #333;">nEleNum</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">lEle</span><span class="p">)</span></span>
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209
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<td class="new_line diff-line-num old" data-linenumber="204" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC209" class="line" lang="python"> <span class="n" style="color: #333;">lScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mi" style="color: #099;">0</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;"><span class="idiff left right deletion">x</span>range</span><span class="p">(</span><span class="n" style="color: #333;">nEleNum</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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210
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<td class="new_line diff-line-num old" data-linenumber="204" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC210" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;"><span class="idiff left right deletion">x</span>range</span><span class="p">(</span><span class="n" style="color: #333;">nEleNum</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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211
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<td class="new_line diff-line-num old" data-linenumber="204" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC211" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">j</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;"><span class="idiff left right deletion">x</span>range</span><span class="p">(</span><span class="n" style="color: #333;">nEleNum</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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<td class="new_line diff-line-num new" data-linenumber="204" 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">
204
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC204" class="line" lang="python"> <span class="n" style="color: #333;">lScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mi" style="color: #099;">0</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">nEleNum</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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<td class="new_line diff-line-num new" data-linenumber="205" 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">
205
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC205" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">nEleNum</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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206
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC206" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">j</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">nEleNum</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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212
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207
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC207" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">lEle</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="n" style="color: #333;">lEle</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]:</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="LC208" class="line" lang="python"> <span class="n" style="color: #333;">lScore</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;">nEleNum</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;">args</span><span class="p">.</span><span class="n" style="color: #333;">nMatch</span></span>
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209
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC209" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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215
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210
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC210" class="line" lang="python"> <span class="n" style="color: #333;">lScore</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;">nEleNum</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="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">nMismatch</span></span>
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216
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211
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC211" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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217
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<td class="new_line diff-line-num old" data-linenumber="212" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC217" class="line" lang="python"> <span class="n" style="color: #333;">lEle</span><span class="p">,</span> <span class="n" style="color: #333;">dEle2Int</span><span class="p">,</span> <span class="n" style="color: #333;">dInt2Ele</span><span class="p">,</span> <span class="n" style="color: #333;">lScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ssw</span><span class="p">.</span><span class="n" style="color: #333;">read_matrix</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">sMatrix</span><span class="p">)</span></span>
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212
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC212" class="line" lang="python"> <span class="n" style="color: #333;">lEle</span><span class="p">,</span> <span class="n" style="color: #333;">dEle2Int</span><span class="p">,</span> <span class="n" style="color: #333;">dInt2Ele</span><span class="p">,</span> <span class="n" style="color: #333;">lScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ssw<span class="idiff left right addition">_lib</span></span><span class="p">.</span><span class="n" style="color: #333;">read_matrix</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">sMatrix</span><span class="p">)</span></span>
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218
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213
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC213" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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214
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC214" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># load AA score matrix</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="LC215" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">sMatrix</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">@@ -227,10 +222,10 @@ def main(args):</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC222" class="line" lang="python"> <span class="n" style="color: #333;">lScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ssw_lib</span><span class="p">.</span><span class="n" style="color: #333;">lBlosum50</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="LC223" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</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="LC224" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># assume the format of the input score matrix is the same as that of http://www.ncbi.nlm.nih.gov/Class/FieldGuide/BLOSUM62.txt</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC230" class="line" lang="python"> <span class="n" style="color: #333;">lEle</span><span class="p">,</span> <span class="n" style="color: #333;">dEle2Int</span><span class="p">,</span> <span class="n" style="color: #333;">dInt2Ele</span><span class="p">,</span> <span class="n" style="color: #333;">lScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ssw</span><span class="p">.</span><span class="n" style="color: #333;">read_matrix</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">sMatrix</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="225" 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">
225
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC225" class="line" lang="python"> <span class="n" style="color: #333;">lEle</span><span class="p">,</span> <span class="n" style="color: #333;">dEle2Int</span><span class="p">,</span> <span class="n" style="color: #333;">dInt2Ele</span><span class="p">,</span> <span class="n" style="color: #333;">lScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ssw<span class="idiff left right addition">_lib</span></span><span class="p">.</span><span class="n" style="color: #333;">read_matrix</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">sMatrix</span><span class="p">)</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="LC226" class="line" lang="python"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC227" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">bBest</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">bProtien</span><span class="p">:</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC233" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left deletion">print</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">>></span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p"><span class="idiff deletion">,</span></span><span class="idiff deletion"> </span><span class="s" style="color: #d14;">'Reverse complement alignment is not available for protein sequences.<span class="idiff right deletion">'</span></span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC228" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p"><span class="idiff left addition">.</span></span><span class="n" style="color: #333;"><span class="idiff addition">write</span></span><span class="p"><span class="idiff addition">(</span></span><span class="s" style="color: #d14;">'Reverse complement alignment is not available for protein sequences.</span><span class="se" style="color: #d14;"><span class="idiff addition">\n</span></span><span class="s" style="color: #d14;"><span class="idiff addition">'</span></span><span class="p"><span class="idiff right addition">)</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="LC229" class="line" lang="python"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC230" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># translate score matrix to ctypes</span></span>
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236
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231
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC231" class="line" lang="python"> <span class="n" style="color: #333;">mat</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">lScore</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ct</span><span class="p">.</span><span class="n" style="color: #333;">c_int8</span><span class="p">)</span> <span class="p">()</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="236" 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">@@ -241,11 +236,11 @@ def main(args):</td>
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241
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236
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC236" class="line" lang="python"> <span class="n" style="color: #333;">nFlag</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span></span>
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242
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237
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC237" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># print sam head</span></span>
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243
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<td class="new_line diff-line-num" data-linenumber="238" 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">
238
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC238" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">bSam</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">bHeader</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">bPath</span><span class="p">:</span></span>
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244
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC244" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left right deletion"> </span><span class="s" style="color: #d14;">'@HD</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">VN:1.4</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">SO:queryname'</span></span>
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245
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<td class="new_line diff-line-num old" data-linenumber="239" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC245" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">sRId</span><span class="p">,</span><span class="n" style="color: #333;">sRSeq</span><span class="p">,</span><span class="n" style="color: #333;">_</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">read</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right deletion">sT</span>arget</span><span class="p">):</span></span>
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246
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<td class="new_line diff-line-num old" data-linenumber="239" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC246" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left right deletion"> </span><span class="s" style="color: #d14;">'@SQ</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">SN:{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">LN:{}'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">sRId</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sRSeq</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="239" 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">
239
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC239" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left addition">(</span></span><span class="s" style="color: #d14;">'@HD</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">VN:1.4</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">SO:queryname'</span><span class="p"><span class="idiff right addition">)</span></span></span>
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<td class="new_line diff-line-num new" data-linenumber="240" 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">
240
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC240" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">sRId</span><span class="p">,</span><span class="n" style="color: #333;">sRSeq</span><span class="p">,</span><span class="n" style="color: #333;">_</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">read</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left addition">args</span></span><span class="p"><span class="idiff addition">.</span></span><span class="n" style="color: #333;"><span class="idiff right addition">t</span>arget</span><span class="p">):</span></span>
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241
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC241" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left addition">(</span></span><span class="s" style="color: #d14;">'@SQ</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">SN:{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">LN:{}'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">sRId</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sRSeq</span><span class="p">))<span class="idiff right addition">)</span></span></span>
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247
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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">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC242" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">bSam</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">bPath</span><span class="p">:</span></span>
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248
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<td class="new_line diff-line-num old" data-linenumber="243" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC248" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left deletion">print</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">>></span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p"><span class="idiff deletion">,</span></span><span class="idiff right deletion"> </span><span class="s" style="color: #d14;">'SAM format output is only available together with option -c.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC243" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p"><span class="idiff left addition">.</span></span><span class="n" style="color: #333;"><span class="idiff addition">write</span></span><span class="p"><span class="idiff addition">(</span></span><span class="s" style="color: #d14;">'SAM format output is only available together with option -c.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p"><span class="idiff right addition">)</span></span></span>
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249
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC244" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">bSam</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</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="LC245" class="line" lang="python"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC246" class="line" lang="python"> <span class="n" style="color: #333;">ssw</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ssw_lib</span><span class="p">.</span><span class="n" style="color: #333;">CSsw</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">sLibPath</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="255" 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="250" 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">@@ -255,25 +250,21 @@ def main(args):</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC250" class="line" lang="python"> <span class="n" style="color: #333;">qNum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">to_int</span><span class="p">(</span><span class="n" style="color: #333;">sQSeq</span><span class="p">,</span> <span class="n" style="color: #333;">lEle</span><span class="p">,</span> <span class="n" style="color: #333;">dEle2Int</span><span class="p">)</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="LC251" class="line" lang="python"> <span class="n" style="color: #333;">qProfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ssw</span><span class="p">.</span><span class="n" style="color: #333;">ssw_init</span><span class="p">(</span><span class="n" style="color: #333;">qNum</span><span class="p">,</span> <span class="n" style="color: #333;">ct</span><span class="p">.</span><span class="n" style="color: #333;">c_int32</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sQSeq</span><span class="p">)),</span> <span class="n" style="color: #333;">mat</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">lEle</span><span class="p">),</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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257
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC252" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># build rc query profile</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC258" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">bBest</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">bProt<span class="idiff left right deletion">i</span>en</span><span class="p">:</span></span>
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253
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC253" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">bBest</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">bProte<span class="idiff left right addition">i</span>n</span><span class="p">:</span></span>
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259
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC254" class="line" lang="python"> <span class="n" style="color: #333;">sQRcSeq</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">''</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="n" style="color: #333;">dRc</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sQSeq</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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260
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC255" class="line" lang="python"> <span class="n" style="color: #333;">qRcNum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">to_int</span><span class="p">(</span><span class="n" style="color: #333;">sQRcSeq</span><span class="p">,</span> <span class="n" style="color: #333;">lEle</span><span class="p">,</span> <span class="n" style="color: #333;">dEle2Int</span><span class="p">)</span></span>
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261
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC256" class="line" lang="python"> <span class="n" style="color: #333;">qRcProfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ssw</span><span class="p">.</span><span class="n" style="color: #333;">ssw_init</span><span class="p">(</span><span class="n" style="color: #333;">qRcNum</span><span class="p">,</span> <span class="n" style="color: #333;">ct</span><span class="p">.</span><span class="n" style="color: #333;">c_int32</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sQSeq</span><span class="p">)),</span> <span class="n" style="color: #333;">mat</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">lEle</span><span class="p">),</span> <span class="mi" style="color: #099;">2</span><span class="p">)</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="LC257" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># set mask len</span></span>
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<td class="new_line diff-line-num old" data-linenumber="258" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC263" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sQSeq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">30</span><span class="p">:</span></span>
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264
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<td class="new_line diff-line-num old" data-linenumber="258" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC264" class="line" lang="python"> <span class="n" style="color: #333;">nMaskLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sQSeq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span></span>
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<td class="new_line diff-line-num old" data-linenumber="258" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC265" class="line" lang="python"> <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 old" data-linenumber="258" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC266" class="line" lang="python"> <span class="n" style="color: #333;">nMaskLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">15</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC267" class="line" lang="python"></span>
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258
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC258" class="line" lang="python"> <span class="n" style="color: #333;">nMaskLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sQSeq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">//</span> <span class="mi" style="color: #099;">2</span></span>
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259
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC259" class="line" lang="python"> </span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC260" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># iter target sequence</span></span>
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269
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC261" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">sRId</span><span class="p">,</span><span class="n" style="color: #333;">sRSeq</span><span class="p">,</span><span class="n" style="color: #333;">_</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">read</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">target</span><span class="p">):</span></span>
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270
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC262" class="line" lang="python"> <span class="n" style="color: #333;">rNum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">to_int</span><span class="p">(</span><span class="n" style="color: #333;">sRSeq</span><span class="p">,</span> <span class="n" style="color: #333;">lEle</span><span class="p">,</span> <span class="n" style="color: #333;">dEle2Int</span><span class="p">)</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC271" class="line" lang="python"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC272" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># format ofres: (nScore, nScore2, nRefBeg, nRefEnd, nQryBeg, nQryEnd, nRefEnd2, nCigarLen, lCigar)</span></span>
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263
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC263" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># format of res: (nScore, nScore2, nRefBeg, nRefEnd, nQryBeg, nQryEnd, nRefEnd2, nCigarLen, lCigar)</span></span>
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273
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264
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC264" class="line" lang="python"> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">align_one</span><span class="p">(</span><span class="n" style="color: #333;">ssw</span><span class="p">,</span> <span class="n" style="color: #333;">qProfile</span><span class="p">,</span> <span class="n" style="color: #333;">rNum</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sRSeq</span><span class="p">),</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">nOpen</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">nExt</span><span class="p">,</span> <span class="n" style="color: #333;">nFlag</span><span class="p">,</span> <span class="n" style="color: #333;">nMaskLen</span><span class="p">)</span></span>
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274
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265
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC265" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># align rc query</span></span>
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275
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266
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC266" class="line" lang="python"> <span class="n" style="color: #333;">resRc</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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276
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC276" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">bBest</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">bProt<span class="idiff left right deletion">i</span>en</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="267" 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">
267
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC267" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">bBest</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">bProte<span class="idiff left right addition">i</span>n</span><span class="p">:</span></span>
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277
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<td class="new_line diff-line-num" data-linenumber="268" 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">
268
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC268" class="line" lang="python"> <span class="n" style="color: #333;">resRc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">align_one</span><span class="p">(</span><span class="n" style="color: #333;">ssw</span><span class="p">,</span> <span class="n" style="color: #333;">qRcProfile</span><span class="p">,</span> <span class="n" style="color: #333;">rNum</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sRSeq</span><span class="p">),</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">nOpen</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">nExt</span><span class="p">,</span> <span class="n" style="color: #333;">nFlag</span><span class="p">,</span> <span class="n" style="color: #333;">nMaskLen</span><span class="p">)</span></span>
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278
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269
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC269" class="line" lang="python"></span>
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279
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270
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC270" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># build cigar and trace back path</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -289,89 +280,89 @@ def main(args):</td>
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280
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC280" class="line" lang="python"></span>
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290
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281
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC281" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># print results</span></span>
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291
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282
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC282" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">bSam</span><span class="p">:</span></span>
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292
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<td class="new_line diff-line-num old" data-linenumber="283" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC292" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left right deletion"> </span><span class="s" style="color: #d14;">'target_name: {}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">query_name: {}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">optimal_alignment_score: {}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">sRId</span><span class="p">,</span> <span class="n" style="color: #333;">sQId</span><span class="p">,</span> <span class="n" style="color: #333;">resPrint</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]),</span></span>
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<td class="new_line diff-line-num new" data-linenumber="283" 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">
283
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC283" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left addition">(</span></span><span class="s" style="color: #d14;">'target_name: {}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">query_name: {}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">optimal_alignment_score: {}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">sRId</span><span class="p">,</span> <span class="n" style="color: #333;">sQId</span><span class="p">,</span> <span class="n" style="color: #333;">resPrint</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])<span class="idiff right addition">)</span>,</span></span>
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293
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<td class="new_line diff-line-num" data-linenumber="284" 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">
284
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC284" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">resPrint</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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294
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<td class="new_line diff-line-num old" data-linenumber="285" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC294" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left right deletion"> </span><span class="s" style="color: #d14;">'suboptimal_alignment_score: {}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">resPrint</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="285" 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">
285
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC285" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left addition">(</span></span><span class="s" style="color: #d14;">'suboptimal_alignment_score: {}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">resPrint</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])<span class="idiff right addition">)</span>,</span></span>
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295
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<td class="new_line diff-line-num" data-linenumber="286" 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">
286
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC286" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">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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296
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC296" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left right deletion"> </span><span class="s" style="color: #d14;">'strand: +</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">,</span></span>
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287
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC287" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left addition">(</span></span><span class="s" style="color: #d14;">'strand: +</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p"><span class="idiff right addition">)</span>,</span></span>
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297
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288
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC288" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span> </span>
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298
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<td class="new_line diff-line-num old" data-linenumber="289" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC298" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left right deletion"> </span><span class="s" style="color: #d14;">'strand: -</span><span class="se" style="color: #d14;">\t</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="289" 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">
289
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC289" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left addition">(</span></span><span class="s" style="color: #d14;">'strand: -</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p"><span class="idiff right addition">)</span>,</span></span>
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299
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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC290" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">resPrint</span><span class="p">[</span><span class="mi" style="color: #099;">2</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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300
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<td class="new_line diff-line-num old" data-linenumber="291" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC300" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left right deletion"> </span><span class="s" style="color: #d14;">'target_begin: {}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">resPrint</span><span class="p">[</span><span class="mi" style="color: #099;">2</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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301
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<td class="new_line diff-line-num old" data-linenumber="291" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC301" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left right deletion"> </span><span class="s" style="color: #d14;">'target_end: {}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">resPrint</span><span class="p">[</span><span class="mi" style="color: #099;">3</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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<td class="new_line diff-line-num new" data-linenumber="291" 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">
291
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC291" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left addition">(</span></span><span class="s" style="color: #d14;">'target_begin: {}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">resPrint</span><span class="p">[</span><span class="mi" style="color: #099;">2</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 class="idiff right addition">)</span>,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="292" 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">
292
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC292" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left addition">(</span></span><span class="s" style="color: #d14;">'target_end: {}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">resPrint</span><span class="p">[</span><span class="mi" style="color: #099;">3</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 class="idiff right addition">)</span>,</span></span>
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302
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293
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC293" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">resPrint</span><span class="p">[</span><span class="mi" style="color: #099;">4</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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303
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<td class="new_line diff-line-num old" data-linenumber="294" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC303" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left right deletion"> </span><span class="s" style="color: #d14;">'query_begin: {}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">resPrint</span><span class="p">[</span><span class="mi" style="color: #099;">4</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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304
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<td class="new_line diff-line-num old" data-linenumber="294" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC304" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left right deletion"> </span><span class="s" style="color: #d14;">'query_end: {}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">resPrint</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="p">)</span></span>
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294
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC294" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left addition">(</span></span><span class="s" style="color: #d14;">'query_begin: {}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">resPrint</span><span class="p">[</span><span class="mi" style="color: #099;">4</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 class="idiff right addition">)</span>,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="295" 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">
295
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC295" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left addition">(</span></span><span class="s" style="color: #d14;">'query_end: {}</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">resPrint</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="p">)<span class="idiff right addition">)</span></span></span>
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305
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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC296" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">resPrint</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 class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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306
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<td class="new_line diff-line-num" data-linenumber="297" 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">
297
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC297" class="line" lang="python"> <span class="n" style="color: #333;">n1</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;">resPrint</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span></span>
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307
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<td class="new_line diff-line-num" data-linenumber="298" 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">
298
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC298" class="line" lang="python"> <span class="n" style="color: #333;">n2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="mi" style="color: #099;">60</span><span class="p">,</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sR</span><span class="p">))</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">resPrint</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">sR</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">'-'</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">60</span><span class="p">)</span></span>
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308
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC299" class="line" lang="python"> <span class="n" style="color: #333;">n3</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;">resPrint</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span></span>
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309
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300
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC300" class="line" lang="python"> <span class="n" style="color: #333;">n4</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="mi" style="color: #099;">60</span><span class="p">,</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sQ</span><span class="p">))</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">resPrint</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">sQ</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">'-'</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">60</span><span class="p">)</span></span>
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310
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301
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC301" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sQ</span><span class="p">),</span> <span class="mi" style="color: #099;">60</span><span class="p">):</span></span>
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311
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC311" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left right deletion"> </span><span class="s" style="color: #d14;">'Target:{:>8}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">n1</span><span class="p">,</span> <span class="n" style="color: #333;">sR</span><span class="p">[</span><span class="n" style="color: #333;">i</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;">60</span><span class="p">],</span> <span class="n" style="color: #333;">n2</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="302" 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">
302
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC302" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left addition">(</span></span><span class="s" style="color: #d14;">'Target:{:>8}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">n1</span><span class="p">,</span> <span class="n" style="color: #333;">sR</span><span class="p">[</span><span class="n" style="color: #333;">i</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;">60</span><span class="p">],</span> <span class="n" style="color: #333;">n2</span><span class="p">)<span class="idiff right addition">)</span></span></span>
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303
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC303" class="line" lang="python"> <span class="n" style="color: #333;">n1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n2</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span></span>
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304
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC304" class="line" lang="python"> <span class="n" style="color: #333;">n2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n2</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="mi" style="color: #099;">60</span><span class="p">,</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sR</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">60</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">sR</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">'-'</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;">60</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;">120</span><span class="p">)</span></span>
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305
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC305" class="line" lang="python"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC315" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left right deletion"> </span><span class="s" style="color: #d14;">'{: ^15}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="s" style="color: #d14;">''</span><span class="p">,</span> <span class="n" style="color: #333;">sA</span><span class="p">[</span><span class="n" style="color: #333;">i</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;">60</span><span class="p">])</span></span>
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306
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC306" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left addition">(</span></span><span class="s" style="color: #d14;">'{: ^15}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="s" style="color: #d14;">''</span><span class="p">,</span> <span class="n" style="color: #333;">sA</span><span class="p">[</span><span class="n" style="color: #333;">i</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;">60</span><span class="p">])<span class="idiff right addition">)</span></span></span>
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307
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC307" class="line" lang="python"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC317" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left right deletion"> </span><span class="s" style="color: #d14;">'Query:{:>9}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</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 class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">n3</span><span class="p">,</span> <span class="n" style="color: #333;">sQ</span><span class="p">[</span><span class="n" style="color: #333;">i</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;">60</span><span class="p">],</span> <span class="n" style="color: #333;">n4</span><span class="p">)</span></span>
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308
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC308" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left addition">(</span></span><span class="s" style="color: #d14;">'Query:{:>9}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</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 class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">n3</span><span class="p">,</span> <span class="n" style="color: #333;">sQ</span><span class="p">[</span><span class="n" style="color: #333;">i</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;">60</span><span class="p">],</span> <span class="n" style="color: #333;">n4</span><span class="p">)<span class="idiff right addition">)</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="LC309" class="line" lang="python"> <span class="n" style="color: #333;">n3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n4</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span></span>
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310
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC310" class="line" lang="python"> <span class="n" style="color: #333;">n4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n4</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="mi" style="color: #099;">60</span><span class="p">,</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sQ</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">60</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">sQ</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">'-'</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;">60</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;">120</span><span class="p">)</span></span>
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320
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311
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC311" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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321
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<td class="new_line diff-line-num old" data-linenumber="312" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC321" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left right deletion"> </span><span class="s" style="color: #d14;">"{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">sQId</span><span class="p">),</span></span>
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<td class="new_line diff-line-num new" data-linenumber="312" 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">
312
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC312" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left addition">(</span></span><span class="s" style="color: #d14;">"{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">sQId</span><span class="p">)<span class="idiff right addition">)</span>,</span></span>
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322
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<td class="new_line diff-line-num" data-linenumber="313" 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">
313
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC313" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">resPrint</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>
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323
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<td class="new_line diff-line-num old" data-linenumber="314" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC323" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left right deletion"> </span><span class="s" style="color: #d14;">"4</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">*</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">0</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">255</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">*</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">*</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">0</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">0</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">*</span><span class="se" style="color: #d14;">\t</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="314" 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">
314
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC314" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left addition">(</span></span><span class="s" style="color: #d14;">"4</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">*</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">0</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">255</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">*</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">*</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">0</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">0</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">*</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">*"</span><span class="p"><span class="idiff right addition">)</span>,</span></span>
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324
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<td class="new_line diff-line-num" data-linenumber="315" 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">
315
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC315" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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325
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<td class="new_line diff-line-num" data-linenumber="316" 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">
316
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC316" class="line" lang="python"> <span class="n" style="color: #333;">mapq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">4.343</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">math</span><span class="p">.</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="n" style="color: #333;">resPrint</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;">resPrint</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="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">resPrint</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])))</span></span>
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326
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<td class="new_line diff-line-num" data-linenumber="317" 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">
317
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC317" class="line" lang="python"> <span class="n" style="color: #333;">mapq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">mapq</span> <span class="o" style="font-weight: 600;">+</span> <span class="mf" style="color: #099;">4.99</span><span class="p">);</span></span>
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327
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<td class="new_line diff-line-num" data-linenumber="318" 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">
318
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC318" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">mapq</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">254</span><span class="p">:</span></span>
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328
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<td class="new_line diff-line-num" data-linenumber="319" 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">
319
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC319" class="line" lang="python"> <span class="n" style="color: #333;">mapq</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">254</span></span>
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329
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<td class="new_line diff-line-num" data-linenumber="320" 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">
320
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC320" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">strand</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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330
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<td class="new_line diff-line-num old" data-linenumber="321" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC330" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left right deletion"> </span><span class="s" style="color: #d14;">'16</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">,</span></span>
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321
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC321" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left addition">(</span></span><span class="s" style="color: #d14;">'16</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p"><span class="idiff right addition">)</span>,</span></span>
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331
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322
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC322" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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332
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<td class="new_line diff-line-num old" data-linenumber="323" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC332" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left right deletion"> </span><span class="s" style="color: #d14;">'0</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">,</span></span>
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333
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<td class="new_line diff-line-num old" data-linenumber="323" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC333" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left right deletion"> </span><span class="s" style="color: #d14;">'{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">sRId</span><span class="p">,</span> <span class="n" style="color: #333;">resPrint</span><span class="p">[</span><span class="mi" style="color: #099;">2</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;">mapq</span><span class="p">),</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC334" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left right deletion"> </span><span class="n" style="color: #333;">sCigar</span><span class="p">,</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC335" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left right deletion"> </span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">*</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">0</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">0</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">,</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC336" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left right deletion"> </span><span class="n" style="color: #333;">sQSeq</span><span class="p">[</span><span class="n" style="color: #333;">resPrint</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]:</span><span class="n" style="color: #333;">resPrint</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="p">]</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">strand</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">sQRcSeq</span><span class="p">[</span><span class="n" style="color: #333;">resPrint</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]:</span><span class="n" style="color: #333;">resPrint</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="p">],</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC337" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left right deletion"> </span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">,</span></span>
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323
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC323" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left addition">(</span></span><span class="s" style="color: #d14;">'0</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p"><span class="idiff right addition">)</span>,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="324" 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">
324
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC324" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left addition">(</span></span><span class="s" style="color: #d14;">'{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">sRId</span><span class="p">,</span> <span class="n" style="color: #333;">resPrint</span><span class="p">[</span><span class="mi" style="color: #099;">2</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;">mapq</span><span class="p">)<span class="idiff right addition">)</span>,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="325" 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">
325
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC325" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left addition">(</span></span><span class="n" style="color: #333;">sCigar</span><span class="p"><span class="idiff right addition">)</span>,</span></span>
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326
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC326" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left addition">(</span></span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">*</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">0</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">0</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p"><span class="idiff right addition">)</span>,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="327" 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">
327
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC327" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left addition">(</span></span><span class="n" style="color: #333;">sQSeq</span><span class="p">[</span><span class="n" style="color: #333;">resPrint</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]:</span><span class="n" style="color: #333;">resPrint</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="p">]<span class="idiff addition">)</span></span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">strand</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;"><span class="idiff addition">print</span></span><span class="p"><span class="idiff addition">(</span></span><span class="n" style="color: #333;">sQRcSeq</span><span class="p">[</span><span class="n" style="color: #333;">resPrint</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]:</span><span class="n" style="color: #333;">resPrint</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="p">]<span class="idiff right addition">)</span>,</span></span>
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328
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC328" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left addition">(</span></span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p"><span class="idiff right addition">)</span>,</span></span>
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329
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC329" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sQQual</span><span class="p">:</span></span>
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339
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330
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC330" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC340" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left right deletion"> </span><span class="n" style="color: #333;">sQQual</span><span class="p">[</span><span class="n" style="color: #333;">resPrint</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]:</span><span class="n" style="color: #333;">resPrint</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="p">],</span></span>
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331
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC331" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left addition">(</span></span><span class="n" style="color: #333;">sQQual</span><span class="p">[</span><span class="n" style="color: #333;">resPrint</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]:</span><span class="n" style="color: #333;">resPrint</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="p">]<span class="idiff right addition">)</span>,</span></span>
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341
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332
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC332" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC342" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left right deletion"> </span><span class="n" style="color: #333;">sQQual</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">resPrint</span><span class="p">[</span><span class="mi" style="color: #099;">4</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;">resPrint</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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC333" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left addition">(</span></span><span class="n" style="color: #333;">sQQual</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">resPrint</span><span class="p">[</span><span class="mi" style="color: #099;">4</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;">resPrint</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="p">:</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]<span class="idiff right addition">)</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="LC334" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC344" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left right deletion"> </span><span class="s" style="color: #d14;">'*'</span><span class="p">,</span></span>
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335
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC335" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left addition">(</span></span><span class="s" style="color: #d14;">'*'</span><span class="p"><span class="idiff right addition">)</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="LC336" class="line" lang="python"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC346" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left right deletion"> </span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">AS:i:{}'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">resPrint</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]),</span></span>
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347
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC347" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left right deletion"> </span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">NM:i:{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sA</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">sA</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">'|'</span><span class="p">)),</span></span>
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337
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC337" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left addition">(</span></span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">AS:i:{}'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">resPrint</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])<span class="idiff right addition">)</span>,</span></span>
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338
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC338" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left addition">(</span></span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">NM:i:{}</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sA</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">sA</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">'|'</span><span class="p">))<span class="idiff right addition">)</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="LC339" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">resPrint</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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC349" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="idiff left right deletion"> </span><span class="s" style="color: #d14;">'ZS:i:{}'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">resPrint</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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340
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC340" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left addition">(</span></span><span class="s" style="color: #d14;">'ZS:i:{}'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">resPrint</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])<span class="idiff right addition">)</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="LC341" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</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="LC342" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</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="LC343" class="line" lang="python"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC344" class="line" lang="python"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC345" class="line" lang="python"> <span class="n" style="color: #333;">ssw</span><span class="p">.</span><span class="n" style="color: #333;">init_destroy</span><span class="p">(</span><span class="n" style="color: #333;">qProfile</span><span class="p">)</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC355" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">bBest</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">bProt<span class="idiff left right deletion">i</span>en</span><span class="p">:</span></span>
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346
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC346" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">bBest</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">bProte<span class="idiff left right addition">i</span>n</span><span class="p">:</span></span>
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347
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC347" class="line" lang="python"> <span class="n" style="color: #333;">ssw</span><span class="p">.</span><span class="n" style="color: #333;">init_destroy</span><span class="p">(</span><span class="n" style="color: #333;">qRcProfile</span><span class="p">)</span></span>
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348
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC348" class="line" lang="python"></span>
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358
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349
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC349" class="line" lang="python"></span>
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359
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350
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC350" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'__main__'</span><span class="p">:</span></span>
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360
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351
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC351" class="line" lang="python"></span>
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361
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<td class="new_line diff-line-num" data-linenumber="352" 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">
352
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC352" class="line" lang="python"> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ap</span><span class="p">.</span><span class="n" style="color: #333;">ArgumentParser</span><span class="p">()</span></span>
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362
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<td class="new_line diff-line-num old" data-linenumber="353" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC362" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-l'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--sLibPath'</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'path of libssw.so'</span><span class="p">)</span></span>
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353
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC353" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-l'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--sLibPath'</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'<span class="idiff left right addition">./</span>'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'path of libssw.so'</span><span class="p">)</span></span>
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363
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<td class="new_line diff-line-num" data-linenumber="354" 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">
354
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC354" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-m'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--nMatch'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'a positive integer as the score for a match in genome sequence alignment. [default: 2]'</span><span class="p">)</span></span>
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364
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<td class="new_line diff-line-num" data-linenumber="355" 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">
355
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC355" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-x'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--nMismatch'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'a positive integer as the score for a mismatch in genome sequence alignment. [default: 2]'</span><span class="p">)</span></span>
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365
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<td class="new_line diff-line-num" data-linenumber="356" 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">
356
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC356" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-o'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--nOpen'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'a positive integer as the penalty for the gap opening in genome sequence alignment. [default: 3]'</span><span class="p">)</span></span>
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366
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<td class="new_line diff-line-num" data-linenumber="357" 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">
357
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC357" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-e'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--nExt'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="n" style="color: #333;">default</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'a positive integer as the penalty for the gap extension in genome sequence alignment. [default: 1]'</span><span class="p">)</span></span>
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367
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<td class="new_line diff-line-num old" data-linenumber="358" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC367" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-p'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--bProt<span class="idiff left deletion">i</span>en'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Do protein sequence alignment. Without this option, <span class="idiff right deletion">the ssw_test</span> will do genome sequence alignment. [default: False]'</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="358" 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">
358
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC358" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-p'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--bProte<span class="idiff left addition">i</span>n'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Do protein sequence alignment. Without this option, <span class="idiff right addition">pyssw</span> will do genome sequence alignment. [default: False]'</span><span class="p">)</span></span>
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368
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<td class="new_line diff-line-num" data-linenumber="359" 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">
359
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC359" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-a'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--sMatrix'</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'a file for either Blosum or Pam weight matrix. [default: Blosum50]'</span><span class="p">)</span></span>
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369
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<td class="new_line diff-line-num" data-linenumber="360" 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">
360
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC360" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-c'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--bPath'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Return the alignment path. [default: False]'</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="370" 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">
370
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<td class="new_line diff-line-num" data-linenumber="361" 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">
361
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC361" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-f'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--nThr'</span><span class="p">,</span> <span class="n" style="color: #333;">default</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'a positive integer. Only output the alignments with the Smith-Waterman score >= N.'</span><span class="p">)</span></span>
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371
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<td class="new_line diff-line-num" data-linenumber="362" 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">
362
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC362" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-r'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--bBest'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'The best alignment will be picked between the original read alignment and the reverse complement read alignment. [default: False]'</span><span class="p">)</span></span>
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372
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363
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC363" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-s'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--bSam'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Output in SAM format. [default: no header]'</span><span class="p">)</span></span>
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373
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364
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC364" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-header'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--bHeader'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'If -s is used, include header in SAM output.'</span><span class="p">)</span></span>
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374
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<td class="new_line diff-line-num old" data-linenumber="365" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC374" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'target'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'targe file'</span><span class="p">)</span></span>
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365
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC365" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'target'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'targe<span class="idiff left right addition">t</span> file'</span><span class="p">)</span></span>
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375
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366
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC366" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'query'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'query file'</span><span class="p">)</span></span>
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376
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<td class="new_line diff-line-num" data-linenumber="367" 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">
367
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC367" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">argv</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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377
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368
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC368" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">print_help</span><span class="p">()</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="381" 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="372" 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">@@ -381,4 +372,5 @@ if __name__ == '__main__':</td>
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381
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372
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC372" class="line" lang="python"> <span class="n" style="color: #333;">t1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ti</span><span class="p">.</span><span class="n" style="color: #333;">default_timer</span><span class="p">()</span></span>
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382
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373
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC373" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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383
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374
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC374" class="line" lang="python"> <span class="n" style="color: #333;">t2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ti</span><span class="p">.</span><span class="n" style="color: #333;">default_timer</span><span class="p">()</span></span>
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384
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC384" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">'CPU time: {} seconds'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">t2</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">t1</span><span class="p">)</span></span></pre></td>
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375
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC375" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'CPU time: {} seconds</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">t2</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">t1</span><span class="p">))</span></span>
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376
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC376" class="line" lang="python"></span></pre></td>
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<a href="https://salsa.debian.org/med-team/libssw/-/commit/c9c6106f955eac1ec9d8a40cc85495ccf3178810#ab2abe5e4546f527e000acaff4069d4b5d9979e2"><strong>src/sse2neon.h</strong></a>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* The MIT License</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="c"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC3" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Copyright (c) 2012-<span class="idiff left right deletion">1</span>015 Boston College.</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Copyright (c) 2012-<span class="idiff left right addition">2</span>015 Boston College.</span></span>
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4
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4" class="line" lang="c"></span>
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5
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Permission is hereby granted, free of charge, to any person obtaining</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="LC6" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> a copy of this software and associated documentation files (the</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">@@ -23,19 +23,49 @@</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC23" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> SOFTWARE.</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="LC24" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*/</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="LC25" class="line" lang="c"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC26" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* Contact: Mengyao Zhao <zhangmp@bc.edu> */</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC26" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* The 2-clause BSD License</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC28" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Copyright 2006 Michael Farrar. </span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC30" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Redistribution and use in source and binary forms, with or without</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC31" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> modification, are permitted provided that the following conditions are</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC32" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> met:</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC34" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> 1. Redistributions of source code must retain the above copyright</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC37" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> 2. Redistributions in binary form must reproduce the above copyright</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC38" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> notice, this list of conditions and the following disclaimer in the</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC45" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC46" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC47" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,</span></span>
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48
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC48" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY</span></span>
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49
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC49" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT</span></span>
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50
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC50" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE</span></span>
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51
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC51" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></span>
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52
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC52" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*/</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="LC53" class="line" lang="c"></span>
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54
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC54" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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29
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55
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC55" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * ssw.c</span></span>
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56
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC56" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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31
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57
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC57" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Created by Mengyao Zhao on 6/22/10.</span></span>
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58
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC58" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Copyright 2010 Boston College. All rights reserved.</span></span>
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<td class="new_line diff-line-num old" data-linenumber="59" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC33" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Version 0.1.4</span></span>
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<td class="new_line diff-line-num old" data-linenumber="59" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC34" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Last revision by Mengyao Zhao on 07/19/16.</span></span>
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59
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC59" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Version 1.2.4</span></span>
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60
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC60" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Last revision by Mengyao Zhao on 2022-Apr-17.</span></span>
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61
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC61" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<td class="new_line diff-line-num new" data-linenumber="62" 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">
62
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC62" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * The lazy-F loop implementation was derived from SWPS3, which is</span></span>
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63
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC63" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * MIT licensed under ETH Zürich, Institute of Computational Science.</span></span>
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64
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC64" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<td class="new_line diff-line-num new" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
65
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC65" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * The core SW loop referenced the swsse2 implementation, which is</span></span>
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66
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC66" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * BSD licensed under Micharl Farrar.</span></span>
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67
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC67" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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37
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68
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC68" class="line" lang="c"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC38" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <emmintrin.h></span></span>
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39
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69
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC69" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stdint.h></span></span>
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40
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70
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC70" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stdlib.h></span></span>
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71
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC71" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stdio.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">@@ -43,6 +73,13 @@</td>
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43
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73
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC73" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <math.h></span></span>
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44
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74
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC74" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "ssw.h"</span></span>
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45
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75
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC75" class="line" lang="c"></span>
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76
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC76" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __ARM_NEON // (M1)</span></span>
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77
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC77" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "sse2neon.h"</span></span>
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78
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC78" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else // x86 (Intel)</span></span>
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79
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC79" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <emmintrin.h></span></span>
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80
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC80" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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81
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82
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46
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83
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC83" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __GNUC__</span></span>
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47
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84
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC84" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define LIKELY(x) __builtin_expect((x),1)</span></span>
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48
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85
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC85" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define UNLIKELY(x) __builtin_expect((x),0)</span></span>
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<td class="diff-line-num unfold js-unfold new_line" 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">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -85,6 +122,43 @@ struct _profile{</td>
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85
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122
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC122" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">bias</span><span class="p">;</span></span>
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86
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123
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC123" class="line" lang="c"><span class="p">};</span></span>
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87
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124
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC124" class="line" lang="c"></span>
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125
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC125" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* array index is an ASCII character value from a CIGAR, </span></span>
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126
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC126" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> element value is the corresponding integer opcode between 0 and 8 */</span></span>
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127
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC127" class="line" lang="c"><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">encoded_ops</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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128
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC128" 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>
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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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC129" 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>
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<td class="new_line diff-line-num new" data-linenumber="130" 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">
130
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC130" 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>
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<td class="new_line diff-line-num new" data-linenumber="131" 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">
131
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC131" 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>
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<td class="new_line diff-line-num new" data-linenumber="132" 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">
132
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC132" 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>
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<td class="new_line diff-line-num new" data-linenumber="133" 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">
133
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC133" 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>
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<td class="new_line diff-line-num new" data-linenumber="134" 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">
134
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC134" 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>
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<td class="new_line diff-line-num new" data-linenumber="135" 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">
135
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC135" 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>
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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_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">
136
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC136" class="line" lang="c"> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* ! */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* " */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* # */</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="137" 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">
137
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC137" class="line" lang="c"> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* $ */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* % */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* & */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* ' */</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="138" 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">
138
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC138" class="line" lang="c"> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* ( */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* ) */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* * */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* + */</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="139" 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">
139
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC139" class="line" lang="c"> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* , */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* - */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* . */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* / */</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="140" 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">
140
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC140" class="line" lang="c"> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* 0 */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* 1 */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* 2 */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* 3 */</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="141" 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">
141
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC141" class="line" lang="c"> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* 4 */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* 5 */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* 6 */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* 7 */</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="142" 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">
142
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC142" class="line" lang="c"> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* 8 */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* 9 */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* : */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* ; */</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC143" class="line" lang="c"> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* < */</span><span class="p">,</span> <span class="mi" style="color: #099;">7</span> <span class="cm" style="color: #998; font-style: italic;">/* = */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* > */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* ? */</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC144" class="line" lang="c"> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* @ */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* A */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* B */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* C */</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC145" class="line" lang="c"> <span class="mi" style="color: #099;">2</span> <span class="cm" style="color: #998; font-style: italic;">/* D */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* E */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* F */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* G */</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
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC146" class="line" lang="c"> <span class="mi" style="color: #099;">5</span> <span class="cm" style="color: #998; font-style: italic;">/* H */</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span> <span class="cm" style="color: #998; font-style: italic;">/* I */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* J */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* K */</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="147" 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">
147
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC147" class="line" lang="c"> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* L */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* M */</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span> <span class="cm" style="color: #998; font-style: italic;">/* N */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* O */</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="148" 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">
148
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC148" class="line" lang="c"> <span class="mi" style="color: #099;">6</span> <span class="cm" style="color: #998; font-style: italic;">/* P */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* Q */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* R */</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span> <span class="cm" style="color: #998; font-style: italic;">/* S */</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="149" 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">
149
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC149" class="line" lang="c"> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* T */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* U */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* V */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* W */</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="150" 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">
150
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC150" class="line" lang="c"> <span class="mi" style="color: #099;">8</span> <span class="cm" style="color: #998; font-style: italic;">/* X */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* Y */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* Z */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* [ */</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="151" 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">
151
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC151" class="line" lang="c"> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* \ */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* ] */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* ^ */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* _ */</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="152" 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">
152
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC152" class="line" lang="c"> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* ` */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* a */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* b */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* c */</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="153" 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">
153
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC153" class="line" lang="c"> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* d */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* e */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* f */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* g */</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="154" 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">
154
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC154" class="line" lang="c"> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* h */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* i */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* j */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* k */</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="155" 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">
155
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC155" class="line" lang="c"> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* l */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* m */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* n */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* o */</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="156" 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">
156
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC156" class="line" lang="c"> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* p */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* q */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* r */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* s */</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="157" 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">
157
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC157" class="line" lang="c"> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* t */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* u */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* v */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* w */</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="158" 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">
158
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC158" class="line" lang="c"> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* x */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* y */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* z */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* { */</span><span class="p">,</span></span>
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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="159" 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">
159
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC159" class="line" lang="c"> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* | */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* } */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* ~ */</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="cm" style="color: #998; font-style: italic;">/* */</span></span>
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<td class="old_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="160" 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">
160
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC160" class="line" lang="c"><span class="p">};</span></span>
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<td class="new_line diff-line-num new" data-linenumber="161" 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">
161
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC161" class="line" lang="c"></span>
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<td class="old_line diff-line-num" data-linenumber="88" 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">
88
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<td class="new_line diff-line-num" data-linenumber="162" 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">
162
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC162" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* Generate query profile rearrange query sequence & calculate the weight of match/mismatch. */</span></span>
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163
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC163" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">__m128i</span><span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">qP_byte</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <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;">read_num</span><span class="p">,</span></span>
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164
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC164" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <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;">mat</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="134" 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="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">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -134,6 +208,7 @@ static alignment_end* sw_sse2_byte (const int8_t* ref,</td>
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134
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208
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC208" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">bias</span><span class="p">,</span> <span class="cm" style="color: #998; font-style: italic;">/* Shift 0 point to a positive value. */</span></span>
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135
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209
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC209" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">maskLen</span><span class="p">)</span> <span class="p">{</span></span>
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136
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210
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC210" class="line" lang="c"></span>
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<td class="new_line diff-line-num new" data-linenumber="211" 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">
211
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC211" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// Put the largest number of the 16 numbers in vm into m.</span></span>
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137
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212
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC212" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define max16(m, vm) (vm) = _mm_max_epu8((vm), _mm_srli_si128((vm), 8)); \</span></span>
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138
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<td class="new_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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC213" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> (vm) = _mm_max_epu8((vm), _mm_srli_si128((vm), 4)); \</span></span>
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139
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<td class="new_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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC214" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> (vm) = _mm_max_epu8((vm), _mm_srli_si128((vm), 2)); \</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="159" 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="234" 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">@@ -159,7 +234,7 @@ static alignment_end* sw_sse2_byte (const int8_t* ref,</td>
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159
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234
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC234" class="line" lang="c"> <span class="n" style="color: #333;">__m128i</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pvE</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">__m128i</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">calloc</span><span class="p">(</span><span class="n" style="color: #333;">segLen</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">__m128i</span><span class="p">));</span></span>
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160
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235
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC235" class="line" lang="c"> <span class="n" style="color: #333;">__m128i</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pvHmax</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">__m128i</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">calloc</span><span class="p">(</span><span class="n" style="color: #333;">segLen</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">__m128i</span><span class="p">));</span></span>
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161
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236
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC236" class="line" lang="c"></span>
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162
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC162" 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;">j</span><span class="p">;</span></span>
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237
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC237" 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;">j</span><span class="p"><span class="idiff left addition">,</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff right addition">k</span></span><span class="p">;</span></span>
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163
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238
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC238" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* 16 byte insertion begin vector */</span></span>
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164
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC239" class="line" lang="c"> <span class="n" style="color: #333;">__m128i</span> <span class="n" style="color: #333;">vGapO</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_set1_epi8</span><span class="p">(</span><span class="n" style="color: #333;">weight_gapO</span><span class="p">);</span></span>
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165
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240
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC240" class="line" lang="c"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="298" 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">@@ -223,39 +298,21 @@ static alignment_end* sw_sse2_byte (const int8_t* ref,</td>
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223
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC298" class="line" lang="c"> <span class="n" style="color: #333;">vH</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_si128</span><span class="p">(</span><span class="n" style="color: #333;">pvHLoad</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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224
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC299" class="line" lang="c"> <span class="p">}</span></span>
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300
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC300" class="line" lang="c"></span>
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226
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC226" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Lazy_F loop: has been revised to disallow adjecent insertion and then deletion, so don't update E(i, j), learn from SWPS3 */</span></span>
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227
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<td class="new_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">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC227" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* reset pointers to the start of the saved data */</span></span>
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228
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<td class="new_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">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC228" 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;">0</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="229" 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">
229
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<td class="new_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">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC229" class="line" lang="c"> <span class="n" style="color: #333;">vH</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_si128</span> <span class="p">(</span><span class="n" style="color: #333;">pvHStore</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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230
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<td class="new_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">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC230" class="line" lang="c"></span>
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<td class="old_line diff-line-num old" data-linenumber="231" 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">
231
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<td class="new_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">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC231" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* the computed vF value is for the given column. since */</span></span>
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<td class="old_line diff-line-num old" data-linenumber="232" 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">
232
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<td class="new_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">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC232" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* we are at the end, we need to shift the vF value over */</span></span>
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233
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<td class="new_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">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC233" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* to the next column. */</span></span>
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<td class="old_line diff-line-num old" data-linenumber="234" 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">
234
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<td class="new_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">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC234" class="line" lang="c"> <span class="n" style="color: #333;">vF</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_slli_si128</span> <span class="p">(</span><span class="n" style="color: #333;">vF</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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235
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<td class="new_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">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC235" class="line" lang="c"> <span class="n" style="color: #333;">vTemp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_subs_epu8</span> <span class="p">(</span><span class="n" style="color: #333;">vH</span><span class="p">,</span> <span class="n" style="color: #333;">vGapO</span><span class="p">);</span></span>
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236
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<td class="new_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">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC236" class="line" lang="c"> <span class="n" style="color: #333;">vTemp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_subs_epu8</span> <span class="p">(</span><span class="n" style="color: #333;">vF</span><span class="p">,</span> <span class="n" style="color: #333;">vTemp</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="237" 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">
237
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<td class="new_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">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC237" class="line" lang="c"> <span class="n" style="color: #333;">vTemp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cmpeq_epi8</span> <span class="p">(</span><span class="n" style="color: #333;">vTemp</span><span class="p">,</span> <span class="n" style="color: #333;">vZero</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="238" 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">
238
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<td class="new_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">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC238" class="line" lang="c"> <span class="n" style="color: #333;">cmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_movemask_epi8</span> <span class="p">(</span><span class="n" style="color: #333;">vTemp</span><span class="p">);</span></span>
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239
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<td class="new_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">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC239" class="line" lang="c"></span>
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240
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<td class="new_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">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC240" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">cmp</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mh" style="color: #099;">0xffff</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="241" 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">
241
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<td class="new_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">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC241" class="line" lang="c"> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="242" 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">
242
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<td class="new_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">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC242" class="line" lang="c"> <span class="n" style="color: #333;">vH</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_max_epu8</span> <span class="p">(</span><span class="n" style="color: #333;">vH</span><span class="p">,</span> <span class="n" style="color: #333;">vF</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="243" 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">
243
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<td class="new_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">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC243" class="line" lang="c"> <span class="n" style="color: #333;">vMaxColumn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_max_epu8</span><span class="p">(</span><span class="n" style="color: #333;">vMaxColumn</span><span class="p">,</span> <span class="n" style="color: #333;">vH</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="244" 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">
244
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<td class="new_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">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC244" class="line" lang="c"> <span class="n" style="color: #333;">_mm_store_si128</span> <span class="p">(</span><span class="n" style="color: #333;">pvHStore</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">vH</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="245" 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">
245
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<td class="new_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">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC245" class="line" lang="c"> <span class="n" style="color: #333;">vF</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_subs_epu8</span> <span class="p">(</span><span class="n" style="color: #333;">vF</span><span class="p">,</span> <span class="n" style="color: #333;">vGapE</span><span class="p">);</span></span>
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246
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<td class="new_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">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC246" class="line" lang="c"> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC247" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">segLen</span><span class="p">)</span></span>
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248
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<td class="new_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">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC248" class="line" lang="c"> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="249" 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">
249
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<td class="new_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">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC249" 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;">0</span><span class="p">;</span></span>
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250
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<td class="new_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">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC250" class="line" lang="c"> <span class="n" style="color: #333;">vF</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_slli_si128</span> <span class="p">(</span><span class="n" style="color: #333;">vF</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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251
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<td class="new_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">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC251" class="line" lang="c"> <span class="p">}</span></span>
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252
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<td class="new_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">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC252" class="line" lang="c"> <span class="n" style="color: #333;">vH</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_si128</span> <span class="p">(</span><span class="n" style="color: #333;">pvHStore</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="253" 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">
253
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<td class="new_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">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC253" class="line" lang="c"></span>
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<td class="old_line diff-line-num old" data-linenumber="254" 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">
254
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<td class="new_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">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC254" class="line" lang="c"> <span class="n" style="color: #333;">vTemp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_subs_epu8</span> <span class="p">(</span><span class="n" style="color: #333;">vH</span><span class="p">,</span> <span class="n" style="color: #333;">vGapO</span><span class="p">);</span></span>
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255
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<td class="new_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">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC255" class="line" lang="c"> <span class="n" style="color: #333;">vTemp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_subs_epu8</span> <span class="p">(</span><span class="n" style="color: #333;">vF</span><span class="p">,</span> <span class="n" style="color: #333;">vTemp</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="256" 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">
256
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<td class="new_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">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC256" class="line" lang="c"> <span class="n" style="color: #333;">vTemp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cmpeq_epi8</span> <span class="p">(</span><span class="n" style="color: #333;">vTemp</span><span class="p">,</span> <span class="n" style="color: #333;">vZero</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="257" 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">
257
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<td class="new_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">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC257" class="line" lang="c"> <span class="n" style="color: #333;">cmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_movemask_epi8</span> <span class="p">(</span><span class="n" style="color: #333;">vTemp</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="258" 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">
258
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<td class="new_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">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC258" class="line" lang="c"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="301" 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">
301
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC301" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Lazy_F loop: has been revised to disallow adjecent insertion and then deletion, so don't update E(i, j), learn from SWPS3 */</span></span>
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<td class="new_line diff-line-num new" data-linenumber="302" 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">
302
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC302" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">k</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;">LIKELY</span><span class="p">(</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">16</span><span class="p">);</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">k</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="303" 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">
303
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC303" class="line" lang="c"> <span class="n" style="color: #333;">vF</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_slli_si128</span> <span class="p">(</span><span class="n" style="color: #333;">vF</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="304" 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">
304
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC304" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</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;">0</span><span class="p">;</span> <span class="n" style="color: #333;">LIKELY</span><span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">segLen</span><span class="p">);</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="305" 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">
305
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC305" class="line" lang="c"> <span class="n" style="color: #333;">vH</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_load_si128</span><span class="p">(</span><span class="n" style="color: #333;">pvHStore</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 new" data-linenumber="259" 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="306" 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">
306
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC306" class="line" lang="c"> <span class="n" style="color: #333;">vH</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_max_epu8</span><span class="p">(</span><span class="n" style="color: #333;">vH</span><span class="p">,</span> <span class="n" style="color: #333;">vF</span><span class="p">);</span></span>
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<td class="old_line diff-line-num new" data-linenumber="259" 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="307" 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">
307
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC307" class="line" lang="c"> <span class="n" style="color: #333;">vMaxColumn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_max_epu8</span><span class="p">(</span><span class="n" style="color: #333;">vMaxColumn</span><span class="p">,</span> <span class="n" style="color: #333;">vH</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// newly added line</span></span>
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<td class="new_line diff-line-num new" data-linenumber="308" 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">
308
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC308" class="line" lang="c"> <span class="n" style="color: #333;">_mm_store_si128</span><span class="p">(</span><span class="n" style="color: #333;">pvHStore</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">vH</span><span class="p">);</span></span>
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309
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC309" class="line" lang="c"> <span class="n" style="color: #333;">vH</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_subs_epu8</span><span class="p">(</span><span class="n" style="color: #333;">vH</span><span class="p">,</span> <span class="n" style="color: #333;">vGapO</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="310" 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">
310
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC310" class="line" lang="c"> <span class="n" style="color: #333;">vF</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_subs_epu8</span><span class="p">(</span><span class="n" style="color: #333;">vF</span><span class="p">,</span> <span class="n" style="color: #333;">vGapE</span><span class="p">);</span></span>
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311
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC311" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">UNLIKELY</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span> <span class="n" style="color: #333;">_mm_movemask_epi8</span><span class="p">(</span><span class="n" style="color: #333;">_mm_cmpgt_epi8</span><span class="p">(</span><span class="n" style="color: #333;">vF</span><span class="p">,</span> <span class="n" style="color: #333;">vH</span><span class="p">))))</span> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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312
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC312" class="line" lang="c"> <span class="p">}</span></span>
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313
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC313" class="line" lang="c"> <span class="p">}</span></span>
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314
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC314" class="line" lang="c"></span>
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315
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC315" class="line" lang="c"><span class="nl">end:</span> </span>
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316
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC316" class="line" lang="c"></span>
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260
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317
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC317" class="line" lang="c"> <span class="n" style="color: #333;">vMaxScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_max_epu8</span><span class="p">(</span><span class="n" style="color: #333;">vMaxScore</span><span class="p">,</span> <span class="n" style="color: #333;">vMaxColumn</span><span class="p">);</span></span>
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261
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318
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC318" class="line" lang="c"> <span class="n" style="color: #333;">vTemp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cmpeq_epi8</span><span class="p">(</span><span class="n" style="color: #333;">vMaxMark</span><span class="p">,</span> <span class="n" style="color: #333;">vMaxScore</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="586" 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">@@ -529,37 +586,6 @@ end:</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC586" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">bests</span><span class="p">;</span></span>
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587
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC587" class="line" lang="c"><span class="p">}</span></span>
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588
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC588" class="line" lang="c"></span>
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532
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<td class="new_line diff-line-num old" data-linenumber="589" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC532" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*! @function Produce CIGAR 32-bit unsigned integer from CIGAR operation and CIGAR length</span></span>
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533
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<td class="new_line diff-line-num old" data-linenumber="589" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC533" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> @param length length of CIGAR</span></span>
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534
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<td class="new_line diff-line-num old" data-linenumber="589" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC534" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> @param op_letter CIGAR operation character ('M', 'I', etc)</span></span>
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535
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<td class="new_line diff-line-num old" data-linenumber="589" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC535" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> @return 32-bit unsigned integer, representing encoded CIGAR operation and length</span></span>
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536
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<td class="new_line diff-line-num old" data-linenumber="589" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC536" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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<td class="new_line diff-line-num old" data-linenumber="589" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC537" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="nf" style="color: #900; font-weight: 600;">to_cigar_int</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">op_letter</span><span class="p">)</span></span>
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538
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC538" class="line" lang="c"><span class="p">{</span></span>
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539
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC539" class="line" lang="c"> <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span><span class="n" style="color: #333;">op_letter</span><span class="p">)</span> <span class="p">{</span></span>
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540
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<td class="new_line diff-line-num old" data-linenumber="589" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC540" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'M'</span><span class="p">:</span> <span class="cm" style="color: #998; font-style: italic;">/* alignment match (can be a sequence match or mismatch */</span></span>
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541
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC541" class="line" lang="c"> <span class="nl">default:</span></span>
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542
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<td class="new_line diff-line-num old" data-linenumber="589" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC542" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">BAM_CIGAR_SHIFT</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="543" 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">
543
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<td class="new_line diff-line-num old" data-linenumber="589" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC543" 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="cm" style="color: #998; font-style: italic;">/* soft clipping (clipped sequences present in SEQ) */</span></span>
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<td class="old_line diff-line-num old" data-linenumber="544" 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">
544
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<td class="new_line diff-line-num old" data-linenumber="589" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC544" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">BAM_CIGAR_SHIFT</span><span class="p">)</span> <span class="o" style="font-weight: 600;">|</span> <span class="p">(</span><span class="mi" style="color: #099;">4u</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="545" 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">
545
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<td class="new_line diff-line-num old" data-linenumber="589" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC545" 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="cm" style="color: #998; font-style: italic;">/* deletion from the reference */</span></span>
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<td class="old_line diff-line-num old" data-linenumber="546" 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">
546
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<td class="new_line diff-line-num old" data-linenumber="589" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC546" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">BAM_CIGAR_SHIFT</span><span class="p">)</span> <span class="o" style="font-weight: 600;">|</span> <span class="p">(</span><span class="mi" style="color: #099;">2u</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="547" 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">
547
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<td class="new_line diff-line-num old" data-linenumber="589" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC547" 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="cm" style="color: #998; font-style: italic;">/* insertion to the reference */</span></span>
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<td class="old_line diff-line-num old" data-linenumber="548" 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">
548
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<td class="new_line diff-line-num old" data-linenumber="589" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC548" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">BAM_CIGAR_SHIFT</span><span class="p">)</span> <span class="o" style="font-weight: 600;">|</span> <span class="p">(</span><span class="mi" style="color: #099;">1u</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="549" 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">
549
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<td class="new_line diff-line-num old" data-linenumber="589" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC549" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'H'</span><span class="p">:</span> <span class="cm" style="color: #998; font-style: italic;">/* hard clipping (clipped sequences NOT present in SEQ) */</span></span>
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<td class="old_line diff-line-num old" data-linenumber="550" 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">
550
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<td class="new_line diff-line-num old" data-linenumber="589" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC550" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">BAM_CIGAR_SHIFT</span><span class="p">)</span> <span class="o" style="font-weight: 600;">|</span> <span class="p">(</span><span class="mi" style="color: #099;">5u</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="551" 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">
551
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<td class="new_line diff-line-num old" data-linenumber="589" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC551" 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="cm" style="color: #998; font-style: italic;">/* skipped region from the reference */</span></span>
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<td class="old_line diff-line-num old" data-linenumber="552" 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">
552
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<td class="new_line diff-line-num old" data-linenumber="589" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC552" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">BAM_CIGAR_SHIFT</span><span class="p">)</span> <span class="o" style="font-weight: 600;">|</span> <span class="p">(</span><span class="mi" style="color: #099;">3u</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="553" 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">
553
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<td class="new_line diff-line-num old" data-linenumber="589" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC553" 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="cm" style="color: #998; font-style: italic;">/* padding (silent deletion from padded reference) */</span></span>
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<td class="old_line diff-line-num old" data-linenumber="554" 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">
554
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<td class="new_line diff-line-num old" data-linenumber="589" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC554" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">BAM_CIGAR_SHIFT</span><span class="p">)</span> <span class="o" style="font-weight: 600;">|</span> <span class="p">(</span><span class="mi" style="color: #099;">6u</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="555" 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">
555
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<td class="new_line diff-line-num old" data-linenumber="589" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC555" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'='</span><span class="p">:</span> <span class="cm" style="color: #998; font-style: italic;">/* sequence match */</span></span>
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<td class="old_line diff-line-num old" data-linenumber="556" 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">
556
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<td class="new_line diff-line-num old" data-linenumber="589" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC556" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">BAM_CIGAR_SHIFT</span><span class="p">)</span> <span class="o" style="font-weight: 600;">|</span> <span class="p">(</span><span class="mi" style="color: #099;">7u</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="557" 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">
557
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<td class="new_line diff-line-num old" data-linenumber="589" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC557" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'X'</span><span class="p">:</span> <span class="cm" style="color: #998; font-style: italic;">/* sequence mismatch */</span></span>
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<td class="old_line diff-line-num old" data-linenumber="558" 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">
558
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<td class="new_line diff-line-num old" data-linenumber="589" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC558" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">BAM_CIGAR_SHIFT</span><span class="p">)</span> <span class="o" style="font-weight: 600;">|</span> <span class="p">(</span><span class="mi" style="color: #099;">8u</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="559" 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">
559
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<td class="new_line diff-line-num old" data-linenumber="589" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC559" class="line" lang="c"> <span class="p">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="560" 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">
560
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<td class="new_line diff-line-num old" data-linenumber="589" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC560" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</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="c1" style="color: #998; font-style: italic;">// This never happens</span></span>
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<td class="old_line diff-line-num old" data-linenumber="561" 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">
561
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<td class="new_line diff-line-num old" data-linenumber="589" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC561" class="line" lang="c"><span class="p">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="562" 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">
562
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<td class="new_line diff-line-num old" data-linenumber="589" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC562" class="line" lang="c"></span>
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563
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589
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC589" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">cigar</span><span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">banded_sw</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <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;">ref</span><span class="p">,</span></span>
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564
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590
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC590" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <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;">read</span><span class="p">,</span></span>
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565
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591
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC591" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">refLen</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="598" 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">@@ -572,11 +598,12 @@ static cigar* banded_sw (const int8_t* ref,</td>
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572
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598
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC598" class="line" lang="c"> <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 class="p">{</span></span>
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573
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599
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC599" class="line" lang="c"></span>
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574
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600
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC600" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</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="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="mi" style="color: #099;">16</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)),</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">c1</span><span class="p">;</span></span>
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575
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<td class="new_line diff-line-num old" data-linenumber="601" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC575" 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;">j</span><span class="p">,</span> <span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">temp1</span><span class="p">,</span> <span class="n" style="color: #333;">temp2</span><span class="p">,</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">16</span><span class="p">,</span> <span class="n" style="color: #333;">s1</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">max</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="new_line diff-line-num new" data-linenumber="601" 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">
601
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC601" 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;">j</span><span class="p">,</span> <span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">temp1</span><span class="p">,</span> <span class="n" style="color: #333;">temp2</span><span class="p">,</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">16</span><span class="p">,</span> <span class="n" style="color: #333;">s1</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">max</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p"><span class="idiff left addition">,</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff right addition">len</span></span><span class="p">;</span></span>
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576
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602
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC602" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">s2</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1024</span><span class="p">;</span></span>
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577
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<td class="new_line diff-line-num" data-linenumber="603" 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">
603
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC603" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">op</span><span class="p">,</span> <span class="n" style="color: #333;">prev_op</span><span class="p">;</span></span>
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578
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<td class="new_line diff-line-num" data-linenumber="604" 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">
604
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC604" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">width</span><span class="p">,</span> <span class="n" style="color: #333;">width_d</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">h_b</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">e_b</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">h_c</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="579" 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">
579
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<td class="new_line diff-line-num" 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">
605
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC605" 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;">direction</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">direction_line</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="606" 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">
606
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC606" class="line" lang="c"> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refLen</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">readLen</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">refLen</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">readLen</span><span class="p">;</span></span>
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580
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<td class="new_line diff-line-num" data-linenumber="607" 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">
607
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC607" class="line" lang="c"> <span class="n" style="color: #333;">cigar</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">cigar</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">cigar</span><span class="p">));</span></span>
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581
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<td class="new_line diff-line-num" data-linenumber="608" 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">
608
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC608" class="line" lang="c"> <span class="n" style="color: #333;">h_b</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">s1</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">));</span></span>
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582
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609
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC609" class="line" lang="c"> <span class="n" style="color: #333;">e_b</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">s1</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">));</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="592" 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="619" 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">@@ -592,13 +619,9 @@ static cigar* banded_sw (const int8_t* ref,</td>
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592
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619
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC619" class="line" lang="c"> <span class="n" style="color: #333;">e_b</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">realloc</span><span class="p">(</span><span class="n" style="color: #333;">e_b</span><span class="p">,</span> <span class="n" style="color: #333;">s1</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">));</span></span>
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593
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620
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC620" class="line" lang="c"> <span class="n" style="color: #333;">h_c</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">realloc</span><span class="p">(</span><span class="n" style="color: #333;">h_c</span><span class="p">,</span> <span class="n" style="color: #333;">s1</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">));</span></span>
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594
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621
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC621" class="line" lang="c"> <span class="p">}</span></span>
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595
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC595" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">width_d</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">readLen</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">s2</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="622" 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">
622
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC622" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">width_d</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">readLen</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">s2</span><span class="p">)</span> <span class="p">{</span><span class="idiff left addition"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right addition">// width_d*readLen* overflow before s2</span></span></span>
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596
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623
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC623" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">s2</span><span class="p">;</span></span>
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597
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624
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC624" class="line" lang="c"> <span class="n" style="color: #333;">kroundup32</span><span class="p">(</span><span class="n" style="color: #333;">s2</span><span class="p">);</span></span>
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598
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC598" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">s2</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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599
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC599" 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;">"Alignment score and position are not consensus.</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="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC600" 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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601
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC601" class="line" lang="c"> <span class="p">}</span></span>
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602
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625
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC625" class="line" lang="c"> <span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int8_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">realloc</span><span class="p">(</span><span class="n" style="color: #333;">direction</span><span class="p">,</span> <span class="n" style="color: #333;">s2</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int8_t</span><span class="p">));</span></span>
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603
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626
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC626" class="line" lang="c"> <span class="p">}</span></span>
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627
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC627" class="line" lang="c"> <span class="n" style="color: #333;">direction_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">direction</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="621" 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">@@ -621,6 +644,7 @@ static cigar* banded_sw (const int8_t* ref,</td>
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621
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644
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC644" class="line" lang="c"></span>
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622
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645
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC645" class="line" lang="c"> <span class="n" style="color: #333;">temp1</span> <span class="o" style="font-weight: 600;">=</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="o" style="font-weight: 600;">?</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">weight_gapO</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">h_b</span><span class="p">[</span><span class="n" style="color: #333;">e</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">weight_gapO</span><span class="p">;</span></span>
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623
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646
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC646" class="line" lang="c"> <span class="n" style="color: #333;">temp2</span> <span class="o" style="font-weight: 600;">=</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="o" style="font-weight: 600;">?</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">weight_gapE</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">e_b</span><span class="p">[</span><span class="n" style="color: #333;">e</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">weight_gapE</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="647" 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">
647
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC647" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//fprintf(stderr, "e_b length: %d, u: %d\n", s1, u);</span></span>
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624
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648
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC648" class="line" lang="c"> <span class="n" style="color: #333;">e_b</span><span class="p">[</span><span class="n" style="color: #333;">u</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">temp1</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">temp2</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">temp1</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">temp2</span><span class="p">;</span></span>
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649
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC649" class="line" lang="c"> <span class="n" style="color: #333;">direction_line</span><span class="p">[</span><span class="n" style="color: #333;">de</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">temp1</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">temp2</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">3</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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650
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC650" class="line" lang="c"></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">@@ -643,7 +667,7 @@ static cigar* banded_sw (const int8_t* ref,</td>
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667
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC667" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</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 class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">u</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="n" style="color: #333;">h_b</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;">h_c</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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668
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC668" class="line" lang="c"> <span class="p">}</span></span>
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669
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC669" class="line" lang="c"> <span class="n" style="color: #333;">band_width</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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC646" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">while</span> <span class="p"><span class="idiff left deletion">(</span></span><span class="n" style="color: #333;"><span class="idiff deletion">LIKELY</span></span><span class="p">(</span><span class="n" style="color: #333;">max</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">score</span><span class="p"><span class="idiff right deletion">));</span></span></span>
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670
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC670" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">max</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">score</span><span class="idiff left addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">&&</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">band_width</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition"><=</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">len</span></span><span class="p"><span class="idiff addition">);</span></span><span class="idiff addition"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right addition">// 2022-Apr-08</span></span></span>
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671
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC671" class="line" lang="c"> <span class="n" style="color: #333;">band_width</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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672
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC672" class="line" lang="c"></span>
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649
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673
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC673" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// trace back</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="653" 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="677" 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">@@ -653,7 +677,7 @@ static cigar* banded_sw (const int8_t* ref,</td>
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653
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677
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC677" class="line" lang="c"> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// record length of current cigar</span></span>
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654
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678
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC678" class="line" lang="c"> <span class="n" style="color: #333;">op</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prev_op</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'M'</span><span class="p">;</span></span>
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655
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679
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC679" class="line" lang="c"> <span class="n" style="color: #333;">temp2</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// h</span></span>
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656
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC656" class="line" lang="c"><span class="idiff left right deletion"> </span><span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">LIKELY</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="p">{</span></span>
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680
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC680" class="line" lang="c"><span class="idiff left addition"> </span><span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">LIKELY</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><span class="idiff addition">>=</span></span><span class="idiff addition"> </span><span class="mi" style="color: #099;"><span class="idiff addition">0</span></span><span class="idiff addition"> </span><span class="o" style="font-weight: 600;"><span class="idiff addition">&&</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff addition">j</span></span><span class="idiff right addition"> </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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657
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681
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC681" class="line" lang="c"> <span class="n" style="color: #333;">set_d</span><span class="p">(</span><span class="n" style="color: #333;">temp1</span><span class="p">,</span> <span class="n" style="color: #333;">band_width</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">temp2</span><span class="p">);</span></span>
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658
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682
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC682" class="line" lang="c"> <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span><span class="n" style="color: #333;">direction_line</span><span class="p">[</span><span class="n" style="color: #333;">temp1</span><span class="p">])</span> <span class="p">{</span></span>
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659
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683
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC683" 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>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="716" 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">@@ -692,7 +716,7 @@ static cigar* banded_sw (const int8_t* ref,</td>
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692
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716
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC716" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">e_b</span><span class="p">);</span></span>
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693
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717
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC717" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">h_b</span><span class="p">);</span></span>
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694
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718
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC718" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">);</span></span>
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695
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC695" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="719" 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">
719
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC719" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">);</span><span class="idiff left right addition"> </span></span>
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696
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<td class="new_line diff-line-num" data-linenumber="720" 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">
720
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC720" 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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<td class="old_line diff-line-num" data-linenumber="697" 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">
697
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721
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC721" class="line" lang="c"> <span class="p">}</span></span>
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698
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722
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC722" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">op</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">prev_op</span><span class="p">)</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">e</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="810" 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="834" 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">@@ -810,6 +834,7 @@ s_align* ssw_align (const s_profile* prof,</td>
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810
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<td class="new_line diff-line-num" data-linenumber="834" 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">
834
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC834" class="line" lang="c"> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_begin1</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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<td class="old_line diff-line-num" data-linenumber="811" 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">
811
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<td class="new_line diff-line-num" data-linenumber="835" 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">
835
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC835" class="line" lang="c"> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cigar</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="old_line diff-line-num" data-linenumber="812" 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">
812
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<td class="new_line diff-line-num" data-linenumber="836" 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">
836
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC836" class="line" lang="c"> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cigarLen</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="new_line diff-line-num new" data-linenumber="837" 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">
837
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC837" class="line" lang="c"> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">flag</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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813
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838
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC838" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">maskLen</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">15</span><span class="p">)</span> <span class="p">{</span></span>
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814
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839
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC839" 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;">"When maskLen < 15, the function ssw_align doesn't return 2nd best alignment information.</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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815
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840
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC840" 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="835" 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="860" 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">@@ -835,8 +860,8 @@ s_align* ssw_align (const s_profile* prof,</td>
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835
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<td class="new_line diff-line-num" data-linenumber="860" 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">
860
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC860" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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836
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861
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC861" class="line" lang="c"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="837" 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">
837
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<td class="new_line diff-line-num" data-linenumber="862" 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">
862
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC862" class="line" lang="c"> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">score1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bests</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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838
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<td class="new_line diff-line-num old" data-linenumber="863" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC838" class="line" lang="c"> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ref_end1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bests</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">ref</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="839" 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">
839
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<td class="new_line diff-line-num old" data-linenumber="863" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC839" class="line" lang="c"> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_end1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bests</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">read</span><span class="p">;</span></span>
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863
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC863" class="line" lang="c"> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ref_end1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bests</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">ref</span><span class="p">;</span><span class="idiff left addition"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right addition">// 0_based, always count from the input seq begin</span></span></span>
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864
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC864" class="line" lang="c"> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_end1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bests</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">read</span><span class="p">;</span><span class="idiff left addition"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right addition">// 0_based, count from the alignment begin (aligned length of the read)</span></span></span>
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840
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865
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC865" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">maskLen</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">15</span><span class="p">)</span> <span class="p">{</span></span>
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841
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866
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC866" class="line" lang="c"> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">score2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bests</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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842
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867
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC867" class="line" lang="c"> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ref_end2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bests</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">ref</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">@@ -860,7 +885,13 @@ s_align* ssw_align (const s_profile* prof,</td>
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860
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885
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC885" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">read_reverse</span><span class="p">);</span></span>
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861
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886
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC886" class="line" lang="c"> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ref_begin1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bests_reverse</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">ref</span><span class="p">;</span></span>
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862
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887
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC887" class="line" lang="c"> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_begin1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_end1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">bests_reverse</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">read</span><span class="p">;</span></span>
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863
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC863" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">bests_reverse</span><span class="p">);</span></span>
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888
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC888" class="line" lang="c"></span>
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889
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC889" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">UNLIKELY</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">score1</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">bests_reverse</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">score</span><span class="p">))</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// banded_sw result will miss a small part</span></span>
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890
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC890" 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: The alignment path of one pair of sequences may miss a small part. [ssw.c ssw_align]</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="891" 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">
891
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC891" class="line" lang="c"> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">flag</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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892
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC892" class="line" lang="c"> <span class="p">}</span></span>
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893
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC893" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">bests_reverse</span><span class="p">);</span></span>
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894
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC894" class="line" lang="c"></span>
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895
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC895" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="mi" style="color: #099;">7</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">flag</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="p">((</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">flag</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;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">score1</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">filters</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">((</span><span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">flag</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="p">(</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ref_end1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ref_begin1</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">filterd</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_end1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_begin1</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">filterd</span><span class="p">)))</span> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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865
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896
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC896" class="line" lang="c"></span>
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897
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC897" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Generate cigar.</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">@@ -868,11 +899,18 @@ s_align* ssw_align (const s_profile* prof,</td>
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868
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899
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC899" class="line" lang="c"> <span class="n" style="color: #333;">readLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_end1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_begin1</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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900
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC900" class="line" lang="c"> <span class="n" style="color: #333;">band_width</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">refLen</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">readLen</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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870
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901
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC901" class="line" lang="c"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">banded_sw</span><span class="p">(</span><span class="n" style="color: #333;">ref</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ref_begin1</span><span class="p">,</span> <span class="n" style="color: #333;">prof</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read_begin1</span><span class="p">,</span> <span class="n" style="color: #333;">refLen</span><span class="p">,</span> <span class="n" style="color: #333;">readLen</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">score1</span><span class="p">,</span> <span class="n" style="color: #333;">weight_gapO</span><span class="p">,</span> <span class="n" style="color: #333;">weight_gapE</span><span class="p">,</span> <span class="n" style="color: #333;">band_width</span><span class="p">,</span> <span class="n" style="color: #333;">prof</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mat</span><span class="p">,</span> <span class="n" style="color: #333;">prof</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n</span><span class="p">);</span></span>
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871
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC871" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">path</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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872
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC872" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">);</span></span>
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873
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<td class="new_line diff-line-num old" data-linenumber="902" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC873" class="line" lang="c"> <span class="n" style="color: #333;">r</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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874
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC874" class="line" lang="c"> <span class="p">}</span></span>
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875
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<td class="new_line diff-line-num old" data-linenumber="902" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC875" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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902
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC902" class="line" lang="c"></span>
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903
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC903" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*int32_t i, length;</span></span>
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904
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC904" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> char op;</span></span>
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905
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC905" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> for (i = 0; i < path->length; ++i) {</span></span>
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906
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC906" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> op = cigar_int_to_op(path->seq[i]);</span></span>
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907
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC907" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> length = cigar_int_to_len(path->seq[i]);</span></span>
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908
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC908" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> fprintf(stderr, "%d%c", length, op);</span></span>
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909
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC909" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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910
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC910" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> fprintf(stderr, "\n");*/</span></span>
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911
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912
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC912" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">path</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;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// banded_sw is failed.</span></span>
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913
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC913" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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876
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914
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC914" class="line" lang="c"> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cigar</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">;</span></span>
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877
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915
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC915" class="line" lang="c"> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cigarLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span><span class="p">;</span></span>
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878
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916
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC916" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="925" 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="963" 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">@@ -925,8 +963,8 @@ uint32_t* store_previous_m (int8_t choice, // 0: current not M, 1: current match</td>
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925
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<td class="new_line diff-line-num" data-linenumber="963" 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">
963
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC963" 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;">mark_mismatch</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">ref_begin1</span><span class="p">,</span></span>
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<td class="old_line diff-line-num" data-linenumber="926" 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">
926
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<td class="new_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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC964" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">read_begin1</span><span class="p">,</span></span>
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<td class="old_line diff-line-num" data-linenumber="927" 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">
927
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<td class="new_line diff-line-num" data-linenumber="965" 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">
965
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC965" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">read_end1</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="928" 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">
928
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<td class="new_line diff-line-num old" data-linenumber="966" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC928" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right deletion">char</span></span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ref</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="929" 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">
929
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<td class="new_line diff-line-num old" data-linenumber="966" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC929" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right deletion">char</span></span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">read</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="966" 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">
966
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC966" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right addition">int8_t</span></span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ref</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="967" 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">
967
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC967" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right addition">int8_t</span></span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">read</span><span class="p">,</span></span>
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930
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<td class="new_line diff-line-num" data-linenumber="968" 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">
968
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC968" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">readLen</span><span class="p">,</span></span>
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931
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969
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC969" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">cigar</span><span class="p">,</span></span>
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932
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970
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC970" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cigarLen</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="943" 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="981" 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">@@ -943,10 +981,8 @@ int32_t mark_mismatch (int32_t ref_begin1,</td>
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<td class="old_line diff-line-num" data-linenumber="943" 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">
943
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<td class="new_line diff-line-num" data-linenumber="981" 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">
981
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC981" class="line" lang="c"> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cigar_int_to_len</span><span class="p">((</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cigar</span><span class="p">)[</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" data-linenumber="944" 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">
944
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<td class="new_line diff-line-num" data-linenumber="982" 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">
982
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC982" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">op</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'M'</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="945" 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">
945
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<td class="new_line diff-line-num" data-linenumber="983" 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">
983
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC983" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</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;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">length</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="946" 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">
946
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<td class="new_line diff-line-num old" data-linenumber="984" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC946" 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;">"ref[%d]: %c</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">read[%d]: %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;">j</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ref</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;">read</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="947" 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">
947
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<td class="new_line diff-line-num" data-linenumber="984" 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">
984
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC984" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ref</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">read</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num" data-linenumber="948" 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">
948
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<td class="new_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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC985" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span> <span class="n" style="color: #333;">mismatch_length</span><span class="p">;</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC949" 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;">"length_m: %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;">length_m</span><span class="p">);</span></span>
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986
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC986" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// the previous is match; however the current one is mismatche</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="LC987" class="line" lang="c"> <span class="n" style="color: #333;">new_cigar</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">store_previous_m</span> <span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">length_m</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">length_x</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">p</span><span class="p">,</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;">new_cigar</span><span class="p">);</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="LC988" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span> <span class="n" style="color: #333;">length_x</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/libssw/-/commit/c9c6106f955eac1ec9d8a40cc85495ccf3178810#ceb1970521a5592e0be98b926f55977493e48a5b"><strong>src/ssw.h</strong></a>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC3" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</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="LC4" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Created by Mengyao Zhao on 6/22/10.</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="LC5" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Copyright 2010 Boston College. All rights reserved.</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC6" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Version <span class="idiff left right deletion">0.1.4</span></span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC7" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Last revision by Mengyao Zhao on <span class="idiff left right deletion">07/19/16</span>.</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC6" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Version <span class="idiff left right addition">1.2.3</span></span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC7" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Last revision by Mengyao Zhao on <span class="idiff left right addition">2022-Apr-15</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="LC8" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</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="LC9" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</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="LC10" class="line" lang="c"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC14" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stdio.h></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="LC15" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stdint.h></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="LC16" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <string.h></span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC18" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __ARM_NEON // (M1)</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC19" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "sse2neon.h"</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC20" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else // x86 (Intel)</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="LC21" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <emmintrin.h></span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC22" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</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="LC24" class="line" lang="c"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC25" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __cplusplus</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="LC26" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="s" style="color: #d14;">"C"</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">@@ -25,24 +31,26 @@ extern "C" {</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC31" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define BAM_CIGAR_SHIFT 4u</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="LC32" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</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="LC33" class="line" lang="c"></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC34" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">encoded_ops</span><span class="p">[];</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="LC35" class="line" lang="c"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC36" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*! @typedef structure of the query profile */</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="LC37" class="line" lang="c"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">_profile</span><span class="p">;</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="LC38" class="line" lang="c"><span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">_profile</span> <span class="n" style="color: #333;">s_profile</span><span class="p">;</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="LC39" class="line" lang="c"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC40" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*! @typedef structure of the alignment result</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC34" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right deletion"> </span>@field score1 the best alignment score</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC35" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right deletion"> </span>@field score2 sub-optimal alignment score</span></span>
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<td class="new_line diff-line-num old" data-linenumber="41" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC36" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right deletion"> </span>@field ref_begin1 0-based best alignment beginning position on reference; ref_begin1 = -1 when the best alignment beginning</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC41" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right addition"> </span>@field score1 the best alignment score</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC42" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right addition"> </span>@field score2 sub-optimal alignment score</span></span>
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<td class="new_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC43" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right addition"> </span>@field ref_begin1 0-based best alignment beginning position on reference; ref_begin1 = -1 when the best alignment beginning</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="LC44" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> position is not available</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC38" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right deletion"> </span>@field ref_end1 0-based best alignment ending position on reference</span></span>
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<td class="new_line diff-line-num old" data-linenumber="45" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC39" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right deletion"> </span>@field read_begin1 0-based best alignment beginning position on read; read_begin1 = -1 when the best alignment beginning</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC45" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right addition"> </span>@field ref_end1 0-based best alignment ending position on reference</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC46" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right addition"> </span>@field read_begin1 0-based best alignment beginning position on read; read_begin1 = -1 when the best alignment beginning</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="LC47" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> position is not available</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC41" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right deletion"> </span>@field read_end1 0-based best alignment ending position on read</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC42" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right deletion"> </span>@field read_end2 0-based sub-optimal alignment ending position on read</span></span>
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<td class="new_line diff-line-num old" data-linenumber="48" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC43" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right deletion"> </span>@field cigar best alignment cigar; stored the same as that in BAM format, high 28 bits: length, low 4 bits: M/I/D (0/1/2);</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC48" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right addition"> </span>@field read_end1 0-based best alignment ending position on read</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC49" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right addition"> </span>@field read_end2 0-based sub-optimal alignment ending position on read</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC50" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right addition"> </span>@field cigar best alignment cigar; stored the same as that in BAM format, high 28 bits: length, low 4 bits: M/I/D (0/1/2);</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="LC51" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> cigar = 0 when the best alignment path is not available</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC45" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> @field cigarLen length of the cigar string; cigarLen = 0 when the best alignment path is not available</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC52" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> @field cigarLen length of the cigar string; cigarLen = 0 when the best alignment path is not available</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC53" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> @field flag If the alignment path is accurate (or has missing part). 0: accurate; 1: banded_sw is totally failed; 2: banded_sw returned path has missing part</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="LC54" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*/</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="LC55" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC56" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">score1</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">@@ -54,6 +62,7 @@ typedef struct {</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC62" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">ref_end2</span><span class="p">;</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="LC63" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cigar</span><span class="p">;</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="LC64" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">cigarLen</span><span class="p">;</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC65" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">flag</span><span class="p">;</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="LC66" class="line" lang="c"><span class="p">}</span> <span class="n" style="color: #333;">s_align</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">@@ -148,8 +157,8 @@ void align_destroy (s_align* a);</td>
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148
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157
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC157" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">mark_mismatch</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">ref_begin1</span><span class="p">,</span></span>
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149
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158
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC158" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">read_begin1</span><span class="p">,</span></span>
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150
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159
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC159" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">read_end1</span><span class="p">,</span></span>
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151
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC151" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right deletion">char</span></span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ref</span><span class="p">,</span></span>
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152
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<td class="new_line diff-line-num old" data-linenumber="160" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC152" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right deletion">char</span></span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">read</span><span class="p">,</span></span>
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160
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC160" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right addition">int8_t</span></span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ref</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="161" 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">
161
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC161" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right addition">int8_t</span></span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">read</span><span class="p">,</span></span>
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153
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<td class="new_line diff-line-num" data-linenumber="162" 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">
162
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC162" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">readLen</span><span class="p">,</span></span>
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154
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163
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC163" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">cigar</span><span class="p">,</span> </span>
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155
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164
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC164" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cigarLen</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="159" 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="168" 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">@@ -159,28 +168,27 @@ int32_t mark_mismatch (int32_t ref_begin1,</td>
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159
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168
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC168" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> @param op_letter CIGAR operation character ('M', 'I', etc)</span></span>
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160
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169
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC169" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> @return 32-bit unsigned integer, representing encoded CIGAR operation and length</span></span>
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161
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170
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC170" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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162
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC162" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">to_cigar_int</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">op_letter</span><span class="p">);</span></span>
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171
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC171" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">to_cigar_int</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">op_letter</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="172" 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">
172
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC172" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">BAM_CIGAR_SHIFT</span><span class="p">)</span> <span class="o" style="font-weight: 600;">|</span> <span class="p">(</span><span class="n" style="color: #333;">encoded_ops</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;">op_letter</span><span class="p">]);</span></span>
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173
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC173" class="line" lang="c"><span class="p">}</span></span>
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174
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC174" class="line" lang="c"></span>
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164
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC175" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*! @function Extract CIGAR operation character from CIGAR 32-bit unsigned integer</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="LC176" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> @param cigar_int 32-bit unsigned integer, representing encoded CIGAR operation and length</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="LC177" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> @return CIGAR operation character ('M', 'I', etc)</span></span>
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178
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC178" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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179
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC179" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//char cigar_int_to_op (uint32_t cigar_int);</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC169" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">cigar_int_to_op</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cigar_int</span><span class="p">)</span> </span>
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170
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC170" class="line" lang="c"><span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="180" 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">
180
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC180" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">cigar_int_to_op</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cigar_int</span><span class="p">)</span> <span class="p">{</span></span>
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171
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<td class="new_line diff-line-num" data-linenumber="181" 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">
181
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC181" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">cigar_int</span> <span class="o" style="font-weight: 600;">&</span> <span class="mh" style="color: #099;">0xfU</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">8</span> <span class="o" style="font-weight: 600;">?</span> <span class="sc" style="color: #d14;">'M'</span><span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">MAPSTR</span><span class="p">[</span><span class="n" style="color: #333;">cigar_int</span> <span class="o" style="font-weight: 600;">&</span> <span class="mh" style="color: #099;">0xfU</span><span class="p">];</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="LC182" class="line" lang="c"><span class="p">}</span></span>
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183
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC183" class="line" lang="c"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC174" class="line" lang="c"></span>
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175
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<td class="new_line diff-line-num" data-linenumber="184" 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">
184
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC184" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*! @function Extract length of a CIGAR operation from CIGAR 32-bit unsigned integer</span></span>
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185
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC185" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> @param cigar_int 32-bit unsigned integer, representing encoded CIGAR operation and length</span></span>
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177
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186
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC186" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> @return length of CIGAR operation</span></span>
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178
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187
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC187" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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179
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<td class="new_line diff-line-num old" data-linenumber="188" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC179" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//uint32_t cigar_int_to_len (uint32_t cigar_int);</span></span>
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180
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<td class="new_line diff-line-num old" data-linenumber="188" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC180" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cigar_int_to_len</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cigar_int</span><span class="p">)</span></span>
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181
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<td class="new_line diff-line-num old" data-linenumber="188" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC181" class="line" lang="c"><span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="188" 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">
188
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC188" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cigar_int_to_len</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">cigar_int</span><span class="p">)</span> <span class="p">{</span></span>
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182
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<td class="new_line diff-line-num" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC189" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">cigar_int</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">BAM_CIGAR_SHIFT</span><span class="p">;</span></span>
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183
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190
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC190" class="line" lang="c"><span class="p">}</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC191" class="line" lang="c"></span>
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184
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192
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC192" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __cplusplus</span></span>
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193
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC193" class="line" lang="c"><span class="p">}</span></span>
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186
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194
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC194" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif // __cplusplus</span></span>
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<a href="https://salsa.debian.org/med-team/libssw/-/commit/c9c6106f955eac1ec9d8a40cc85495ccf3178810#5efc6e752ca883c31747f028085e413c59f4ecfb"><strong>src/ssw_cpp.cpp</strong></a>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// ssw_cpp.cpp</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC2" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Created by Wan-Ping Lee</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Last revision by Mengyao Zhao on 2017-05-30</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="LC5" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "ssw_cpp.h"</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="LC6" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "ssw.h"</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="LC7" class="line" lang="cpp"></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">@@ -323,7 +327,7 @@ int Aligner::TranslateBase(const char* bases, const int& length,</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC328" class="line" lang="cpp"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC329" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">Aligner</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Align</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</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;">query</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Filter</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">filter</span><span class="p">,</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC326" class="line" lang="cpp"> <span class="n" style="color: #333;">Alignment</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">alignment</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC330" class="line" lang="cpp"> <span class="n" style="color: #333;">Alignment</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">alignment</span><span class="p"><span class="idiff left addition">,</span></span><span class="idiff addition"> </span><span class="k" style="font-weight: 600;"><span class="idiff addition">const</span></span><span class="idiff addition"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff addition">int32_t</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff right addition">maskLen</span></span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</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="LC331" class="line" lang="cpp"><span class="p">{</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="LC332" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">translation_matrix_</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</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="LC333" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">reference_length_</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;">return</span> <span class="nb" style="color: #0086b3;">false</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">@@ -342,7 +346,7 @@ bool Aligner::Align(const char* query, const Filter& filter,</td>
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342
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC346" class="line" lang="cpp"> <span class="n" style="color: #333;">s_align</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">s_al</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ssw_align</span><span class="p">(</span><span class="n" style="color: #333;">profile</span><span class="p">,</span> <span class="n" style="color: #333;">translated_reference_</span><span class="p">,</span> <span class="n" style="color: #333;">reference_length_</span><span class="p">,</span></span>
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347
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC347" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">gap_opening_penalty_</span><span class="p">),</span></span>
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348
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC348" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">gap_extending_penalty_</span><span class="p">),</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC345" class="line" lang="cpp"> <span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="n" style="color: #333;">filter</span><span class="p">.</span><span class="n" style="color: #333;">score_filter</span><span class="p">,</span> <span class="n" style="color: #333;">filter</span><span class="p">.</span><span class="n" style="color: #333;">distance_filter</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right deletion">query_l</span>en</span><span class="p">);</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC349" class="line" lang="cpp"> <span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="n" style="color: #333;">filter</span><span class="p">.</span><span class="n" style="color: #333;">score_filter</span><span class="p">,</span> <span class="n" style="color: #333;">filter</span><span class="p">.</span><span class="n" style="color: #333;">distance_filter</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right addition">maskL</span>en</span><span class="p">);</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="LC351" class="line" lang="cpp"> <span class="n" style="color: #333;">alignment</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Clear</span><span class="p">();</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="LC352" class="line" lang="cpp"> <span class="n" style="color: #333;">ConvertAlignment</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s_al</span><span class="p">,</span> <span class="n" style="color: #333;">query_len</span><span class="p">,</span> <span class="n" style="color: #333;">alignment</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">@@ -359,7 +363,7 @@ bool Aligner::Align(const char* query, const Filter& filter,</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC364" class="line" lang="cpp"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC365" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">Aligner</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Align</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</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;">query</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</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;">ref</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ref_len</span><span class="p">,</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC362" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Filter</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">filter</span><span class="p">,</span> <span class="n" style="color: #333;">Alignment</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">alignment</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC366" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Filter</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">filter</span><span class="p">,</span> <span class="n" style="color: #333;">Alignment</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">alignment</span><span class="p"><span class="idiff left addition">,</span></span><span class="idiff addition"> </span><span class="k" style="font-weight: 600;"><span class="idiff addition">const</span></span><span class="idiff addition"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff addition">int32_t</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff right addition">maskLen</span></span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</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="LC367" class="line" lang="cpp"><span class="p">{</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="LC368" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">translation_matrix_</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</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">@@ -369,9 +373,6 @@ bool Aligner::Align(const char* query, const char* ref, const int& ref_len,</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC373" class="line" lang="cpp"> <span class="n" style="color: #333;">TranslateBase</span><span class="p">(</span><span class="n" style="color: #333;">query</span><span class="p">,</span> <span class="n" style="color: #333;">query_len</span><span class="p">,</span> <span class="n" style="color: #333;">translated_query</span><span class="p">);</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="LC375" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// calculate the valid length</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC372" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//int calculated_ref_length = static_cast<int>(strlen(ref));</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC373" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//int valid_ref_len = (calculated_ref_length > ref_len)</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC374" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// ? ref_len : calculated_ref_length;</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="LC376" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">valid_ref_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ref_len</span><span class="p">;</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="LC377" class="line" lang="cpp"> <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;">translated_ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">int8_t</span><span class="p">[</span><span class="n" style="color: #333;">valid_ref_len</span><span class="p">];</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="LC378" class="line" lang="cpp"> <span class="n" style="color: #333;">TranslateBase</span><span class="p">(</span><span class="n" style="color: #333;">ref</span><span class="p">,</span> <span class="n" style="color: #333;">valid_ref_len</span><span class="p">,</span> <span class="n" style="color: #333;">translated_ref</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">@@ -386,7 +387,7 @@ bool Aligner::Align(const char* query, const char* ref, const int& ref_len,</td>
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386
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387
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC387" class="line" lang="cpp"> <span class="n" style="color: #333;">s_align</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">s_al</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ssw_align</span><span class="p">(</span><span class="n" style="color: #333;">profile</span><span class="p">,</span> <span class="n" style="color: #333;">translated_ref</span><span class="p">,</span> <span class="n" style="color: #333;">valid_ref_len</span><span class="p">,</span></span>
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387
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388
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC388" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">gap_opening_penalty_</span><span class="p">),</span></span>
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388
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389
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC389" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">gap_extending_penalty_</span><span class="p">),</span></span>
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389
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC389" class="line" lang="cpp"> <span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="n" style="color: #333;">filter</span><span class="p">.</span><span class="n" style="color: #333;">score_filter</span><span class="p">,</span> <span class="n" style="color: #333;">filter</span><span class="p">.</span><span class="n" style="color: #333;">distance_filter</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right deletion">query_l</span>en</span><span class="p">);</span></span>
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390
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC390" class="line" lang="cpp"> <span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="n" style="color: #333;">filter</span><span class="p">.</span><span class="n" style="color: #333;">score_filter</span><span class="p">,</span> <span class="n" style="color: #333;">filter</span><span class="p">.</span><span class="n" style="color: #333;">distance_filter</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right addition">maskL</span>en</span><span class="p">);</span></span>
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390
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391
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC391" class="line" lang="cpp"></span>
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391
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392
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC392" class="line" lang="cpp"> <span class="n" style="color: #333;">alignment</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Clear</span><span class="p">();</span></span>
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392
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393
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC393" class="line" lang="cpp"> <span class="n" style="color: #333;">ConvertAlignment</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s_al</span><span class="p">,</span> <span class="n" style="color: #333;">query_len</span><span class="p">,</span> <span class="n" style="color: #333;">alignment</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/libssw/-/commit/c9c6106f955eac1ec9d8a40cc85495ccf3178810#270c7e3fe1b863d7de4d54f2eb71337caf6c7bb7"><strong>src/ssw_cpp.h</strong></a>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// ssw_cpp.h</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC2" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Created by Wan-Ping Lee</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Last revision by Mengyao Zhao on 2017-05-30</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="LC5" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifndef COMPLETE_STRIPED_SMITH_WATERMAN_CPP_H_</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="LC6" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define COMPLETE_STRIPED_SMITH_WATERMAN_CPP_H_</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="LC7" class="line" lang="cpp"></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">@@ -127,9 +131,12 @@ class Aligner {</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC131" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// @param query The query sequence.</span></span>
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128
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC132" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// @param filter The filter for the alignment.</span></span>
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129
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133
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC133" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// @param alignment The container contains the result.</span></span>
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134
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC134" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// @param maskLen The distance between the optimal and suboptimal alignment ending position will >= maskLen. We suggest to </span></span>
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135
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC135" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// use readLen/2, if you don't have special concerns. Note: maskLen has to be >= 15, otherwise this function </span></span>
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136
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC136" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// will NOT return the suboptimal alignment information.</span></span>
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130
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137
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC137" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// @return True: succeed; false: fail.</span></span>
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131
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138
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC138" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// =========</span></span>
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132
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<td class="new_line diff-line-num old" data-linenumber="139" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC132" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">Align</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</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;">query</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Filter</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">filter</span><span class="p">,</span> <span class="n" style="color: #333;">Alignment</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">alignment</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="139" 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">
139
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC139" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">Align</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</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;">query</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Filter</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">filter</span><span class="p">,</span> <span class="n" style="color: #333;">Alignment</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">alignment</span><span class="p"><span class="idiff left addition">,</span></span><span class="idiff addition"> </span><span class="k" style="font-weight: 600;"><span class="idiff addition">const</span></span><span class="idiff addition"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff addition">int32_t</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff right addition">maskLen</span></span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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140
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC140" class="line" lang="cpp"></span>
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134
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141
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC141" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// =========</span></span>
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142
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC142" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// @function Align the query againt the reference.</span></span>
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<td class="diff-line-num unfold js-unfold new_line" 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">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -141,10 +148,13 @@ class Aligner {</td>
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141
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148
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC148" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// @param ref_len The length of the reference sequence.</span></span>
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142
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149
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC149" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// @param filter The filter for the alignment.</span></span>
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143
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150
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC150" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// @param alignment The container contains the result.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="151" 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">
151
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC151" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// @param maskLen The distance between the optimal and suboptimal alignment ending position will >= maskLen. We suggest to </span></span>
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<td class="new_line diff-line-num new" data-linenumber="152" 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">
152
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC152" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// use readLen/2, if you don't have special concerns. Note: maskLen has to be >= 15, otherwise this function </span></span>
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<td class="new_line diff-line-num new" data-linenumber="153" 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">
153
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC153" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// will NOT return the suboptimal alignment information.</span></span>
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144
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154
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC154" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// @return True: succeed; false: fail.</span></span>
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145
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155
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC155" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// =========</span></span>
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156
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC156" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">Align</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</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;">query</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</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;">ref</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ref_len</span><span class="p">,</span></span>
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147
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<td class="new_line diff-line-num old" data-linenumber="157" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC147" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Filter</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">filter</span><span class="p">,</span> <span class="n" style="color: #333;">Alignment</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">alignment</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="157" 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">
157
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC157" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Filter</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">filter</span><span class="p">,</span> <span class="n" style="color: #333;">Alignment</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">alignment</span><span class="p"><span class="idiff left addition">,</span></span><span class="idiff addition"> </span><span class="k" style="font-weight: 600;"><span class="idiff addition">const</span></span><span class="idiff addition"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff addition">int32_t</span></span><span class="idiff addition"> </span><span class="n" style="color: #333;"><span class="idiff right addition">maskLen</span></span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</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="LC158" class="line" lang="cpp"></span>
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159
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC159" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// @function Clear up all containers and thus the aligner is disabled.</span></span>
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150
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160
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC160" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// To rebuild the aligner please use Build functions.</span></span>
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<li id="f4f800a405a82d8bf6aaeae378544be7bf776510">
<a href="https://salsa.debian.org/med-team/libssw/-/commit/c9c6106f955eac1ec9d8a40cc85495ccf3178810#f4f800a405a82d8bf6aaeae378544be7bf776510"><strong>src/ssw_lib.py</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">@@ -3,6 +3,7 @@</td>
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3
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="s" style="color: #d14;">Simple python wrapper for SSW library</span></span>
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4
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4
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="s" style="color: #d14;">Please put the path of libssw.so into LD_LIBRARY_PATH or pass it explicitly as a parameter</span></span>
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5
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="s" style="color: #d14;">By Yongan Zhao (March 2016)</span></span>
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6
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="s" style="color: #d14;">Revised by Mengyao Zhao on 2022-May-19</span></span>
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7
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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8
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC8" class="line" lang="python"></span>
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8
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9
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</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">@@ -101,10 +102,10 @@ class CSsw(object):</td>
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102
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC102" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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102
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103
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC103" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># load libssw</span></span>
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103
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104
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">sLibName</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'libssw.so'</span></span>
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104
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<td class="new_line diff-line-num old" data-linenumber="105" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC104" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;"><span class="idiff left deletion">not</span></span><span class="idiff right deletion"> </span><span class="n" style="color: #333;">sLibPath</span><span class="p">:</span></span>
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105
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<td class="new_line diff-line-num old" data-linenumber="105" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC105" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># user does<span class="idiff left right deletion">n't</span> give the path explicitly</span></span>
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105
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sLibPath</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="106" 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">
106
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC106" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># user does give the path explicitly</span></span>
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106
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<td class="new_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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC107" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">sLibPath</span><span class="p">,</span> <span class="n" style="color: #333;">sLibName</span><span class="p">)):</span></span>
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107
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<td class="new_line diff-line-num old" data-linenumber="108" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC107" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left deletion">print</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">>></span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p"><span class="idiff deletion">,</span></span><span class="idiff deletion"> </span><span class="s" style="color: #d14;">'libssw.so does not exist in the input path<span class="idiff right deletion">'</span></span></span>
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<td class="new_line diff-line-num new" data-linenumber="108" 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">
108
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p"><span class="idiff left addition">.</span></span><span class="n" style="color: #333;"><span class="idiff addition">write</span></span><span class="p"><span class="idiff addition">(</span></span><span class="s" style="color: #d14;">'libssw.so does not exist in the input path<span class="idiff addition">.'</span></span><span class="p"><span class="idiff right addition">)</span></span></span>
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108
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109
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">()</span></span>
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109
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110
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC110" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ssw</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ct</span><span class="p">.</span><span class="n" style="color: #333;">cdll</span><span class="p">.</span><span class="n" style="color: #333;">LoadLibrary</span><span class="p">(</span><span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">sLibPath</span><span class="p">,</span><span class="n" style="color: #333;">sLibName</span><span class="p">))</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="LC111" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>
<td class="diff-line-num unfold js-unfold new_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="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -115,7 +116,7 @@ class CSsw(object):</td>
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115
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116
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC116" class="line" lang="python"> <span class="n" style="color: #333;">bFound</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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116
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117
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC117" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ssw</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ct</span><span class="p">.</span><span class="n" style="color: #333;">cdll</span><span class="p">.</span><span class="n" style="color: #333;">LoadLibrary</span><span class="p">(</span><span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">,</span><span class="n" style="color: #333;">sLibName</span><span class="p">))</span></span>
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117
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC118" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">bFound</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">False</span><span class="p">:</span></span>
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118
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC118" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left deletion">print</span></span><span class="idiff deletion"> </span><span class="o" style="font-weight: 600;"><span class="idiff deletion">>></span></span><span class="idiff deletion"> </span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p"><span class="idiff deletion">,</span></span><span class="idiff right deletion"> </span><span class="s" style="color: #d14;">'libssw.so does not exist in PATH'</span></span>
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119
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC119" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p"><span class="idiff left addition">.</span></span><span class="n" style="color: #333;"><span class="idiff addition">write</span></span><span class="p"><span class="idiff addition">(</span></span><span class="s" style="color: #d14;">'libssw.so does not exist in PATH'</span><span class="p"><span class="idiff right addition">)</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="LC120" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">()</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="LC121" class="line" lang="python"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC122" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># init ssw_init</span></span>
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