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<h3>

Michael R. Crusoe pushed to branch upstream

at <a href="https://salsa.debian.org/med-team/libvcflib">Debian Med / libvcflib</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/libvcflib/commit/18f9a56680d84676eadf8905cf2bd95b76fc9841">18f9a566</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2019-09-04T00:51:02Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.0.0+dfsg</pre>

</li>

</ul>

<h4>18 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">

Makefile

</a>

</li>

<li class="file-stats">

<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

README.md

</a>

</li>

<li class="file-stats">

<a href="#a3605ce2e71fe99d64663ab3128baf72f749037e">

scripts/vcf2bed.py

</a>

</li>

<li class="file-stats">

<a href="#a6b7f423610de5f7b91ca6f058e43ed89c5fe2c5">

scripts/vcf2sqlite.py

</a>

</li>

<li class="file-stats">

<a href="#2f6457546dd9b17dda7980dfec7f910ad32c6fa5">

scripts/vcfclearid

</a>

</li>

<li class="file-stats">

<a href="#427a79153566b7170203310fb39d886b8affc023">

scripts/vcfclearinfo

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<li class="file-stats">

<a href="#698eb6a3f16b693cec023ddbdc3df2295eded77a">

scripts/vcffirstheader

</a>

</li>

<li class="file-stats">

<a href="#13db7414b0966cb9ed1bb9968327fd5e1af9863c">

scripts/vcfnulldotslashdot

</a>

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<li class="file-stats">

<a href="#064f6f30b2ef573145e550cf01828d6462d0f335">

src/BedReader.h

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<li class="file-stats">

<a href="#1e0994915779ecf5b7b7fc9ddefc94353c73476f">

src/Variant.cpp

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<li class="file-stats">

<a href="#652b96bba65afc5f190351f4ffa54108321ad32e">

src/Variant.h

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<li class="file-stats">

<a href="#9189853d8f456e526b136ecd561456f45ecc315b">

src/cdflib.cpp

</a>

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<li class="file-stats">

<a href="#de10b670208808941807d0db7069159f2749af37">

src/split.h

</a>

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<li class="file-stats">

<a href="#3dc965d7809a4f1703d452c230376064628bf793">

src/vcfintersect.cpp

</a>

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<li class="file-stats">

<a href="#b7af15dcd85a3603e7a069c58654922f58cb13f0">

src/vcfnormalizesvs.cpp

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<li class="file-stats">

<a href="#40f4482121a1441df05d09168d44fe98200323c7">

src/vcfroc.cpp

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<li class="file-stats">

<a href="#ece78a032e8effb46b4cccead2e1d42469704a62">

test/Makefile

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<li class="file-stats">

<a href="#18cfe6cfeda7aa16dcc24f1650282d1367a79a65">

<span class="deleted-file">

−

test/tests/main

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</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">

<a href="https://salsa.debian.org/med-team/libvcflib/commit/18f9a56680d84676eadf8905cf2bd95b76fc9841#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c"><strong>Makefile</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="128" style="width: 35px; color: rgba(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">@@ -128,8 +128,16 @@ LEFTALIGN = smithwaterman/LeftAlign.o</td>

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<td class="diff-line-num old_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="make"><span class="nv" style="color: #008080;">FSOM</span> <span class="o" style="font-weight: 600;">=</span> fsom/fsom.o</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC129" class="line" lang="make"><span class="nv" style="color: #008080;">FILEVERCMP</span> <span class="o" style="font-weight: 600;">=</span> filevercmp/filevercmp.o</span>

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<td class="diff-line-num old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC130" class="line" lang="make"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); 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="diff-line-num new_line old" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC131" class="line" lang="make"><span class="nv" style="color: #008080;">INCLUDES</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-Itabixpp</span>/htslib <span class="nt" style="color: #000080;">-I</span><span class="nv" style="color: #008080;">$(INC_DIR)</span> <span class="nt" style="color: #000080;">-L</span><span class="nb" style="color: #0086b3;">.</span> <span class="nt" style="color: #000080;">-Ltabixpp</span>/htslib</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); 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="diff-line-num new_line old" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC132" class="line" lang="make"><span class="nv" style="color: #008080;">LDFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-L</span><span class="nv" style="color: #008080;">$(LIB_DIR)</span> <span class="nt" style="color: #000080;">-lvcflib</span> <span class="nt" style="color: #000080;">-lhts</span> <span class="nt" style="color: #000080;">-lpthread</span> <span class="nt" style="color: #000080;">-lz</span> <span class="nt" style="color: #000080;">-lm</span> <span class="nt" style="color: #000080;">-llzma</span> <span class="nt" style="color: #000080;">-lbz2</span></span>

</pre>

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC131" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Work out how to find htslib</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC132" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Use the one we ship in tabixpp unless told otherwise by the environment</span></span>

</pre>

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC133" class="line" lang="make"><span class="nv" style="color: #008080;">HTS_LIB</span> <span class="o" style="font-weight: 600;">?=</span> <span class="nv" style="color: #008080;">$(VCF_LIB_LOCAL)</span>/tabixpp/htslib/libhts.a</span>

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC134" class="line" lang="make"><span class="nv" style="color: #008080;">HTS_INCLUDES</span> <span class="o" style="font-weight: 600;">?=</span> <span class="nt" style="color: #000080;">-I</span><span class="nv" style="color: #008080;">$(VCF_LIB_LOCAL)</span>/tabixpp/htslib</span>

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC135" class="line" lang="make"><span class="nv" style="color: #008080;">HTS_LDFLAGS</span> <span class="o" style="font-weight: 600;">?=</span> <span class="nt" style="color: #000080;">-L</span><span class="nv" style="color: #008080;">$(VCF_LIB_LOCAL)</span>/tabixpp/htslib <span class="nt" style="color: #000080;">-lhts</span> <span class="nt" style="color: #000080;">-lbz2</span> <span class="nt" style="color: #000080;">-lm</span> <span class="nt" style="color: #000080;">-lz</span> <span class="nt" style="color: #000080;">-llzma</span> <span class="nt" style="color: #000080;">-pthread</span></span>

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<td class="diff-line-num new new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC136" class="line" lang="make"></span>

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<pre style="margin: 0;">+<span id="LC137" class="line" lang="make"></span>

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<pre style="margin: 0;">+<span id="LC138" class="line" lang="make"><span class="nv" style="color: #008080;">INCLUDES</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$(HTS_INCLUDES)</span> <span class="nt" style="color: #000080;">-I</span><span class="nv" style="color: #008080;">$(INC_DIR)</span> </span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC139" class="line" lang="make"><span class="nv" style="color: #008080;">LDFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-L</span><span class="nv" style="color: #008080;">$(LIB_DIR)</span> <span class="nt" style="color: #000080;">-lvcflib</span> <span class="nv" style="color: #008080;">$(HTS_LDFLAGS)</span> <span class="nt" style="color: #000080;">-lpthread</span> <span class="nt" style="color: #000080;">-lz</span> <span class="nt" style="color: #000080;">-lm</span> <span class="nt" style="color: #000080;">-llzma</span> <span class="nt" style="color: #000080;">-lbz2</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC140" class="line" lang="make"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

141

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="make"></span>

</pre>

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<td class="diff-line-num 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">

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<td class="diff-line-num new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

142

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<pre style="margin: 0;"> <span id="LC142" class="line" lang="make"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC143" 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;">$(OBJECTS) $(BINS) scriptToBin</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -167,7 +175,7 @@ intervaltree: pre</td>

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<td class="diff-line-num old_line" 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">

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<td class="diff-line-num new_line" 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">

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<pre style="margin: 0;"> <span id="LC175" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cd </span>intervaltree <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$(MAKE)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cp</span> <span class="k" style="font-weight: 600;">*</span>.h<span class="k" style="font-weight: 600;">*</span> <span class="nv" style="color: #008080;">$(VCF_LIB_LOCAL)</span>/<span class="nv" style="color: #008080;">$(INC_DIR)</span>/</span>

</pre>

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<td class="diff-line-num old_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">

168

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<td class="diff-line-num new_line" 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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<pre style="margin: 0;"> <span id="LC176" class="line" lang="make"></span>

</pre>

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<td class="diff-line-num old_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">

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<td class="diff-line-num new_line" 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">

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<pre style="margin: 0;"> <span id="LC177" class="line" lang="make"><span class="nl">$(TABIX)</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">pre</span></span>

</pre>

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<td class="diff-line-num old old_line" 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="diff-line-num new_line old" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC170" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cd </span>tabixpp <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$(MAKE)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cp</span> <span class="k" style="font-weight: 600;">*</span>.h<span class="k" style="font-weight: 600;">*</span> <span class="nv" style="color: #008080;">$(VCF_LIB_LOCAL)</span>/<span class="nv" style="color: #008080;">$(INC_DIR)</span>/</span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC178" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cd </span>tabixpp <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;"><span class="idiff left">INCLUDES</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: #008080;"><span class="idiff">$(HTS_INCLUDES)</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">LIBPATH</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s2" style="color: #d14;"><span class="idiff">"-L. </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(HTS_LDFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">HTSLIB</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: #008080;"><span class="idiff">$(HTS_LIB)</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff right"> </span><span class="nv" style="color: #008080;">$(MAKE)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cp</span> <span class="k" style="font-weight: 600;">*</span>.h<span class="k" style="font-weight: 600;">*</span> <span class="nv" style="color: #008080;">$(VCF_LIB_LOCAL)</span>/<span class="nv" style="color: #008080;">$(INC_DIR)</span>/</span>

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<td class="diff-line-num new_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC179" class="line" lang="make"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC180" class="line" lang="make"><span class="nl">$(SMITHWATERMAN)</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">pre</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="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">

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<pre style="margin: 0;"> <span id="LC181" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cd </span>smithwaterman <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$(MAKE)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cp</span> <span class="k" style="font-weight: 600;">*</span>.h<span class="k" style="font-weight: 600;">*</span> <span class="nv" style="color: #008080;">$(VCF_LIB_LOCAL)</span>/<span class="nv" style="color: #008080;">$(INC_DIR)</span>/ <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cp</span> <span class="k" style="font-weight: 600;">*</span>.o <span class="nv" style="color: #008080;">$(VCF_LIB_LOCAL)</span>/<span class="nv" style="color: #008080;">$(OBJ_DIR)</span>/</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -223,8 +231,14 @@ clean:</td>

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<td class="diff-line-num old_line" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC231" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> <span class="nv" style="color: #008080;">$(LIB_DIR)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC232" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> <span class="nv" style="color: #008080;">$(INC_DIR)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC233" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> <span class="nv" style="color: #008080;">$(OBJ_DIR)</span></span>

</pre>

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226

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<pre style="margin: 0;">-<span id="LC226" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cd </span>tabixpp <span class="o" style="font-weight: 600;">&&</span> make clean</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

227

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</td>

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<pre style="margin: 0;">-<span id="LC227" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cd </span>smithwaterman <span class="o" style="font-weight: 600;">&&</span> make clean</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

228

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</td>

<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="make"> <span class="nb" style="color: #0086b3;">cd </span>fastahack <span class="o" style="font-weight: 600;">&&</span> make clean</span>

</pre>

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<td class="diff-line-num old old_line" 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="diff-line-num new_line 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">

</td>

<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="make"></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC234" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cd </span>tabixpp <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$(MAKE)</span> clean</span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC235" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cd </span>smithwaterman <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$(MAKE)</span> clean</span>

</pre>

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC236" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cd </span>fastahack <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$(MAKE)</span> clean</span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC237" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cd </span>multichoose <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$(MAKE)</span> clean</span>

</pre>

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<td class="diff-line-num new new_line" 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="make"> <span class="nb" style="color: #0086b3;">cd </span>fsom <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$(MAKE)</span> clean</span>

</pre>

</td>

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC239" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cd </span>libVCFH <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$(MAKE)</span> clean</span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC240" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cd test</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$(MAKE)</span> clean</span>

</pre>

</td>

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<td class="diff-line-num new new_line" 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">

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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="make"> <span class="nb" style="color: #0086b3;">cd </span>filevercmp <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$(MAKE)</span> clean</span>

</pre>

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC242" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cd </span>intervaltree <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$(MAKE)</span> clean</span>

</pre>

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC243" class="line" lang="make"> </span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC244" 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;">clean all test pre</span></span></pre>

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<br>

</li>

<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

<a href="https://salsa.debian.org/med-team/libvcflib/commit/18f9a56680d84676eadf8905cf2bd95b76fc9841#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="144" style="width: 35px; color: rgba(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="144" style="width: 35px; color: rgba(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">@@ -144,13 +144,13 @@ This makes installation easy, as users can add vcflib/bin to their path, or copy</td>

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144

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<pre style="margin: 0;"> <span id="LC144" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### vcf2tsv</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC145" class="line" lang="markdown">    </span>

</pre>

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="markdown">    usage: vcf2tsv <span class="p">[</span><span class="nv" style="color: #008080;">-n null_string</span><span class="p">]</span> <span class="p">[</span><span class="ss" style="color: #990073;">-g</span><span class="p">]</span> <span class="p">[</span><span class="nv" style="color: #008080;">vcf file</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC147" class="line" lang="markdown"><span class="idiff left right">    </span>Converts stdin or given VCF file to tab-delimited format, using null string to replace empty values in the table.</span>

</pre>

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<pre style="margin: 0;">-<span id="LC148" class="line" lang="markdown"><span class="idiff left right">    </span>Specifying -g will output one line per sample with genotype information.</span>

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC147" class="line" lang="markdown">Converts stdin or given VCF file to tab-delimited format, using null string to replace empty values in the table.</span>

</pre>

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC148" class="line" lang="markdown">Specifying -g will output one line per sample with genotype information.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC149" class="line" lang="markdown">    </span>

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### vcfaddinfo</span></span>

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<pre style="margin: 0;"> <span id="LC151" class="line" lang="markdown">    </span>

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<td class="diff-line-num old_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC152" class="line" lang="markdown">    usage: vcfaddinfo <span class="nt" style="color: #000080;"><vcf</span> <span class="na" style="color: #008080;">file</span><span class="nt" style="color: #000080;">></span> <span class="nt" style="color: #000080;"><vcf</span> <span class="na" style="color: #008080;">file</span><span class="nt" style="color: #000080;">></span></span>

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<pre style="margin: 0;">-<span id="LC153" class="line" lang="markdown"><span class="idiff left right">    </span>Adds info fields from the second file which are not present in the first vcf file.</span>

</pre>

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC153" class="line" lang="markdown">Adds info fields from the second file which are not present in the first vcf file.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="markdown">    </span>

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<td class="diff-line-num old_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC155" class="line" lang="markdown">    </span>

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<td class="diff-line-num old_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC156" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### vcfafpath</span></span>

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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -167,11 +167,9 @@ Uses allele frequencies in the AF info column to estimate phylogeny at multialle</td>

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<pre style="margin: 0;"> <span id="LC167" class="line" lang="markdown">        -t, --tag-parsed FLAG   Tag records which are split apart of a complex allele</span>

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<pre style="margin: 0;"> <span id="LC168" class="line" lang="markdown">                                with this flag</span>

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<pre style="margin: 0;"> <span id="LC169" class="line" lang="markdown">    </span>

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<pre style="margin: 0;">-<span id="LC170" class="line" lang="markdown">    If multiple alleleic primitives (gaps or mismatches) are specified in</span>

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<pre style="margin: 0;">-<span id="LC171" class="line" lang="markdown">    a single VCF record, split the record into multiple lines, but drop all</span>

</pre>

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<pre style="margin: 0;">-<span id="LC172" class="line" lang="markdown">    INFO fields.  "Pure" MNPs are split into multiple SNPs unless the -m</span>

</pre>

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<pre style="margin: 0;">-<span id="LC173" class="line" lang="markdown">    flag is provided.  Genotypes are phased where complex alleles have been</span>

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<pre style="margin: 0;">-<span id="LC174" class="line" lang="markdown">    decomposed, provided genotypes in the input.</span>

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<pre style="margin: 0;">+<span id="LC170" class="line" lang="markdown">If multiple alleleic primitives (gaps or mismatches) are specified in a single VCF record, split the record into multiple lines, but drop all INFO fields.</span>

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<pre style="margin: 0;">+<span id="LC171" class="line" lang="markdown">"Pure" MNPs are split into multiple SNPs unless the -m flag is provided.</span>

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<pre style="margin: 0;">+<span id="LC172" class="line" lang="markdown">Genotypes are phased where complex alleles have been decomposed, provided genotypes in the input.</span>

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<pre style="margin: 0;"> <span id="LC173" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC174" class="line" lang="markdown"><span class="sb" style="color: #d14;">    </span></span>

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<pre style="margin: 0;"> <span id="LC175" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### vcfaltcount</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">@@ -188,29 +186,25 @@ Counts the number of alternate alleles in the record.</td>

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<pre style="margin: 0;"> <span id="LC186" class="line" lang="markdown"><span class="sb" style="color: #d14;">        -k, --key   use this INFO field key for the annotations</span></span>

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<pre style="margin: 0;"> <span id="LC187" class="line" lang="markdown"><span class="sb" style="color: #d14;">        -d, --default  use this INFO field key for records without annotations</span></span>

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<pre style="margin: 0;"> <span id="LC188" class="line" lang="markdown"></span>

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<pre style="margin: 0;">-<span id="LC191" class="line" lang="markdown"><span class="sb" style="color: #d14;">    Intersect the records in the VCF file with targets provided in a BED file.</span></span>

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<pre style="margin: 0;">-<span id="LC192" class="line" lang="markdown"><span class="sb" style="color: #d14;">    Intersections are done on the reference sequences in the VCF file.</span></span>

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<pre style="margin: 0;">-<span id="LC193" class="line" lang="markdown"><span class="sb" style="color: #d14;">    If no VCF filename is specified on the command line (last argument) the VCF</span></span>

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<pre style="margin: 0;">-<span id="LC194" class="line" lang="markdown"><span class="sb" style="color: #d14;">    read from stdin.</span></span>

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<pre style="margin: 0;">+<span id="LC189" class="line" lang="markdown">Intersect the records in the VCF file with targets provided in a BED file.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC190" class="line" lang="markdown">Intersections are done on the reference sequences in the VCF file.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC191" class="line" lang="markdown">If no VCF filename is specified on the command line (last argument) the VCF read from stdin.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC192" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC193" class="line" lang="markdown"><span class="sb" style="color: #d14;">    </span></span>

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<pre style="margin: 0;"> <span id="LC194" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### vcfannotategenotypes</span></span>

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<pre style="margin: 0;"> <span id="LC195" class="line" lang="markdown">    </span>

</pre>

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<pre style="margin: 0;"> <span id="LC196" class="line" lang="markdown">    usage: vcfannotategenotypes <span class="nt" style="color: #000080;"><annotation-tag></span> <span class="nt" style="color: #000080;"><vcf</span> <span class="na" style="color: #008080;">file</span><span class="nt" style="color: #000080;">></span> <span class="nt" style="color: #000080;"><vcf</span> <span class="na" style="color: #008080;">file</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC197" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old old_line" 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">

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<pre style="margin: 0;">-<span id="LC201" class="line" lang="markdown"><span class="sb" style="color: #d14;">    annotates genotypes in the first file with genotypes in the second adding the</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC202" class="line" lang="markdown"><span class="sb" style="color: #d14;">    genotype as another flag to each sample filed in the first file.</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC203" class="line" lang="markdown"><span class="sb" style="color: #d14;">    annotation-tag is the name of the sample flag which is added to store the</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC204" class="line" lang="markdown"><span class="sb" style="color: #d14;">    annotation.  also adds a 'has\_variant' flag for sites where the second file has</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC205" class="line" lang="markdown"><span class="sb" style="color: #d14;">    a variant.</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<pre style="margin: 0;">+<span id="LC198" class="line" lang="markdown">Annotates genotypes in the first file with genotypes in the second adding the genotype as another flag to each sample filed in the first file.</span>

</pre>

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC199" class="line" lang="markdown">Annotation-tag is the name of the sample flag which is added to store the annotation.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC200" class="line" lang="markdown">Also adds a 'has<span class="se" style="color: #d14;">\_</span>variant' flag for sites where the second file has a variant.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC201" class="line" lang="markdown">    </span>

</pre>

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<pre style="margin: 0;"> <span id="LC202" class="line" lang="markdown">    </span>

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<td class="diff-line-num old_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">

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<pre style="margin: 0;"> <span id="LC203" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### vcfbreakmulti</span></span>

</pre>

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<td class="diff-line-num old_line" 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">

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<pre style="margin: 0;"> <span id="LC204" class="line" lang="markdown">    </span>

</pre>

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<pre style="margin: 0;"> <span id="LC205" class="line" lang="markdown">    usage: vcfbreakmulti <span class="p">[</span><span class="nv" style="color: #008080;">options</span><span class="p">]</span> <span class="p">[</span><span class="ss" style="color: #990073;">file</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC206" class="line" lang="markdown">    </span>

</pre>

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<td class="diff-line-num new_line 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">

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<pre style="margin: 0;">-<span id="LC212" class="line" lang="markdown">    If multiple alleles are specified in a single record, break the record into</span>

</pre>

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<pre style="margin: 0;">-<span id="LC213" class="line" lang="markdown">    multiple lines, preserving allele-specific INFO fields.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC207" class="line" lang="markdown">If multiple alleles are specified in a single record, break the record into multiple lines, preserving allele-specific INFO fields.</span>

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<pre style="margin: 0;"> <span id="LC208" class="line" lang="markdown">    </span>

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<pre style="margin: 0;"> <span id="LC209" class="line" lang="markdown">    </span>

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<pre style="margin: 0;"> <span id="LC210" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### vcfcheck</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">@@ -220,7 +214,7 @@ Counts the number of alternate alleles in the record.</td>

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<pre style="margin: 0;"> <span id="LC214" class="line" lang="markdown">    options: -f, --fasta-reference  FASTA reference file to use to obtain</span>

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<pre style="margin: 0;"> <span id="LC215" class="line" lang="markdown">                                    primer sequences</span>

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<pre style="margin: 0;"> <span id="LC216" class="line" lang="markdown">    </span>

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<pre style="margin: 0;">-<span id="LC223" class="line" lang="markdown"><span class="idiff left right">    </span>Verifies that the VCF REF field matches the reference as described.</span>

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<pre style="margin: 0;">+<span id="LC217" class="line" lang="markdown">Verifies that the VCF REF field matches the reference as described.</span>

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<pre style="margin: 0;"> <span id="LC218" class="line" lang="markdown">    </span>

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<pre style="margin: 0;"> <span id="LC219" class="line" lang="markdown">    </span>

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<pre style="margin: 0;"> <span id="LC220" class="line" lang="markdown">    </span>

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<pre style="margin: 0;"> <span id="LC233" class="line" lang="markdown"><span class="sb" style="color: #d14;">        -r --region REGION  A region specifier of the form chrN:x-y to bound the merge</span></span>

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<pre style="margin: 0;"> <span id="LC234" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC235" class="line" lang="markdown">Combines VCF files positionally, combining samples when sites and alleles are identical.</span>

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<pre style="margin: 0;">-<span id="LC242" class="line" lang="markdown">Any number of VCF files may be combined.  The INFO field and other columns are taken from</span>

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<pre style="margin: 0;">-<span id="LC243" class="line" lang="markdown">one of the files which are combined when records in multiple files match.  Alleles must</span>

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<pre style="margin: 0;">-<span id="LC244" class="line" lang="markdown">have identical ordering to be combined into one record.  If they do not, multiple records</span>

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<pre style="margin: 0;">-<span id="LC245" class="line" lang="markdown">will be emitted.</span>

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<pre style="margin: 0;">+<span id="LC236" class="line" lang="markdown">Any number of VCF files may be combined.</span>

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<pre style="margin: 0;">+<span id="LC237" class="line" lang="markdown">The INFO field and other columns are taken from one of the files which are combined when records in multiple files match.</span>

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<pre style="margin: 0;">+<span id="LC238" class="line" lang="markdown">Alleles must</span>

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<pre style="margin: 0;">+<span id="LC239" class="line" lang="markdown">have identical ordering to be combined into one record.</span>

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<pre style="margin: 0;">+<span id="LC240" class="line" lang="markdown">If they do not, multiple records will be emitted.</span>

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<pre style="margin: 0;"> <span id="LC241" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC242" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC243" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### vcfcommonsamples</span></span>

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<pre style="margin: 0;"> <span id="LC244" class="line" lang="markdown">    </span>

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<pre style="margin: 0;">-<span id="LC250" class="line" lang="markdown">    usage: vcfcommonsamples <span class="nt" style="color: #000080;"><vcf</span> <span class="na" style="color: #008080;">file</span><span class="nt" style="color: #000080;">></span> <span class="nt" style="color: #000080;"><vcf</span> <span class="na" style="color: #008080;">file</span><span class="nt" style="color: #000080;">></span> outputs each record in the</span>

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<pre style="margin: 0;">-<span id="LC251" class="line" lang="markdown">    first file, removing samples not present in the second</span>

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<pre style="margin: 0;">+<span id="LC245" class="line" lang="markdown">    usage: vcfcommonsamples <span class="nt" style="color: #000080;"><vcf</span> <span class="na" style="color: #008080;">file</span><span class="nt" style="color: #000080;">></span> <span class="nt" style="color: #000080;"><vcf</span> <span class="na" style="color: #008080;">file</span><span class="nt" style="color: #000080;">></span></span>

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<pre style="margin: 0;">+<span id="LC246" class="line" lang="markdown">    </span>

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<pre style="margin: 0;">+<span id="LC247" class="line" lang="markdown">Outputs each record in the first file, removing samples not present in the second.</span>

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<pre style="margin: 0;"> <span id="LC248" class="line" lang="markdown">    </span>

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<pre style="margin: 0;"> <span id="LC249" class="line" lang="markdown">    </span>

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<pre style="margin: 0;"> <span id="LC250" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### vcfcountalleles</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">@@ -270,11 +266,11 @@ in the file.</td>

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<pre style="margin: 0;"> <span id="LC266" class="line" lang="markdown">    </span>

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<pre style="margin: 0;"> <span id="LC267" class="line" lang="markdown">    usage: vcfentropy <span class="p">[</span><span class="nv" style="color: #008080;">options</span><span class="p">]</span> <span class="nt" style="color: #000080;"><vcf</span> <span class="na" style="color: #008080;">file</span><span class="nt" style="color: #000080;">></span></span>

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<pre style="margin: 0;"> <span id="LC268" class="line" lang="markdown">    </span>

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<pre style="margin: 0;">-<span id="LC273" class="line" lang="markdown">    options:<span class="idiff left right"> -f, --fasta-reference  FASTA reference file to use to obtain</span></span>

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<pre style="margin: 0;">-<span id="LC274" class="line" lang="markdown"><span class="idiff left right">primer sequences -w, --window-size      Size of the window over which to</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC275" class="line" lang="markdown">calculate entropy</span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<pre style="margin: 0;">+<span id="LC269" class="line" lang="markdown">    options:</span>

</pre>

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC270" class="line" lang="markdown"><span class="idiff left right">        -f, --fasta-reference  FASTA reference file to use to obtain primer sequences</span></span>

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC271" class="line" lang="markdown"><span class="idiff left right">        -w, --window-size      Size of the window over which to </span>calculate entropy</span>

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<pre style="margin: 0;"> <span id="LC272" class="line" lang="markdown">    </span>

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<pre style="margin: 0;">-<span id="LC277" class="line" lang="markdown"><span class="idiff left right">    </span>Anotates the output VCF file with, for each record, EntropyLeft,</span>

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<pre style="margin: 0;">+<span id="LC273" class="line" lang="markdown">Anotates the output VCF file with, for each record, EntropyLeft,</span>

</pre>

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<pre style="margin: 0;"> <span id="LC274" class="line" lang="markdown">EntropyRight, EntropyCenter, which are the entropies of the sequence of the</span>

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<pre style="margin: 0;"> <span id="LC275" class="line" lang="markdown">given window size to the left, right, and center  of the record.</span>

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<pre style="margin: 0;"> <span id="LC276" class="line" lang="markdown">    </span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -299,26 +295,23 @@ given window size to the left, right, and center  of the record.</td>

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<pre style="margin: 0;"> <span id="LC295" class="line" lang="markdown"><span class="sb" style="color: #d14;">                              compressed file which has been indexed with tabix.  any number of</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC296" class="line" lang="markdown"><span class="sb" style="color: #d14;">                              regions may be specified.</span></span>

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<pre style="margin: 0;"> <span id="LC297" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC302" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right">    </span>Filter the specified vcf file using the set of filters.</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC303" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right">    </span>Filters are specified in the form "<ID> <operator> <value>:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); 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="diff-line-num new_line old" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC304" class="line" lang="markdown"><span class="sb" style="color: #d14;">    <span class="idiff left right"> </span>-f "DP > 10"  # for info fields</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); 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="diff-line-num new_line old" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC305" class="line" lang="markdown"><span class="sb" style="color: #d14;">    <span class="idiff left right"> </span>-g "GT = 1|1" # for genotype fields</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC306" class="line" lang="markdown"><span class="sb" style="color: #d14;">    <span class="idiff left right"> </span>-f "CpG"  # for 'flag' fields</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<pre style="margin: 0;">+<span id="LC298" class="line" lang="markdown">Filter the specified vcf file using the set of filters.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC299" class="line" lang="markdown">Filters are specified in the form "<span class="nt" style="color: #000080;"><ID></span> <span class="nt" style="color: #000080;"><operator></span> <span class="nt" style="color: #000080;"><value></span>:</span>

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<pre style="margin: 0;">+<span id="LC300" class="line" lang="markdown">    -f "DP > 10"  # for info fields</span>

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<pre style="margin: 0;">+<span id="LC301" class="line" lang="markdown">    -g "GT = 1|1" # for genotype fields</span>

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<pre style="margin: 0;">+<span id="LC302" class="line" lang="markdown">    -f "CpG"  # for 'flag' fields</span>

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<pre style="margin: 0;"> <span id="LC303" class="line" lang="markdown"></span>

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<pre style="margin: 0;">-<span id="LC308" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right">    </span>Operators can be any of: =, !, <, >, |, &</span></span>

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<pre style="margin: 0;">+<span id="LC304" class="line" lang="markdown">Operators can be any of: =, !, <span class="nt" style="color: #000080;"><</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="nt" style="color: #000080;">></span>, |, &</span>

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<pre style="margin: 0;"> <span id="LC305" class="line" lang="markdown"></span>

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<pre style="margin: 0;">-<span id="LC310" class="line" lang="markdown"><span class="sb" style="color: #d14;">    Any number of filters may be specified.  They are combined via logical AND</span></span>

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<pre style="margin: 0;">-<span id="LC311" class="line" lang="markdown"><span class="sb" style="color: #d14;">    unless --or is specified on the command line.  Obtain logical negation through</span></span>

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<pre style="margin: 0;">-<span id="LC312" class="line" lang="markdown"><span class="sb" style="color: #d14;">    the use of parentheses, e.g. "! ( DP = 10 )"</span></span>

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<pre style="margin: 0;">+<span id="LC306" class="line" lang="markdown">Any number of filters may be specified.  They are combined via logical AND unless --or is specified on the command line.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC307" class="line" lang="markdown">Obtain logical negation through the use of parentheses, e.g. "! ( DP = 10 )"</span>

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<pre style="margin: 0;"> <span id="LC308" class="line" lang="markdown"></span>

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<pre style="margin: 0;">-<span id="LC314" class="line" lang="markdown"><span class="sb" style="color: #d14;">    For convenience, you can specify "QUAL" to refer to the quality of the site, even</span></span>

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<pre style="margin: 0;">-<span id="LC315" class="line" lang="markdown"><span class="sb" style="color: #d14;">    though it does not appear in the INFO fields.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC309" class="line" lang="markdown">For convenience, you can specify "QUAL" to refer to the quality of the site, even though it does not appear in the INFO fields.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC310" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC311" class="line" lang="markdown"><span class="sb" style="color: #d14;">    </span></span>

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<pre style="margin: 0;"> <span id="LC312" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### vcffixup</span></span>

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<pre style="margin: 0;"> <span id="LC313" class="line" lang="markdown"></span>

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<td class="diff-line-num new_line 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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<pre style="margin: 0;">-<span id="LC320" class="line" lang="markdown">Count the allele frequencies across alleles present in each record in the </span>

</pre>

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<td class="diff-line-num new_line 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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<pre style="margin: 0;">-<span id="LC321" class="line" lang="markdown">VCF file.  (Similar to vcftools --freq.)</span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC314" class="line" lang="markdown">Count the allele frequencies across alleles present in each record in the VCF file. (Similar to vcftools --freq.)</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC315" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="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">

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<pre style="margin: 0;"> <span id="LC316" class="line" lang="markdown">Uses genotypes from the VCF file to correct AC (alternate allele count), AF</span>

</pre>

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<pre style="margin: 0;"> <span id="LC317" class="line" lang="markdown">(alternate allele frequency), NS (number of called), in the VCF records.  For</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="334" style="width: 35px; color: rgba(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="327" style="width: 35px; color: rgba(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">@@ -334,10 +327,9 @@ was not called as polymorphic.</td>

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<pre style="margin: 0;"> <span id="LC327" class="line" lang="markdown">    </span>

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<td class="diff-line-num new_line" data-linenumber="328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC328" class="line" lang="markdown">    usage: vcfflatten <span class="p">[</span><span class="nv" style="color: #008080;">file</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC329" class="line" lang="markdown">    </span>

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<td class="diff-line-num old old_line" data-linenumber="337" style="width: 35px; color: rgba(0,0,0,0.3); 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="diff-line-num new_line old" data-linenumber="330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC337" class="line" lang="markdown">    Removes multi-allelic sites by picking the most common alternate.  Requires</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC338" class="line" lang="markdown">    allele frequency specification 'AF' and use of 'G' and 'A' to specify the</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="339" style="width: 35px; color: rgba(0,0,0,0.3); 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="diff-line-num new_line old" data-linenumber="330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC339" class="line" lang="markdown">    fields which vary according to the Allele or Genotype. VCF file may be</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

340

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<td class="diff-line-num new_line old" data-linenumber="330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC340" class="line" lang="markdown">    specified on the command line or piped as stdin.</span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC330" class="line" lang="markdown">Removes multi-allelic sites by picking the most common alternate.</span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC331" class="line" lang="markdown">Requires allele frequency specification 'AF' and use of 'G' and 'A' to specify the fields which vary according to the Allele or Genotype.</span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC332" class="line" lang="markdown">VCF file may be specified on the command line or piped as stdin.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC333" class="line" lang="markdown">    </span>

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<td class="diff-line-num old_line" data-linenumber="342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC334" class="line" lang="markdown">    </span>

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<td class="diff-line-num old_line" data-linenumber="343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC335" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### vcfgeno2haplo</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="348" style="width: 35px; color: rgba(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="340" style="width: 35px; color: rgba(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">@@ -348,17 +340,16 @@ was not called as polymorphic.</td>

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<pre style="margin: 0;"> <span id="LC340" class="line" lang="markdown">        -w, --window-size N       compare records up to this many bp away (default 30)</span>

</pre>

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<pre style="margin: 0;"> <span id="LC341" class="line" lang="markdown">        -r, --reference FILE      FASTA reference file, required with -i and -u</span>

</pre>

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<pre style="margin: 0;"> <span id="LC342" class="line" lang="markdown">    </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="351" style="width: 35px; color: rgba(0,0,0,0.3); 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="diff-line-num new_line old" data-linenumber="343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC351" class="line" lang="markdown"><span class="idiff left right">    </span>Convert genotype-based phased alleles within --window-size into haplotype alleles.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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">

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<pre style="margin: 0;">+<span id="LC343" class="line" lang="markdown">Convert genotype-based phased alleles within --window-size into haplotype alleles.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC344" class="line" lang="markdown">    </span>

</pre>

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<pre style="margin: 0;"> <span id="LC345" class="line" lang="markdown">    </span>

</pre>

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<pre style="margin: 0;"> <span id="LC346" class="line" lang="markdown">    </span>

</pre>

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<pre style="margin: 0;"> <span id="LC347" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### vcfgenotypecompare</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC348" class="line" lang="markdown">    </span>

</pre>

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<td class="diff-line-num old_line" 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">

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<pre style="margin: 0;"> <span id="LC349" class="line" lang="markdown">    usage: vcfgenotypecompare <span class="nt" style="color: #000080;"><other-genotype-tag></span> <span class="nt" style="color: #000080;"><vcf</span> <span class="na" style="color: #008080;">file</span><span class="nt" style="color: #000080;">></span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC358" class="line" lang="markdown">    adds statistics to the INFO field of the vcf file describing the</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="359" style="width: 35px; color: rgba(0,0,0,0.3); 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="diff-line-num new_line old" data-linenumber="350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC359" class="line" lang="markdown">    amount of discrepancy between the genotypes (GT) in the vcf file and the</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="360" style="width: 35px; color: rgba(0,0,0,0.3); 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="diff-line-num new_line old" data-linenumber="350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC360" class="line" lang="markdown">    genotypes reported in the <span class="nt" style="color: #000080;"><other-genotype-tag></span>.  use this after</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="361" style="width: 35px; color: rgba(0,0,0,0.3); 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="diff-line-num new_line old" data-linenumber="350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC361" class="line" lang="markdown">    vcfannotategenotypes to get correspondence statistics for two vcfs.</span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC350" class="line" lang="markdown">    </span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC351" class="line" lang="markdown">Adds statistics to the INFO field of the vcf file describing the amount of discrepancy between the genotypes (GT) in the vcf file and the genotypes reported in the <span class="nt" style="color: #000080;"><other-genotype-tag></span>.</span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC352" class="line" lang="markdown">Use this after vcfannotategenotypes to get correspondence statistics for two vcfs.</span>

</pre>

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<td class="diff-line-num old_line" 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">

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<pre style="margin: 0;"> <span id="LC353" class="line" lang="markdown">    </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="363" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC354" class="line" lang="markdown">    </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC355" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### vcfgenotypes</span></span>

</pre>

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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">@@ -373,8 +364,8 @@ alleles provided in the call's ALT/REF fields.</td>

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<pre style="margin: 0;"> <span id="LC364" class="line" lang="markdown">    </span>

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<pre style="margin: 0;"> <span id="LC365" class="line" lang="markdown">    options:</span>

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<pre style="margin: 0;"> <span id="LC366" class="line" lang="markdown">        -n, --fix-null-genotypes   only apply to null and partly-null genotypes</span>

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<pre style="margin: 0;">-<span id="LC376" class="line" lang="markdown"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">-<span id="LC377" class="line" lang="markdown"><span class="idiff left right">    </span>Set genotypes using the maximum genotype likelihood for each sample.</span>

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<pre style="margin: 0;">+<span id="LC367" class="line" lang="markdown"></span>

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<pre style="margin: 0;">+<span id="LC368" class="line" lang="markdown">Set genotypes using the maximum genotype likelihood for each sample.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC369" class="line" lang="markdown">    </span>

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<pre style="margin: 0;"> <span id="LC370" class="line" lang="markdown">    </span>

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<pre style="margin: 0;"> <span id="LC371" class="line" lang="markdown">    </span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="411" style="width: 35px; color: rgba(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="402" style="width: 35px; color: rgba(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">@@ -411,30 +402,31 @@ Adds a field (id) which contains an allele-specific numerical index.</td>

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<pre style="margin: 0;"> <span id="LC402" class="line" lang="markdown">        -M, --merge-from FROM-TAG</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC403" class="line" lang="markdown">        -T, --merge-to   TO-TAG   merge from FROM-TAG used in the -i file, setting TO-TAG</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC404" class="line" lang="markdown">                                  in the current file.</span>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC405" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC406" class="line" lang="markdown">For bed-vcf intersection, alleles which fall into the targets are retained.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC407" class="line" lang="markdown">    </span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC415" class="line" lang="markdown">    For bed-vcf intersection, alleles which fall into the targets are retained.</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="416" style="width: 35px; color: rgba(0,0,0,0.3); 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="diff-line-num new_line old" data-linenumber="408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC416" class="line" lang="markdown">    </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); 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="diff-line-num new_line old" data-linenumber="408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC417" class="line" lang="markdown">    For vcf-vcf intersection and union, unify on equivalent alleles within window-size bp</span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC418" class="line" lang="markdown">    as determined by haplotype comparison alleles.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC408" class="line" lang="markdown">For vcf-vcf intersection and union, unify on equivalent alleles within window-size bp as determined by haplotype comparison alleles.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC409" class="line" lang="markdown">    </span>

</pre>

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<pre style="margin: 0;"> <span id="LC410" class="line" lang="markdown">    </span>

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<pre style="margin: 0;"> <span id="LC411" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### vcfkeepgeno</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC412" class="line" lang="markdown">    </span>

</pre>

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<pre style="margin: 0;"> <span id="LC413" class="line" lang="markdown">    usage: vcfkeepgeno <span class="nt" style="color: #000080;"><vcf</span> <span class="na" style="color: #008080;">file</span><span class="nt" style="color: #000080;">></span> <span class="p">[</span><span class="nv" style="color: #008080;">FIELD1</span><span class="p">]</span> <span class="p">[</span><span class="ss" style="color: #990073;">FIELD2</span><span class="p">]</span> ...</span>

</pre>

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<pre style="margin: 0;">-<span id="LC424" class="line" lang="markdown">    <span class="idiff left right">outputs each record in the vcf file, removing FORMAT fields not listed</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC425" class="line" lang="markdown"><span class="idiff left right">    on the command line from sample specifications in the output</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC414" class="line" lang="markdown">    </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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">

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<pre style="margin: 0;">+<span id="LC415" class="line" lang="markdown"><span class="idiff left right">Outputs each record in the vcf file, removing FORMAT fields not listed on the command line from sample specifications in the output.</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC416" class="line" lang="markdown">    </span>

</pre>

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<pre style="margin: 0;"> <span id="LC417" class="line" lang="markdown">    </span>

</pre>

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<pre style="margin: 0;"> <span id="LC418" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### vcfkeepinfo</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC419" class="line" lang="markdown">    </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC420" class="line" lang="markdown">    usage: vcfkeepinfo <span class="nt" style="color: #000080;"><vcf</span> <span class="na" style="color: #008080;">file</span><span class="nt" style="color: #000080;">></span> <span class="p">[</span><span class="nv" style="color: #008080;">FIELD1</span><span class="p">]</span> <span class="p">[</span><span class="ss" style="color: #990073;">FIELD2</span><span class="p">]</span> ...</span>

</pre>

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431

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<td class="diff-line-num new_line old" data-linenumber="421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC431" class="line" lang="markdown">    outputs each record in the vcf file, removing INFO fields not listed on the command line</span>

</pre>

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<pre style="margin: 0;">+<span id="LC421" class="line" lang="markdown">    </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="422" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC422" class="line" lang="markdown"> Outputs each record in the vcf file, removing INFO fields not listed on the command line.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC423" class="line" lang="markdown">    </span>

</pre>

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<pre style="margin: 0;"> <span id="LC424" class="line" lang="markdown">    </span>

</pre>

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<pre style="margin: 0;"> <span id="LC425" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### vcfkeepsamples</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC426" class="line" lang="markdown">    </span>

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<pre style="margin: 0;"> <span id="LC427" class="line" lang="markdown">    usage: vcfkeepsamples <span class="nt" style="color: #000080;"><vcf</span> <span class="na" style="color: #008080;">file</span><span class="nt" style="color: #000080;">></span> <span class="p">[</span><span class="nv" style="color: #008080;">SAMPLE1</span><span class="p">]</span> <span class="p">[</span><span class="ss" style="color: #990073;">SAMPLE2</span><span class="p">]</span> ...</span>

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<pre style="margin: 0;">-<span id="LC437" class="line" lang="markdown">    outputs each record in the vcf file, removing samples not listed on the command line</span>

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<pre style="margin: 0;">+<span id="LC428" class="line" lang="markdown"></span>

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<pre style="margin: 0;">+<span id="LC429" class="line" lang="markdown">Outputs each record in the vcf file, removing samples not listed on the command line.</span>

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<pre style="margin: 0;"> <span id="LC430" class="line" lang="markdown">    </span>

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<pre style="margin: 0;"> <span id="LC431" class="line" lang="markdown">    </span>

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<pre style="margin: 0;"> <span id="LC432" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### vcfleftalign</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">@@ -453,9 +445,9 @@ alignments.</td>

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<pre style="margin: 0;"> <span id="LC445" class="line" lang="markdown"><span class="sb" style="color: #d14;">        -r, --reference FILE  Use this reference as a basis for realignment.</span></span>

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<pre style="margin: 0;"> <span id="LC446" class="line" lang="markdown"><span class="sb" style="color: #d14;">        -w, --window N        Use a window of this many bp when left aligning (150).</span></span>

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<pre style="margin: 0;"> <span id="LC447" class="line" lang="markdown"></span>

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<pre style="margin: 0;">-<span id="LC456" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right">    Left-aligns variants in the specified input file or stdin.  Window size is determined</span></span></span>

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<pre style="margin: 0;">-<span id="LC457" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right">    dynamically according to the entropy of the regions flanking the indel.  These must have</span></span></span>

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<pre style="margin: 0;">-<span id="LC458" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right">   </span> entropy > 1 bit/bp, or be shorter than ~5kb.</span></span>

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<pre style="margin: 0;">+<span id="LC448" class="line" lang="markdown"><span class="idiff left right">Left-aligns variants in the specified input file or stdin.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC449" class="line" lang="markdown"><span class="idiff left right">Window size is determined dynamically according to the entropy of the regions flanking the indel.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC450" class="line" lang="markdown"><span class="idiff left right">These must have</span> entropy > 1 bit/bp, or be shorter than ~5kb.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC451" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC452" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC453" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### vcflength</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">@@ -495,12 +487,11 @@ Use `vcfallelicprimitives` to decompose records while preserving format.</td>

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<pre style="margin: 0;"> <span id="LC487" class="line" lang="markdown">        -f, --fasta-reference  FASTA reference file to use to obtain primer sequences</span>

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<pre style="margin: 0;"> <span id="LC488" class="line" lang="markdown">        -l, --primer-length    The length of the primer sequences on each side of the variant</span>

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<pre style="margin: 0;"> <span id="LC489" class="line" lang="markdown">    </span>

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<pre style="margin: 0;">-<span id="LC498" class="line" lang="markdown">    For each VCF record, extract the flanking sequences, and write them to stdout as FASTA</span>

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<pre style="margin: 0;">-<span id="LC499" class="line" lang="markdown">    records suitable for alignment.  This tool is intended for use in designing validation</span>

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<pre style="margin: 0;">-<span id="LC500" class="line" lang="markdown">    experiments.  Primers extracted which would flank all of the alleles at multi-allelic</span>

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<pre style="margin: 0;">-<span id="LC501" class="line" lang="markdown">    sites.  The name of the FASTA "reads" indicates the VCF record which they apply to.</span>

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<pre style="margin: 0;">-<span id="LC502" class="line" lang="markdown">    The form is >CHROM_POS_LEFT for the 3' primer and >CHROM_POS_RIGHT for the 5' primer,</span>

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<pre style="margin: 0;">-<span id="LC503" class="line" lang="markdown">    for example:</span>

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<pre style="margin: 0;">+<span id="LC490" class="line" lang="markdown">For each VCF record, extract the flanking sequences, and write them to stdout as FASTA records suitable for alignment.</span>

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<td class="diff-line-num new new_line" data-linenumber="491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC491" class="line" lang="markdown">This tool is intended for use in designing validation experiments.</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC492" class="line" lang="markdown">Primers extracted which would flank all of the alleles at multi-allelic sites.</span>

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<pre style="margin: 0;">+<span id="LC493" class="line" lang="markdown">The name of the FASTA "reads" indicates the VCF record which they apply to.</span>

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<pre style="margin: 0;">+<span id="LC494" class="line" lang="markdown">The form is >CHROM_POS_LEFT for the 3' primer and >CHROM_POS_RIGHT for the 5' primer, for example:</span>

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<pre style="margin: 0;"> <span id="LC495" class="line" lang="markdown"><span class="gt" style="color: #a00;">    </span></span>

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<pre style="margin: 0;"> <span id="LC496" class="line" lang="markdown"><span class="gt" style="color: #a00;">    >20_233255_LEFT</span></span>

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<pre style="margin: 0;"> <span id="LC497" class="line" lang="markdown">    CCATTGTATATATAGACCATAATTTCTTTATCCAATCATCTGTTGATGGA</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="518" style="width: 35px; color: rgba(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="509" style="width: 35px; color: rgba(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">@@ -518,9 +509,9 @@ Use `vcfallelicprimitives` to decompose records while preserving format.</td>

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<pre style="margin: 0;"> <span id="LC509" class="line" lang="markdown">        -s, --scale-by KEY   scale sampling likelihood by this Float info field</span>

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<pre style="margin: 0;"> <span id="LC510" class="line" lang="markdown">        -p, --random-seed N  use this random seed</span>

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520

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511

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<pre style="margin: 0;"> <span id="LC511" class="line" lang="markdown">    </span>

</pre>

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521

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<td class="diff-line-num new_line old" data-linenumber="512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC521" class="line" lang="markdown"><span class="idiff left right">    </span>Randomly sample sites from an input VCF file, which may be provided as stdin.</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

522

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<td class="diff-line-num new_line old" data-linenumber="512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC522" class="line" lang="markdown"><span class="idiff left right">    Scale the sampling probability by the field specified in KEY.  This may be</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

523

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<td class="diff-line-num new_line old" data-linenumber="512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC523" class="line" lang="markdown"><span class="idiff left right">   </span> used to provide uniform sampling across allele frequencies, for instance.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

512

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<pre style="margin: 0;">+<span id="LC512" class="line" lang="markdown">Randomly sample sites from an input VCF file, which may be provided as stdin.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

513

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<pre style="margin: 0;">+<span id="LC513" class="line" lang="markdown"><span class="idiff left right">Scale the sampling probability by the field specified in KEY.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

514

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<pre style="margin: 0;">+<span id="LC514" class="line" lang="markdown"><span class="idiff left right">This may be</span> used to provide uniform sampling across allele frequencies, for instance.</span>

</pre>

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524

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<td class="diff-line-num new_line" data-linenumber="515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

515

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<pre style="margin: 0;"> <span id="LC515" class="line" lang="markdown">    </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

525

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<td class="diff-line-num new_line" data-linenumber="516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

516

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<pre style="margin: 0;"> <span id="LC516" class="line" lang="markdown">    </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

526

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<td class="diff-line-num new_line" data-linenumber="517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

517

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<pre style="margin: 0;"> <span id="LC517" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### vcfremap</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="539" style="width: 35px; color: rgba(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="530" style="width: 35px; color: rgba(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">@@ -539,8 +530,8 @@ Use `vcfallelicprimitives` to decompose records while preserving format.</td>

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<td class="diff-line-num old_line" data-linenumber="539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

539

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<td class="diff-line-num new_line" data-linenumber="530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

530

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<pre style="margin: 0;"> <span id="LC530" class="line" lang="markdown">        -R, --repeat-gap-extend N    penalize non-repeat-unit gaps in repeat sequence</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

540

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<td class="diff-line-num new_line" data-linenumber="531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

531

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<pre style="margin: 0;"> <span id="LC531" class="line" lang="markdown">        -a, --adjust-vcf TAG         supply a new cigar as TAG in the output VCF</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

541

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<td class="diff-line-num new_line" data-linenumber="532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

532

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<pre style="margin: 0;"> <span id="LC532" class="line" lang="markdown">    </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

542

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<td class="diff-line-num new_line old" data-linenumber="533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC542" class="line" lang="markdown"><span class="idiff left right">    </span>For each alternate allele, attempt to realign against the reference with lowered gap open penalty.</span>

</pre>

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543

</td>

<td class="diff-line-num new_line old" data-linenumber="533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC543" class="line" lang="markdown"><span class="idiff left right">    </span>If realignment is possible, adjust the cigar and reference/alternate alleles.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

533

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<pre style="margin: 0;">+<span id="LC533" class="line" lang="markdown">For each alternate allele, attempt to realign against the reference with lowered gap open penalty.</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

534

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<pre style="margin: 0;">+<span id="LC534" class="line" lang="markdown">If realignment is possible, adjust the cigar and reference/alternate alleles.</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

544

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<td class="diff-line-num new_line" data-linenumber="535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

535

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<pre style="margin: 0;"> <span id="LC535" class="line" lang="markdown">    </span>

</pre>

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545

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<td class="diff-line-num new_line" data-linenumber="536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

536

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<pre style="margin: 0;"> <span id="LC536" class="line" lang="markdown">    </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

546

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<td class="diff-line-num new_line" data-linenumber="537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

537

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<pre style="margin: 0;"> <span id="LC537" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### vcfremoveaberrantgenotypes</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="544" style="width: 35px; color: rgba(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">@@ -553,7 +544,8 @@ allele observation) for each genotype.</td>

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<pre style="margin: 0;"> <span id="LC544" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### vcfremovesamples</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC545" class="line" lang="markdown">    </span>

</pre>

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<pre style="margin: 0;"> <span id="LC546" class="line" lang="markdown">    usage: vcfremovesamples <span class="nt" style="color: #000080;"><vcf</span> <span class="na" style="color: #008080;">file</span><span class="nt" style="color: #000080;">></span> <span class="p">[</span><span class="nv" style="color: #008080;">SAMPLE1</span><span class="p">]</span> <span class="p">[</span><span class="ss" style="color: #990073;">SAMPLE2</span><span class="p">]</span> ...</span>

</pre>

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<td class="diff-line-num new_line 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">

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<pre style="margin: 0;">-<span id="LC556" class="line" lang="markdown">    outputs each record in the vcf file, removing samples listed on the command line</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC547" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC548" class="line" lang="markdown">Outputs each record in the vcf file, removing samples listed on the command line.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC549" class="line" lang="markdown">    </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

558

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<pre style="margin: 0;"> <span id="LC550" class="line" lang="markdown">    </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

559

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<td class="diff-line-num new_line" data-linenumber="551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

551

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<pre style="margin: 0;"> <span id="LC551" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### vcfroc</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="565" style="width: 35px; color: rgba(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="557" style="width: 35px; color: rgba(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">@@ -565,17 +557,17 @@ allele observation) for each genotype.</td>

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<td class="diff-line-num old_line" data-linenumber="565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

565

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<pre style="margin: 0;"> <span id="LC557" class="line" lang="markdown">        -w, --window-size N       compare records up to this many bp away (default 30)</span>

</pre>

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566

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558

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<pre style="margin: 0;"> <span id="LC558" class="line" lang="markdown">        -r, --reference FILE      FASTA reference file</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC559" class="line" lang="markdown">    </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="568" style="width: 35px; color: rgba(0,0,0,0.3); 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="diff-line-num new_line 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">

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<pre style="margin: 0;">-<span id="LC568" class="line" lang="markdown"><span class="idiff left right">    Generates a pseudo-ROC curve using sensitivity and specificity estimated against</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

569

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<td class="diff-line-num new_line 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">

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<pre style="margin: 0;">-<span id="LC569" class="line" lang="markdown"><span class="idiff left right">    a putative truth set.  </span>Thresholding is provided by successive QUAL cutoffs.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

560

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<pre style="margin: 0;">+<span id="LC560" class="line" lang="markdown"><span class="idiff left right">Generates a pseudo-ROC curve using sensitivity and specificity estimated against a putative truth set.</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC561" class="line" lang="markdown">Thresholding is provided by successive QUAL cutoffs.</span>

</pre>

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570

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<td class="diff-line-num new_line" data-linenumber="562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

562

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<pre style="margin: 0;"> <span id="LC562" class="line" lang="markdown">    </span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

563

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<pre style="margin: 0;"> <span id="LC563" class="line" lang="markdown">    </span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC564" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### vcfsamplediff</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC565" class="line" lang="markdown">    </span>

</pre>

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<pre style="margin: 0;"> <span id="LC566" class="line" lang="markdown">    usage: vcfsamplediff <span class="nt" style="color: #000080;"><tag></span> <span class="nt" style="color: #000080;"><sample></span> <span class="nt" style="color: #000080;"><sample></span> <span class="p">[</span><span class="nv" style="color: #008080;"> <sample> ... </span><span class="p">]</span> <span class="nt" style="color: #000080;"><vcf</span> <span class="na" style="color: #008080;">file</span><span class="nt" style="color: #000080;">></span></span>

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<pre style="margin: 0;">-<span id="LC575" class="line" lang="markdown">    <span class="idiff left">tags each record where the listed sample genotypes differ with </span><span class="nt" style="color: #000080;"><span class="idiff right"><tag></span></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC576" class="line" lang="markdown"><span class="idiff left right">    The first sample is assumed to be germline, the second somatic.</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC577" class="line" lang="markdown"><span class="idiff left">    Each record is tagged with </span><span class="nt" style="color: #000080;"><span class="idiff"><tag></span></span><span class="idiff right">={germline,somatic,loh} to specify the type of</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC578" class="line" lang="markdown"><span class="idiff left right">   </span> variant given the genotype difference between the two samples.</span>

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<pre style="margin: 0;">+<span id="LC567" class="line" lang="markdown">    </span>

</pre>

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<pre style="margin: 0;">+<span id="LC568" class="line" lang="markdown"><span class="idiff left">Tags each record where the listed sample genotypes differ with </span><span class="nt" style="color: #000080;"><span class="idiff right"><tag></span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

569

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<pre style="margin: 0;">+<span id="LC569" class="line" lang="markdown"><span class="idiff left right">The first sample is assumed to be germline, the second somatic.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC570" class="line" lang="markdown"><span class="idiff left">Each record is tagged with </span><span class="nt" style="color: #000080;"><span class="idiff"><tag></span></span><span class="idiff right">={germline,somatic,loh} to specify the type of</span> variant given the genotype difference between the two samples.</span>

</pre>

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579

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<pre style="margin: 0;"> <span id="LC571" class="line" lang="markdown">    </span>

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<pre style="margin: 0;"> <span id="LC572" class="line" lang="markdown">    </span>

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<td class="diff-line-num new_line" data-linenumber="573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC573" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### vcfsamplenames</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="593" style="width: 35px; color: rgba(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">@@ -593,13 +585,10 @@ Prints the names of the samples in the VCF file.</td>

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<pre style="margin: 0;"> <span id="LC585" class="line" lang="markdown">    application: </span>

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC586" class="line" lang="markdown">        vcfsom -a output.som -f "AF DP ABP" test.vcf >results.vcf</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC587" class="line" lang="markdown">    </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="596" style="width: 35px; color: rgba(0,0,0,0.3); 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="diff-line-num new_line old" data-linenumber="588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC596" class="line" lang="markdown">    vcfsomtrains and/or applies a self-organizing map to the input VCF data</span>

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<td class="diff-line-num new_line old" data-linenumber="588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC597" class="line" lang="markdown">    on stdin, adding two columns for the x and y coordinates of the winning</span>

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<td class="diff-line-num old old_line" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC598" class="line" lang="markdown">    neuron in the network and an optional euclidean distance from a given</span>

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<td class="diff-line-num new_line old" data-linenumber="588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC599" class="line" lang="markdown">    node (--center).</span>

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<pre style="margin: 0;">+<span id="LC588" class="line" lang="markdown">vcfsom trains and/or applies a self-organizing map to the input VCF data on stdin, adding two columns for the x and y coordinates of the winning neuron in the network and an optional euclidean distance from a given node (--center).</span>

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<pre style="margin: 0;"> <span id="LC589" class="line" lang="markdown">    </span>

</pre>

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<td class="diff-line-num old old_line" 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="diff-line-num new_line old" data-linenumber="590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC601" class="line" lang="markdown"><span class="idiff left right">    If a map is provided via --apply,  map will be applied to input without</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC602" class="line" lang="markdown"><span class="idiff left right">    training.  </span>Automated filtering to an estimated FP rate is </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC590" class="line" lang="markdown"><span class="idiff left right">If a map is provided via --apply,  map will be applied to input without training.</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC591" class="line" lang="markdown">Automated filtering to an estimated FP rate is </span>

</pre>

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<pre style="margin: 0;"> <span id="LC592" class="line" lang="markdown">    </span>

</pre>

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<pre style="margin: 0;"> <span id="LC593" class="line" lang="markdown">    options:</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

605

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<td class="diff-line-num new_line" data-linenumber="594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

594

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<pre style="margin: 0;"> <span id="LC594" class="line" lang="markdown">    </span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="642" style="width: 35px; color: rgba(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="631" style="width: 35px; color: rgba(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">@@ -642,7 +631,7 @@ Prints the names of the samples in the VCF file.</td>

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<pre style="margin: 0;"> <span id="LC631" class="line" lang="markdown">        -o, --gap-open-penalty N     gap open penalty for SW algorithm</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC632" class="line" lang="markdown">        -e, --gap-extend-penalty N   gap extension penalty for SW algorithm</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC633" class="line" lang="markdown">    </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

645

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<td class="diff-line-num new_line old" data-linenumber="634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC645" class="line" lang="markdown"><span class="idiff left right">    </span>Prints statistics about variants in the input VCF file.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC634" class="line" lang="markdown">Prints statistics about variants in the input VCF file.</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

635

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<pre style="margin: 0;"> <span id="LC635" class="line" lang="markdown">    </span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC636" class="line" lang="markdown">    </span>

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<td class="diff-line-num new_line" data-linenumber="637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC637" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### vcfstreamsort</span></span>

</pre>

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<br>

</li>

<li id="a3605ce2e71fe99d64663ab3128baf72f749037e">

<a href="https://salsa.debian.org/med-team/libvcflib/commit/18f9a56680d84676eadf8905cf2bd95b76fc9841#a3605ce2e71fe99d64663ab3128baf72f749037e"><strong>scripts/vcf2bed.py</strong></a>

<hr>

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1

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python</span></span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">print_function</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"></span>

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<td class="diff-line-num old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdin</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,4 +13,4 @@ for line in sys.stdin:</td>

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<td class="diff-line-num old_line" 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">

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<td class="diff-line-num new_line" 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">

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python">    <span class="n" style="color: #333;">span</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;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">])</span> <span class="c1" style="color: #998; font-style: italic;"># handle multi-base alleles</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python">    <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">span</span></span>

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<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python">    <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span></span>

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<td class="diff-line-num new_line old" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">map</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff right">,</span></span> <span class="p">[</span><span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">]))</span></span></pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff right">in</span></span> <span class="p">[</span><span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">]))</span></span></pre>

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<br>

</li>

<li id="a6b7f423610de5f7b91ca6f058e43ed89c5fe2c5">

<a href="https://salsa.debian.org/med-team/libvcflib/commit/18f9a56680d84676eadf8905cf2bd95b76fc9841#a6b7f423610de5f7b91ca6f058e43ed89c5fe2c5"><strong>scripts/vcf2sqlite.py</strong></a>

<hr>

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<td class="diff-line-num old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

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<td class="diff-line-num new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); 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="diff-line-num new_line old" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC2" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">print_function</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">re</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sqlite3</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC7" 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="o" style="font-weight: 600;">.</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;">2</span><span class="p">:</span></span>

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<td class="diff-line-num old old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

8

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<td class="diff-line-num new_line old" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"usage"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sys</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">argv</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">" [dbname]"</span></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

9

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<td class="diff-line-num new_line old" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">"reads VCF on stdin, and writes output to a sqlite3 db [dbname]"</span></span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"usage {} [dbname]"</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">format</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">sys</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">argv</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">])</span></span></span>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"reads VCF on stdin, and writes output to a sqlite3 db [dbname]"</span></span><span class="p"><span class="idiff right">)</span></span></span>

</pre>

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<td class="diff-line-num 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">

10

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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python">    <span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="n" style="color: #333;">dbname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="24" style="width: 35px; color: rgba(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="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -24,7 +24,7 @@ for line in sys.stdin:</td>

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<td class="diff-line-num old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python">        <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">search</span><span class="p">(</span><span class="s" style="color: #d14;">"Number=(.*?),"</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python">        <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">search</span><span class="p">(</span><span class="s" style="color: #d14;">"Type=(.*?),"</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">n</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">t</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); 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="diff-line-num new_line old" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python">            <span class="nb" style="color: #0086b3;">id</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="n" style="color: #333;">groups</span><span class="p">()[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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">

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python">            <span class="n" style="color: #333;">id<span class="idiff left right">en</span></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="n" style="color: #333;">groups</span><span class="p">()[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python">            <span class="n" style="color: #333;">number</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">groups</span><span class="p">()[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">number</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"A"</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python">                <span class="n" style="color: #333;">number</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>

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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">@@ -34,8 +34,8 @@ for line in sys.stdin:</td>

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python">                <span class="n" style="color: #333;">number</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;">number</span><span class="p">)</span></span>

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<td class="diff-line-num old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python">            <span class="n" style="color: #333;">typestr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">groups</span><span class="p">()[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

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<td class="diff-line-num new_line old" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python">            <span class="n" style="color: #333;">infotypes</span><span class="p">[</span><span class="nb" style="color: #0086b3;">id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">typestr</span></span>

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<td class="diff-line-num old old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); 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="diff-line-num new_line old" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python">            <span class="n" style="color: #333;">infonumbers</span><span class="p">[</span><span class="nb" style="color: #0086b3;">id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">number</span></span>

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<td class="diff-line-num new old_line" 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">

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python">            <span class="n" style="color: #333;">infotypes</span><span class="p">[</span><span class="n" style="color: #333;">id<span class="idiff left right">en</span></span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">typestr</span></span>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python">            <span class="n" style="color: #333;">infonumbers</span><span class="p">[</span><span class="n" style="color: #333;">id<span class="idiff left right">en</span></span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">number</span></span>

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<td class="diff-line-num old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC39" 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 old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python">            <span class="k" style="font-weight: 600;">continue</span></span>

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<td class="diff-line-num old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python">    <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</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="diff-line-num unfold js-unfold old_line" data-linenumber="78" style="width: 35px; color: rgba(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="78" style="width: 35px; color: rgba(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">@@ -78,13 +78,13 @@ conn.execute(tablecmd)</td>

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python"><span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdin</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python">    <span class="n" style="color: #333;">fields</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</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="diff-line-num new_line old" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python">    <span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">id</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ref</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">alts</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">qual</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">filter</span></span><span class="p">,</span> <span class="n" style="color: #333;">info</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fields</span><span class="p">[:</span><span class="mi" style="color: #099;">8</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python">    <span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="n" style="color: #333;">id<span class="idiff left">en</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ref</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">alts</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">qual</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">filt</span></span><span class="p">,</span> <span class="n" style="color: #333;">info</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fields</span><span class="p">[:</span><span class="mi" style="color: #099;">8</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python">    <span class="n" style="color: #333;">alts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alts</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python">    <span class="n" style="color: #333;">altindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python">    <span class="n" style="color: #333;">chrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">chrom</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;">"</span></span>

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<pre style="margin: 0;">-<span id="LC85" class="line" lang="python">    <span class="nb" style="color: #0086b3;">id</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\'</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">id</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;">"</span></span>

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python">    <span class="n" style="color: #333;">id<span class="idiff left">en</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\'</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">iden</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;">"</span></span>

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python">    <span class="n" style="color: #333;">ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;">"</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="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;">"</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC87" class="line" lang="python">    <span class="nb" style="color: #0086b3;">filt<span class="idiff left">er</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\'</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">filter</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;">"</span></span>

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python">    <span class="n" style="color: #333;">filt</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\'</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">filt</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;">"</span></span>

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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">alt</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">alts</span><span class="p">:</span></span>

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<td class="diff-line-num old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python">        <span class="n" style="color: #333;">alt</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">alt</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;">"</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python">        <span class="n" style="color: #333;">info_values</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -115,7 +115,7 @@ for line in sys.stdin:</td>

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="python">                    <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0"</span></span>

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="python">            <span class="n" style="color: #333;">ordered_insertion</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC117" class="line" lang="python">        <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"insert into alleles values ("</span> \</span>

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<pre style="margin: 0;">-<span id="LC118" class="line" lang="python">            <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;">join</span><span class="p">([</span><span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">id</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ref</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">alt</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">qual</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">filter</span></span><span class="p">])</span> \</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

118

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python">            <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;">join</span><span class="p">([</span><span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="n" style="color: #333;">id<span class="idiff left">en</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ref</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">alt</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">qual</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">filt</span></span><span class="p">])</span> \</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

119

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<td class="diff-line-num new_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

119

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="python">            <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">", "</span> \</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

120

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<td class="diff-line-num new_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

120

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python">            <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;">join</span><span class="p">(</span><span class="n" style="color: #333;">ordered_insertion</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">")"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

121

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<td class="diff-line-num new_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

121

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="python">        <span class="n" style="color: #333;">conn</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">execute</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="p">)</span></span>

</pre>

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</table>

<br>

</li>

<li id="2f6457546dd9b17dda7980dfec7f910ad32c6fa5">

<a href="https://salsa.debian.org/med-team/libvcflib/commit/18f9a56680d84676eadf8905cf2bd95b76fc9841#2f6457546dd9b17dda7980dfec7f910ad32c6fa5"><strong>scripts/vcfclearid</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

</td>

<td class="diff-line-num new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

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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="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2

</td>

<td class="diff-line-num new_line old" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>

</pre>

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<td class="diff-line-num old old_line" 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">

3

</td>

<td class="diff-line-num new_line old" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<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="python"></span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" 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="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">print_function</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

</td>

<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

</td>

<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdin</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

</td>

<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

8

</td>

<td class="diff-line-num new_line old" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC8" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">strip</span></span><span class="p"><span class="idiff right">(</span>)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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="python">        <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">strip</span></span><span class="p"><span class="idiff right">()</span>)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

</td>

<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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 class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num 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">

10

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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python">        <span class="n" style="color: #333;">fields</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

11

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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python">        <span class="n" style="color: #333;">fields</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="s" style="color: #d14;">"."</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

12

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<td class="diff-line-num new_line old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC12" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">fields</span></span><span class="p">)</span></span></pre>

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<td class="diff-line-num new old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">fields</span></span><span class="p"><span class="idiff right">)</span>)</span></span></pre>

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<br>

</li>

<li id="427a79153566b7170203310fb39d886b8affc023">

<a href="https://salsa.debian.org/med-team/libvcflib/commit/18f9a56680d84676eadf8905cf2bd95b76fc9841#427a79153566b7170203310fb39d886b8affc023"><strong>scripts/vcfclearinfo</strong></a>

<hr>

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<td class="diff-line-num old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

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<td class="diff-line-num new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2

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<td class="diff-line-num new_line old" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>

</pre>

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<td class="diff-line-num old old_line" 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">

3

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<td class="diff-line-num new_line old" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC3" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" 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="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">print_function</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdin</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

8

</td>

<td class="diff-line-num new_line old" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC8" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">strip</span></span><span class="p"><span class="idiff right">(</span>)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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="python">        <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">strip</span></span><span class="p"><span class="idiff right">()</span>)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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 class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num 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">

10

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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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="n" style="color: #333;">fields</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

11

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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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="python">        <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"."</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

12

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<td class="diff-line-num new_line old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">fields</span></span><span class="p">)</span></span></pre>

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<td class="diff-line-num new old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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="python">        <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">fields</span></span><span class="p"><span class="idiff right">)</span>)</span></span></pre>

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<br>

</li>

<li id="698eb6a3f16b693cec023ddbdc3df2295eded77a">

<a href="https://salsa.debian.org/med-team/libvcflib/commit/18f9a56680d84676eadf8905cf2bd95b76fc9841#698eb6a3f16b693cec023ddbdc3df2295eded77a"><strong>scripts/vcffirstheader</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

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<td class="diff-line-num new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2

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<td class="diff-line-num new_line old" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" 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="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">print_function</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

</td>

<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

</td>

<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

</td>

<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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="python"><span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdin</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

</td>

<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

</td>

<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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 class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">header</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

9

</td>

<td class="diff-line-num new_line old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<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="python">            <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">strip</span></span><span class="p"><span class="idiff right">(</span>)</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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="python">            <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">strip</span></span><span class="p"><span class="idiff right">()</span>)</span></span>

</pre>

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<td class="diff-line-num 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">

10

</td>

<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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="python">        <span class="k" style="font-weight: 600;">continue</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

11

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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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="python">    <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12

</td>

<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">header</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

13

</td>

<td class="diff-line-num new_line old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<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="python">           <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">strip</span></span><span class="p"><span class="idiff right">(</span>)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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="python">           <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">strip</span></span><span class="p"><span class="idiff right">()</span>)</span></span>

</pre>

</td>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python">           <span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span></span>

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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python">        <span class="k" style="font-weight: 600;">continue</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); 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="diff-line-num new_line old" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">strip</span></span><span class="p"><span class="idiff right">(</span>)</span></span></pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">strip</span></span><span class="p"><span class="idiff right">()</span>)</span></span></pre>

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<br>

</li>

<li id="13db7414b0966cb9ed1bb9968327fd5e1af9863c">

<a href="https://salsa.debian.org/med-team/libvcflib/commit/18f9a56680d84676eadf8905cf2bd95b76fc9841#13db7414b0966cb9ed1bb9968327fd5e1af9863c"><strong>scripts/vcfnulldotslashdot</strong></a>

<hr>

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<td class="diff-line-num old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

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<td class="diff-line-num new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python</span></span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">print_function</span><span class="p">,</span> <span class="n" style="color: #333;">division</span></span>

</pre>

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3

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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">math</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8" style="width: 35px; color: rgba(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="8" style="width: 35px; color: rgba(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">@@ -8,15 +8,15 @@ def multcoeff(n,k): return bincoeff(n+k-1,k)</td>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdin</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num 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">

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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); 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="diff-line-num new_line old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">strip</span></span><span class="p"><span class="idiff right">(</span>)</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">strip</span></span><span class="p"><span class="idiff right">()</span>)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12

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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python">        <span class="k" style="font-weight: 600;">continue</span></span>

</pre>

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<td class="diff-line-num old_line" 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">

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<td class="diff-line-num new_line" 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">

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python">    <span class="n" style="color: #333;">fields</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</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>

</pre>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python">    <span class="n" style="color: #333;">alleles</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;">fields</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;">split</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">))</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># assume that we have GT:GL</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># how many genotypes?  assume diploid</span></span>

</pre>

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<td class="diff-line-num old old_line" 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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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python">    <span class="n" style="color: #333;">flatgls</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;">join</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">map</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">,[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">multcoeff</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">alleles</span></span><span class="p"><span class="idiff">,</span></span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff right">))</span>)</span></span>

</pre>

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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python">    <span class="n" style="color: #333;">flatgls</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;">join</span><span class="p">(<span class="idiff left">[</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">multcoeff</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">alleles</span></span><span class="p"><span class="idiff">,</span></span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff right">)]</span>)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC18" 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;">9</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">)):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fields</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="s" style="color: #d14;">"."</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python">            <span class="n" style="color: #333;">fields</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="s" style="color: #d14;">"./.:"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">flatgls</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">fields</span></span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">fields</span></span><span class="p"><span class="idiff right">)</span>)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python">    </span></pre>

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<br>

</li>

<li id="064f6f30b2ef573145e550cf01828d6462d0f335">

<a href="https://salsa.debian.org/med-team/libvcflib/commit/18f9a56680d84676eadf8905cf2bd95b76fc9841#064f6f30b2ef573145e550cf01828d6462d0f335"><strong>src/BedReader.h</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="93" style="width: 35px; color: rgba(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="93" style="width: 35px; color: rgba(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">@@ -93,7 +93,7 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="c">    <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">isOpen</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_isOpen</span><span class="p">;</span> <span class="p">}</span></span>

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<td class="diff-line-num new_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="c">    <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BedTarget</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">targets</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); 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="diff-line-num new_line old" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC96" class="line" lang="c">    <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">IntervalTree</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BedTarget</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">intervals</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// intervals by reference sequence</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="c">    <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">IntervalTree</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">size_t</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">BedTarget</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">intervals</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// intervals by reference sequence</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

97

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<td class="diff-line-num new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

97

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

98

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<td class="diff-line-num new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

98

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="c">    <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BedTarget</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">entries</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num old_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

99

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<td class="diff-line-num new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

99

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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="c"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -119,20 +119,18 @@ public:</td>

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<td class="diff-line-num old_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

119

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<td class="diff-line-num new_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="c">    <span class="p">}</span></span>

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<td class="diff-line-num old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

120

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="c">    <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BedTarget</span><span class="o" style="font-weight: 600;">*></span> <span class="n" style="color: #333;">targetsContained</span><span class="p">(</span><span class="n" style="color: #333;">BedTarget</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">target</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC122" class="line" lang="c">        <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BedTarget</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">results</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

123

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<td class="diff-line-num new_line old" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC123" class="line" lang="c">        <span class="n" style="color: #333;">intervals</span><span class="p">[</span><span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">].</span><span class="n" style="color: #333;">findContained</span><span class="p">(</span><span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">left</span><span class="p">,</span> <span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">right</span><span class="p">,</span> <span class="n" style="color: #333;">results</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="c">        <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">,</span> <span class="n" style="color: #333;">BedTarget</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">results</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">intervals</span><span class="p">[</span><span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">].</span><span class="n" style="color: #333;">findContained</span><span class="p">(</span><span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">left</span><span class="p">,</span> <span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">right</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC123" class="line" lang="c">        <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BedTarget</span><span class="o" style="font-weight: 600;">*></span> <span class="n" style="color: #333;">contained</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); 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="diff-line-num new_line old" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC125" class="line" lang="c">        <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BedTarget</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">results</span><span class="p">.</span><span class="n" style="color: #333;">begin</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;">results</span><span class="p">.</span><span class="n" style="color: #333;">end</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="p">{</span></span>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC124" class="line" lang="c">        <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">size_t</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">BedTarget</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">results</span><span class="p">.</span><span class="n" style="color: #333;">begin</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;">results</span><span class="p">.</span><span class="n" style="color: #333;">end</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="p">{</span></span>

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<td class="diff-line-num new_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC125" class="line" lang="c">            <span class="n" style="color: #333;">contained</span><span class="p">.</span><span class="n" style="color: #333;">push_back</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;">value</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

127

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<td class="diff-line-num new_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

126

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="c">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

128

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<td class="diff-line-num new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC127" class="line" lang="c">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">contained</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

129

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<td class="diff-line-num new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

129

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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="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC130" class="line" lang="c">    <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BedTarget</span><span class="o" style="font-weight: 600;">*></span> <span class="n" style="color: #333;">targetsOverlapping</span><span class="p">(</span><span class="n" style="color: #333;">BedTarget</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">target</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); 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="diff-line-num new_line old" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC132" class="line" lang="c">        <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BedTarget</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">results</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); 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="diff-line-num new_line old" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC133" class="line" lang="c">        <span class="n" style="color: #333;">intervals</span><span class="p">[</span><span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">].</span><span class="n" style="color: #333;">findOverlapping</span><span class="p">(</span><span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">left</span><span class="p">,</span> <span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">right</span><span class="p">,</span> <span class="n" style="color: #333;">results</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC131" class="line" lang="c">        <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">,</span> <span class="n" style="color: #333;">BedTarget</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">results</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">intervals</span><span class="p">[</span><span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">].</span><span class="n" style="color: #333;">findOverlapping</span><span class="p">(</span><span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">left</span><span class="p">,</span> <span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">right</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num 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">

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<td class="diff-line-num new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC132" class="line" lang="c">        <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BedTarget</span><span class="o" style="font-weight: 600;">*></span> <span class="n" style="color: #333;">overlapping</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); 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="diff-line-num new_line old" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC135" class="line" lang="c">        <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BedTarget</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">results</span><span class="p">.</span><span class="n" style="color: #333;">begin</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;">results</span><span class="p">.</span><span class="n" style="color: #333;">end</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="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC133" class="line" lang="c">        <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">size_t</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">BedTarget</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">results</span><span class="p">.</span><span class="n" style="color: #333;">begin</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;">results</span><span class="p">.</span><span class="n" style="color: #333;">end</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="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

136

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<td class="diff-line-num new_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">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC134" class="line" lang="c">            <span class="n" style="color: #333;">overlapping</span><span class="p">.</span><span class="n" style="color: #333;">push_back</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;">value</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

137

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<td class="diff-line-num new_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="c">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="136" style="width: 35px; color: rgba(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="LC136" class="line" lang="c">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">overlapping</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_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="diff-line-num unfold js-unfold new_line" data-linenumber="146" style="width: 35px; color: rgba(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">@@ -148,12 +146,12 @@ BedReader(string& fname)</td>

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="c">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC147" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC148" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">addTargets</span><span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BedTarget</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">targets</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC151" class="line" lang="c">        <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BedTarget</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">intervalsBySeq</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC149" class="line" lang="c">        <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">size_t</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">BedTarget</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">intervalsBySeq</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="c">        <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BedTarget</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">targets</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">targets</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">t</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC153" class="line" lang="c">            <span class="n" style="color: #333;">intervalsBySeq</span><span class="p">[</span><span class="n" style="color: #333;">t</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;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BedTarget</span><span class="o" style="font-weight: 600;">*></span><span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">left</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">right</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&*</span><span class="n" style="color: #333;">t</span><span class="p">));</span></span>

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<pre style="margin: 0;">+<span id="LC151" class="line" lang="c">            <span class="n" style="color: #333;">intervalsBySeq</span><span class="p">[</span><span class="n" style="color: #333;">t</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;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">size_t</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">BedTarget</span><span class="o" style="font-weight: 600;">*></span><span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">left</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">right</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&*</span><span class="n" style="color: #333;">t</span><span class="p">));</span></span>

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<pre style="margin: 0;"> <span id="LC152" class="line" lang="c">        <span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC155" class="line" lang="c">        <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BedTarget</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">intervalsBySeq</span><span class="p">.</span><span class="n" style="color: #333;">begin</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;">intervalsBySeq</span><span class="p">.</span><span class="n" style="color: #333;">end</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="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC156" class="line" lang="c">            <span class="n" style="color: #333;">intervals</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;">first</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">IntervalTree</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;"><span class="idiff left">BedTarget</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*></span></span><span class="p"><span class="idiff right">(</span></span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC153" class="line" lang="c">        <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">size_t</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">BedTarget</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">intervalsBySeq</span><span class="p">.</span><span class="n" style="color: #333;">begin</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;">intervalsBySeq</span><span class="p">.</span><span class="n" style="color: #333;">end</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="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC154" class="line" lang="c">            <span class="n" style="color: #333;">intervals</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;">first</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">IntervalTree</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">size_t</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">BedTarget</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*></span></span><span class="p"><span class="idiff">((</span></span><span class="n" style="color: #333;"><span class="idiff">vector</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">Interval</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">size_t</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">BedTarget</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*></span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">>&&</span></span><span class="p"><span class="idiff right">)</span></span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC155" class="line" lang="c">        <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC156" class="line" lang="c">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC157" class="line" lang="c"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="161" style="width: 35px; color: rgba(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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -161,12 +159,12 @@ BedReader(string& fname)</td>

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<pre style="margin: 0;"> <span id="LC159" class="line" lang="c">        <span class="n" style="color: #333;">file</span><span class="p">.</span><span class="n" style="color: #333;">open</span><span class="p">(</span><span class="n" style="color: #333;">fname</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>

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<pre style="margin: 0;"> <span id="LC160" class="line" lang="c">        <span class="n" style="color: #333;">_isOpen</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC161" class="line" lang="c">        <span class="n" style="color: #333;">targets</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">entries</span><span class="p">();</span></span>

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<td class="diff-line-num new_line old" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC164" class="line" lang="c">        <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BedTarget</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">intervalsBySeq</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC162" class="line" lang="c">        <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">size_t</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">BedTarget</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">intervalsBySeq</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC163" class="line" lang="c">        <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BedTarget</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">targets</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">targets</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">t</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC166" class="line" lang="c">            <span class="n" style="color: #333;">intervalsBySeq</span><span class="p">[</span><span class="n" style="color: #333;">t</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;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BedTarget</span><span class="o" style="font-weight: 600;">*></span><span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">left</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">right</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&*</span><span class="n" style="color: #333;">t</span><span class="p">));</span></span>

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<pre style="margin: 0;">+<span id="LC164" class="line" lang="c">            <span class="n" style="color: #333;">intervalsBySeq</span><span class="p">[</span><span class="n" style="color: #333;">t</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;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">size_t</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">BedTarget</span><span class="o" style="font-weight: 600;">*></span><span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">left</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">right</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&*</span><span class="n" style="color: #333;">t</span><span class="p">));</span></span>

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<pre style="margin: 0;"> <span id="LC165" class="line" lang="c">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); 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="diff-line-num new_line 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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<pre style="margin: 0;">-<span id="LC168" class="line" lang="c">        <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BedTarget</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">intervalsBySeq</span><span class="p">.</span><span class="n" style="color: #333;">begin</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;">intervalsBySeq</span><span class="p">.</span><span class="n" style="color: #333;">end</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="p">{</span></span>

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<td class="diff-line-num new_line 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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<pre style="margin: 0;">-<span id="LC169" class="line" lang="c">            <span class="n" style="color: #333;">intervals</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;">first</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">IntervalTree</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;"><span class="idiff left">BedTarget</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*></span></span><span class="p"><span class="idiff right">(</span></span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC166" class="line" lang="c">        <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">size_t</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">BedTarget</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">intervalsBySeq</span><span class="p">.</span><span class="n" style="color: #333;">begin</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;">intervalsBySeq</span><span class="p">.</span><span class="n" style="color: #333;">end</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="p">{</span></span>

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<td class="diff-line-num new old_line" 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">

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<pre style="margin: 0;">+<span id="LC167" class="line" lang="c">            <span class="n" style="color: #333;">intervals</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;">first</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">IntervalTree</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">size_t</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">BedTarget</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*></span></span><span class="p"><span class="idiff">((</span></span><span class="n" style="color: #333;"><span class="idiff">vector</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">Interval</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">size_t</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">BedTarget</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*></span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">>&&</span></span><span class="p"><span class="idiff right">)</span></span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC168" class="line" lang="c">        <span class="p">}</span></span>

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC169" class="line" lang="c">    <span class="p">}</span></span>

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<td class="diff-line-num old_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="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">

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<pre style="margin: 0;"> <span id="LC170" class="line" lang="c"></span>

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<br>

</li>

<li id="1e0994915779ecf5b7b7fc9ddefc94353c73476f">

<a href="https://salsa.debian.org/med-team/libvcflib/commit/18f9a56680d84676eadf8905cf2bd95b76fc9841#1e0994915779ecf5b7b7fc9ddefc94353c73476f"><strong>src/Variant.cpp</strong></a>

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "Variant.h"</span></span>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <utility></span></span>

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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

4

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<td class="diff-line-num new_line old" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">vcflib</span> <span class="p">{</span></span>

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6

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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">rev_arr</span> <span class="p">[</span><span class="mi" style="color: #099;">26</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="mi" style="color: #099;">84</span><span class="p">,</span> <span class="mi" style="color: #099;">66</span><span class="p">,</span> <span class="mi" style="color: #099;">71</span><span class="p">,</span> <span class="mi" style="color: #099;">68</span><span class="p">,</span> <span class="mi" style="color: #099;">69</span><span class="p">,</span> <span class="mi" style="color: #099;">70</span><span class="p">,</span> <span class="mi" style="color: #099;">67</span><span class="p">,</span> <span class="mi" style="color: #099;">72</span><span class="p">,</span> <span class="mi" style="color: #099;">73</span><span class="p">,</span> <span class="mi" style="color: #099;">74</span><span class="p">,</span> <span class="mi" style="color: #099;">75</span><span class="p">,</span> <span class="mi" style="color: #099;">76</span><span class="p">,</span> <span class="mi" style="color: #099;">77</span><span class="p">,</span> <span class="mi" style="color: #099;">78</span><span class="p">,</span> <span class="mi" style="color: #099;">79</span><span class="p">,</span> <span class="mi" style="color: #099;">80</span><span class="p">,</span> <span class="mi" style="color: #099;">81</span><span class="p">,</span> <span class="mi" style="color: #099;">82</span><span class="p">,</span> <span class="mi" style="color: #099;">83</span><span class="p">,</span> <span class="mi" style="color: #099;">65</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cpp">                           <span class="mi" style="color: #099;">85</span><span class="p">,</span> <span class="mi" style="color: #099;">86</span><span class="p">,</span> <span class="mi" style="color: #099;">87</span><span class="p">,</span> <span class="mi" style="color: #099;">88</span><span class="p">,</span> <span class="mi" style="color: #099;">89</span><span class="p">,</span> <span class="mi" style="color: #099;">90</span><span class="p">};</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">reverse_complement</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">seq</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// The old implementation of this function forgot to null-terminate its</span></span>

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// returned string. This implementation uses heavier-weight C++ stuff that</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC12" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// may be slower but should ensure that that doesn't happen again.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">size</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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">seq</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" 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">

16

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" 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">

18

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cpp">    <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">ret</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cpp">    <span class="n" style="color: #333;">ret</span><span class="p">.</span><span class="n" style="color: #333;">reserve</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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20

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">transform</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">rbegin</span><span class="p">(),</span> <span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">rend</span><span class="p">(),</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">back_inserter</span><span class="p">(</span><span class="n" style="color: #333;">ret</span><span class="p">),</span> <span class="p">[](</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">in</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">lower_case</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">in</span> <span class="o" style="font-weight: 600;">>=</span> <span class="sc" style="color: #d14;">'a'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">in</span> <span class="o" style="font-weight: 600;"><=</span> <span class="sc" style="color: #d14;">'z'</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">lower_case</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// Convert to upper case</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp">            <span class="n" style="color: #333;">in</span> <span class="o" style="font-weight: 600;">-=</span> <span class="mi" style="color: #099;">32</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">in</span> <span class="o" style="font-weight: 600;"><</span> <span class="sc" style="color: #d14;">'A'</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">in</span> <span class="o" style="font-weight: 600;">></span> <span class="sc" style="color: #d14;">'Z'</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">runtime_error</span><span class="p">(</span><span class="s" style="color: #d14;">"Out of range character "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">to_string</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="p">)</span><span class="n" style="color: #333;">in</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" in inverted sequence"</span><span class="p">);</span></span>

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// Compute RC in terms of letter identity, and then lower-case if necessary.</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">rev_arr</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;">in</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="sc" style="color: #d14;">'A'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">lower_case</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">32</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cpp">    <span class="p">});</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ret</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">toUpper</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">seq</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">size</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>

</pre>

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">seq</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

40

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp">    <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">ret</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp">    <span class="n" style="color: #333;">ret</span><span class="p">.</span><span class="n" style="color: #333;">reserve</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">transform</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">back_inserter</span><span class="p">(</span><span class="n" style="color: #333;">ret</span><span class="p">),</span> <span class="p">[](</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">in</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// If it's lower-case, bring it down in value to upper-case.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">in</span> <span class="o" style="font-weight: 600;">>=</span> <span class="sc" style="color: #d14;">'a'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">in</span> <span class="o" style="font-weight: 600;"><=</span> <span class="sc" style="color: #d14;">'z'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="p">(</span><span class="n" style="color: #333;">in</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">32</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">in</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp">    <span class="p">});</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ret</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">allATGCN</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">allowLowerCase</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">allowLowerCase</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cpp">       <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">const_iterator</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

57

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp">            <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">i</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'A'</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="sc" style="color: #d14;">'a'</span> <span class="o" style="font-weight: 600;">&&</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp">                <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'C'</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="sc" style="color: #d14;">'c'</span> <span class="o" style="font-weight: 600;">&&</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

60

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="cpp">                <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'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="sc" style="color: #d14;">'t'</span> <span class="o" style="font-weight: 600;">&&</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

61

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cpp">                <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'G'</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="sc" style="color: #d14;">'g'</span> <span class="o" style="font-weight: 600;">&&</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp">                <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'N'</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="sc" style="color: #d14;">'n'</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp">                    <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

64

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp">            <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

65

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

66

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

67

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">const_iterator</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

69

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp">            <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">i</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

70

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'A'</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="sc" style="color: #d14;">'C'</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="sc" style="color: #d14;">'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="sc" style="color: #d14;">'G'</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="sc" style="color: #d14;">'N'</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

71

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

72

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp">            <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

73

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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="cpp">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

74

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp">        </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

75

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

76

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<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="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

77

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

78

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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<td class="diff-line-num new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

79

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<td class="diff-line-num new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

80

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

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<td class="diff-line-num new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

81

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">line</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">parseSamples</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,6 +86,7 @@ void Variant::parse(string& line, bool parseSamples) {</td>

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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

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<td class="diff-line-num new_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

86

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp">    <span class="n" style="color: #333;">format</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15

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<td class="diff-line-num new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

87

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp">    <span class="n" style="color: #333;">alt</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16

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<td class="diff-line-num new_line" 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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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp">    <span class="n" style="color: #333;">alleles</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

89

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<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="cpp">    <span class="n" style="color: #333;">canonical</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

17

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<td class="diff-line-num new_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

90

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

18

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<td class="diff-line-num new_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

91

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT [SAMPLE1 .. SAMPLEN]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

19

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<td class="diff-line-num new_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

92

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC92" class="line" lang="cpp">    <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">fields</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">split</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">,</span> <span class="sc" style="color: #d14;">'\t'</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="112" style="width: 35px; color: rgba(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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -112,288 +185,492 @@ void Variant::parse(string& line, bool parseSamples) {</td>

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<td class="diff-line-num old_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

112

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<td class="diff-line-num new_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">

185

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<pre style="margin: 0;"> <span id="LC185" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//return true; // we should be catching exceptions...</span></span>

</pre>

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113

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<td class="diff-line-num new_line" 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">

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<pre style="margin: 0;"> <span id="LC186" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

114

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<td class="diff-line-num new_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC187" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

115

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<td class="diff-line-num new_line 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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<pre style="margin: 0;">-<span id="LC115" class="line" lang="cpp"><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Variant</span><span class="p">,</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">convert_to_breakends</span><span class="p">(</span><span class="n" style="color: #333;">FastaReference</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fasta_reference</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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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<pre style="margin: 0;">+<span id="LC188" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">hasSVTags</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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">

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<pre style="margin: 0;">+<span id="LC189" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">found_svtype</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">getSVTYPE</span><span class="p">().</span><span class="n" style="color: #333;">empty</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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">

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<pre style="margin: 0;">+<span id="LC190" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">found_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="s" style="color: #d14;">"SVLEN"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">()</span> <span class="o" style="font-weight: 600;">||</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="s" style="color: #d14;">"END"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">()</span> <span class="o" style="font-weight: 600;">||</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="s" style="color: #d14;">"SPAN"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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191

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<pre style="margin: 0;"> <span id="LC191" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); 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="diff-line-num new_line old" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC117" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_sv</span><span class="p">()){</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC118" class="line" lang="cpp">        <span class="n" style="color: #333;">Variant</span> <span class="n" style="color: #333;">f</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC119" class="line" lang="cpp">        <span class="n" style="color: #333;">Variant</span> <span class="n" style="color: #333;">s</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); 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="diff-line-num new_line old" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC120" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); 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="diff-line-num new_line old" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC121" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// just copy our old variant to keep our evidence tags and such</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC122" class="line" lang="cpp">        <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); 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="diff-line-num new_line old" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC123" class="line" lang="cpp">        <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

124

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<td class="diff-line-num new_line old" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC124" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// First variant gets our position</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

125

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<td class="diff-line-num new_line old" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC125" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// The second goes at sv end</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC126" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// We need to modify the ALT field</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC127" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// and the SVTYPE</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

128

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<pre style="margin: 0;">-<span id="LC128" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// and the name</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

129

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<pre style="margin: 0;">-<span id="LC129" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// and the pair info field, if there</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

130

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<pre style="margin: 0;">-<span id="LC130" class="line" lang="cpp">        </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

131

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<pre style="margin: 0;">-<span id="LC131" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rand</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC132" class="line" lang="cpp">        <span class="n" style="color: #333;">stringstream</span> <span class="n" style="color: #333;">f_new_alt</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC133" class="line" lang="cpp">        <span class="n" style="color: #333;">stringstream</span> <span class="n" style="color: #333;">s_new_alt</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC134" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

135

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<pre style="margin: 0;">-<span id="LC135" class="line" lang="cpp">        <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">f_new_ref</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

136

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<pre style="margin: 0;">-<span id="LC136" class="line" lang="cpp">        <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">s_new_ref</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<pre style="margin: 0;">+<span id="LC192" class="line" lang="cpp">   <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">found_svtype</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">found_len</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC193" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC194" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC138" class="line" lang="cpp">        <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">f_new_id</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" 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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<pre style="margin: 0;">-<span id="LC139" class="line" lang="cpp">        <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">s_new_id</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC195" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); 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="diff-line-num new_line 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">

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<pre style="margin: 0;">-<span id="LC141" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">opos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_sv_end</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC196" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">isSymbolicSV</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<pre style="margin: 0;">+<span id="LC197" class="line" lang="cpp">    </span>

</pre>

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<pre style="margin: 0;">+<span id="LC198" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">found_svtype</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">getSVTYPE</span><span class="p">().</span><span class="n" style="color: #333;">empty</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC199" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC200" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">ref_valid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">allATGCN</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ref</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC201" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">alts_valid</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC202" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alt</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC203" 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;">allATGCN</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">)){</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC204" class="line" lang="cpp">            <span class="n" style="color: #333;">alts_valid</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC205" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC206" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC207" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC208" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">ref_valid</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">alts_valid</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">found_svtype</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC209" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

142

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<td class="diff-line-num new_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC210" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC211" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getSVTYPE</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">altpos</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC212" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC213" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">altpos</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC214" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// TODO: Implement multi-alt SVs</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC215" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC216" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

143

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<td class="diff-line-num new_line" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

217

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<pre style="margin: 0;"> <span id="LC217" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

144

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<td class="diff-line-num new_line old" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC144" class="line" lang="cpp">        <span class="n" style="color: #333;">f_new_ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">fasta_reference</span><span class="p">.</span><span class="n" style="color: #333;">getSubSequence</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sequenceName</span><span class="p">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

145

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<td class="diff-line-num new_line old" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC145" class="line" lang="cpp">        <span class="n" style="color: #333;">s_new_ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">fasta_reference</span><span class="p">.</span><span class="n" style="color: #333;">getSubSequence</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sequenceName</span><span class="p">,</span> <span class="n" style="color: #333;">opos</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

146

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<td class="diff-line-num new_line" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

218

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<pre style="margin: 0;"> <span id="LC218" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

147

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<td class="diff-line-num new_line old" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC147" class="line" lang="cpp">    <span class="idiff left">    </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">this</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"SVTYPE"</span></span><span class="p"><span class="idiff">][</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"DEL"</span></span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); 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="diff-line-num new_line old" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC148" class="line" lang="cpp">        <span class="idiff left">    </span><span class="n" style="color: #333;"><span class="idiff">f_new_alt</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">f_new_ref</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"["</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">this</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">sequenceName</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">":"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">opos</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"["</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right">  </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

149

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<td class="diff-line-num new_line old" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC149" class="line" lang="cpp">            <span class="n" style="color: #333;"><span class="idiff left">s_new_alt</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">s_new_ref</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"]"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">this</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">sequenceName</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">":"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">opos</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"]</span>"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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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="cpp">    <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">this</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">find</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"SVTYPE"</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">this</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">end</span></span><span class="p"><span class="idiff right">()</span>){</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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="cpp">        <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">altpos</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">>=</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">this</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">at</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"SVTYPE"</span></span><span class="p"><span class="idiff">).</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff">())</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">{</span></span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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="cpp">            <span class="k" style="font-weight: 600;"><span class="idiff left">return</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"</span>"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

150

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<td class="diff-line-num new_line" data-linenumber="222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

222

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC222" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

151

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<td class="diff-line-num new_line old" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC151" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"SVTYPE"</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="s" style="color: #d14;">"INS"</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

152

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<td class="diff-line-num new_line old" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<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="cpp">            <span class="n" style="color: #333;">f_new_alt</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

153

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<td class="diff-line-num new_line old" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC153" class="line" lang="cpp">            <span class="n" style="color: #333;">s_new_alt</span> <span class="o" style="font-weight: 600;"><<</span>  <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>

</pre>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

154

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<td class="diff-line-num new_line old" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC154" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

155

</td>

<td class="diff-line-num new_line old" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<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="cpp">        <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"SVTYPE"</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="s" style="color: #d14;">"INV"</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old old_line" 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">

156

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<td class="diff-line-num new_line old" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<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="cpp">            <span class="n" style="color: #333;">f_new_alt</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" 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">

157

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<td class="diff-line-num new_line old" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC157" class="line" lang="cpp">            <span class="n" style="color: #333;">s_new_alt</span> <span class="o" style="font-weight: 600;"><<</span>  <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" 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">

158

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<td class="diff-line-num new_line old" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<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="cpp">        <span class="p">}</span> </span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" 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="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"SVTYPE"</span><span class="p">)[</span><span class="n" style="color: #333;">altpos</span><span class="p">];</span></span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

224

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<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="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num 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">

159

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<td class="diff-line-num new_line" data-linenumber="225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

225

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC225" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" 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="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" 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="cpp"><span class="p">};</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

160

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<td class="diff-line-num new_line" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

161

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<td class="diff-line-num new_line" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

229

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC229" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

162

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<td class="diff-line-num new_line old" data-linenumber="230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<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="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">make_pair</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

163

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<td class="diff-line-num new_line old" data-linenumber="230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC163" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" 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="diff-line-num new_line" data-linenumber="230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

230

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC230" class="line" lang="cpp"></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

165

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<td class="diff-line-num new_line 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">

</td>

<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="cpp">    <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="s" style="color: #d14;">"SVTYPE"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" 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">

166

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<td class="diff-line-num new_line 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC166" class="line" lang="cpp">               <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"SVTYPE"</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="s" style="color: #d14;">"TRA"</span><span class="p">){</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC231" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getMaxReferencePos</span><span class="p">(){</span></span>

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<td class="diff-line-num new new_line" data-linenumber="232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC232" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">canonical</span> <span class="o" style="font-weight: 600;">&&</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="s" style="color: #d14;">"END"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC233" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// We are cannonicalized and must have a correct END</span></span>

</pre>

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC234" class="line" lang="cpp">        </span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC235" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC236" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"END"</span><span class="p">)){</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC237" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// Get the latest one defined.</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC238" class="line" lang="cpp">            <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">stoi</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)),</span> <span class="n" style="color: #333;">end</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC239" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC240" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// Convert to 0-based.</span></span>

</pre>

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC241" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC242" class="line" lang="cpp">        </span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC243" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" 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">

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<td class="diff-line-num new_line" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC244" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC245" 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="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isSymbolicSV</span><span class="p">()){</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC246" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// We don't necessarily have an END, but we don't need one</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC247" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">zeroBasedPosition</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="k" style="font-weight: 600;">this</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;">length</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>

</pre>

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<td class="diff-line-num new_line" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC248" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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249

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<pre style="margin: 0;"> <span id="LC249" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num old old_line" 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">

170

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<td class="diff-line-num new_line old" data-linenumber="250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC170" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

171

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<td class="diff-line-num new_line old" data-linenumber="250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC171" class="line" lang="cpp">        <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"ERROR: non-SV types cannot be converted to BND format"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

172

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<td class="diff-line-num new_line old" data-linenumber="250" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC172" class="line" lang="cpp">        <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">999</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC250" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">canonicalizable</span><span class="p">()){</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC251" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// We aren't canonical, but we could be.</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

252

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<pre style="margin: 0;">+<span id="LC252" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="s" style="color: #d14;">"END"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">()){</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC253" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// We have an END; blindly trust it</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC254" class="line" lang="cpp">            <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC255" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"END"</span><span class="p">)){</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC256" class="line" lang="cpp">                <span class="c1" style="color: #998; font-style: italic;">// Get the latest one defined.</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC257" class="line" lang="cpp">                <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max</span><span class="p">(</span><span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">stoi</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)),</span> <span class="n" style="color: #333;">end</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC258" class="line" lang="cpp">            <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC259" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// Convert to 0-based.</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC260" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC261" class="line" lang="cpp">            </span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC262" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC263" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="s" style="color: #d14;">"SVLEN"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">()){</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC264" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// There's no endpoint, but we know an SVLEN.</span></span>

</pre>

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC265" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// A negative SVLEN means a deletion, so if we find one we can say we delete that much.</span></span>

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC266" class="line" lang="cpp">            <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">deleted</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC267" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"SVLEN"</span><span class="p">)){</span></span>

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<pre style="margin: 0;">+<span id="LC268" class="line" lang="cpp">                <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alt_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stoi</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC269" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">alt_len</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">){</span></span>

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC270" class="line" lang="cpp">                    <span class="c1" style="color: #998; font-style: italic;">// Not a deletion, so doesn't affect any ref bases</span></span>

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC271" class="line" lang="cpp">                    <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC272" class="line" lang="cpp">                <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC273" class="line" lang="cpp">                <span class="n" style="color: #333;">deleted</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">alt_len</span><span class="p">,</span> <span class="n" style="color: #333;">deleted</span><span class="p">);</span> </span>

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<pre style="margin: 0;">+<span id="LC274" class="line" lang="cpp">            <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC275" class="line" lang="cpp">            </span>

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<pre style="margin: 0;">+<span id="LC276" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// The anchoring base at POS gets added in (because it isn't</span></span>

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<pre style="margin: 0;">+<span id="LC277" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// deleted) but then subtracted out (because we have to do that to</span></span>

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC278" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// match non-SV deletions). For insertions, deleted is 0 and we</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC279" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// return 0-based POS. Inversions must have an END.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">zeroBasedPosition</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">deleted</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC281" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC282" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC283" class="line" lang="cpp">            <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Warning: insufficient length information for "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC284" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC285" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

173

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<td class="diff-line-num new_line" 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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<pre style="margin: 0;"> <span id="LC286" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

174

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<td class="diff-line-num new_line old" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC174" class="line" lang="cpp"><span class="p"><span class="idiff left right">};</span></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

175

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<td class="diff-line-num new_line old" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC175" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" 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="diff-line-num new_line old" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC176" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Variant</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">is_sv</span></span><span class="p"><span class="idiff right">(){</span></span></span>

</pre>

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<td class="diff-line-num old old_line" 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="diff-line-num new_line old" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC177" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;"><span class="idiff left">this</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">find</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"SVTYPE"</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">this</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">end</span></span><span class="p"><span class="idiff right">()</span>;</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC287" class="line" lang="cpp"><span class="idiff left">    </span><span class="k" style="font-weight: 600;"><span class="idiff">else</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">{</span></span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC288" class="line" lang="cpp">        <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Warning: can't get end of non-canonicalizeable variant "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC289" class="line" lang="cpp"><span class="idiff left">    </span><span class="p"><span class="idiff right">}</span></span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC290" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;"><span class="idiff left">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" 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="diff-line-num new_line" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC291" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

179

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<td class="diff-line-num new_line" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

292

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC292" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" 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">

180

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<td class="diff-line-num new_line 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">

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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="cpp"><span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">get_sv_len</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

181

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<td class="diff-line-num new_line 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">

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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="cpp">        <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">sv_len</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

182

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<td class="diff-line-num new_line 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">

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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="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_sv</span><span class="p">()){</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" 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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<pre style="margin: 0;">-<span id="LC183" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="s" style="color: #d14;">"SVLEN"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">()){</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

184

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<td class="diff-line-num new_line 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">

</td>

<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="cpp">                <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">pre_abs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stol</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"SVLEN"</span><span class="p">][</span><span class="n" style="color: #333;">pos</span><span class="p">]);</span> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

185

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<td class="diff-line-num new_line 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">

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<pre style="margin: 0;">-<span id="LC185" class="line" lang="cpp">                <span class="n" style="color: #333;">sv_len</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;">pre_abs</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

186

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<td class="diff-line-num new_line 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">

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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="cpp">                <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"END"</span><span class="p">][</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</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;">sv_len</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num old old_line" 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">

187

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<td class="diff-line-num new_line 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">

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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="cpp">            <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" 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">

188

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<td class="diff-line-num new_line 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">

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<pre style="margin: 0;">-<span id="LC188" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="s" style="color: #d14;">"END"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">()){</span></span>

</pre>

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<td class="diff-line-num old old_line" 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="diff-line-num new_line 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">

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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="cpp">                <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">pre_abs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stol</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"END"</span><span class="p">][</span><span class="n" style="color: #333;">pos</span><span class="p">])</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

190

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<td class="diff-line-num new_line 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">

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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="cpp">                <span class="n" style="color: #333;">sv_len</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;">pre_abs</span> <span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

191

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<td class="diff-line-num new_line 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">

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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="cpp">                <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"SVTYPE"</span><span class="p">][</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"DEL"</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

192

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<td class="diff-line-num new_line 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">

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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="cpp">                    <span class="n" style="color: #333;">sv_len</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="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sv_len</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" 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="diff-line-num new_line 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">

</td>

<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="cpp">                <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" 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="diff-line-num new_line 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">

</td>

<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="cpp">                <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"SVLEN"</span><span class="p">][</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sv_len</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

195

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<td class="diff-line-num new_line" data-linenumber="293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" 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="diff-line-num new_line 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">

</td>

<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="cpp">                <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" 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="diff-line-num new_line 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">

</td>

<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="cpp">                <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" 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="diff-line-num new_line 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="LC198" class="line" lang="cpp">                    <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"NO SV LENGTH INFO"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

</td>

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199

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<td class="diff-line-num new_line 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">

</td>

<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="cpp">                    <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1999</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" 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="diff-line-num new_line 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">

</td>

<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="cpp">                <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

201

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<td class="diff-line-num new_line" data-linenumber="294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

294

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC294" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" 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="diff-line-num new_line 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">

</td>

<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="cpp">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sv_len</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" 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="diff-line-num new_line 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">

</td>

<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="cpp">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" 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="diff-line-num new_line 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">

</td>

<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="cpp">        <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" 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="diff-line-num new_line 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">

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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="cpp">            <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"NOT A STRUCTURAL VARIANT"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" 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="diff-line-num new_line 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">

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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="cpp">            <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1872</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" 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="diff-line-num new_line 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">

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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="cpp">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

208

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<td class="diff-line-num new_line 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">

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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="cpp"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" 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="diff-line-num new_line" data-linenumber="295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

295

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<pre style="margin: 0;"> <span id="LC295" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

210

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<td class="diff-line-num new_line old" data-linenumber="296" style="width: 35px; color: rgba(0,0,0,0.3); 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="cpp"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int64_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Variant</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">get_sv_end</span></span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pos</span></span><span class="p"><span class="idiff right">){</span></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

211

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<td class="diff-line-num new_line old" data-linenumber="296" style="width: 35px; color: rgba(0,0,0,0.3); 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="cpp"><span class="idiff left">    </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">is_sv</span></span><span class="p"><span class="idiff right">()){</span></span></span>

</pre>

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<td class="diff-line-num old old_line" 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="diff-line-num new_line old" data-linenumber="296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<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="cpp"><span class="idiff left">        </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int64_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">slen</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">get_sv_len</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">pos</span></span><span class="p"><span class="idiff right">);</span></span></span>

</pre>

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<td class="diff-line-num old old_line" 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="diff-line-num new_line old" data-linenumber="296" style="width: 35px; color: rgba(0,0,0,0.3); 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="cpp">    <span class="idiff left">    </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">this</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"SVTYPE"</span></span><span class="p"><span class="idiff">][</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"DEL"</span></span><span class="p"><span class="idiff right">){</span></span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

214

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<td class="diff-line-num new_line old" data-linenumber="296" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC214" class="line" lang="cpp">    <span class="idiff left">        </span><span class="k" style="font-weight: 600;"><span class="idiff">return</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">this</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">position</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">slen</span></span><span class="p"><span class="idiff right">);</span></span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

215

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<td class="diff-line-num new_line old" data-linenumber="296" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC215" class="line" lang="cpp">    <span class="idiff left">    </span><span class="p"><span class="idiff right">}</span></span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

216

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<td class="diff-line-num new_line old" data-linenumber="296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC216" class="line" lang="cpp">        <span class="k" style="font-weight: 600;"><span class="idiff left right">else</span></span><span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC217" class="line" lang="cpp">            <span class="k" style="font-weight: 600;"><span class="idiff left">return</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">this</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">position</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">slen</span></span><span class="p"><span class="idiff right">)</span>;</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC296" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">// To canonicalize a variant, we need either both REF and ALT seqs filled in</span></span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC297" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">// or SVTYPE and SVLEN or END or SPAN or SEQ sufficient to define the variant.</span></span></span>

</pre>

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC298" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Variant</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">canonicalizable</span></span><span class="p"><span class="idiff right">(){</span></span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC299" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pre_canon</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">allATGCN</span></span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">this</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">ref</span></span><span class="p"><span class="idiff right">);</span></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC300" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<pre style="margin: 0;">+<span id="LC301" class="line" lang="cpp">    <span class="k" style="font-weight: 600;"><span class="idiff left">for</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">auto</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">a</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">this</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">alt</span></span><span class="p"><span class="idiff right">){</span></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC302" class="line" lang="cpp">        <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff">allATGCN</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">a</span></span><span class="p"><span class="idiff right">))</span>{</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC303" class="line" lang="cpp">            <span class="n" style="color: #333;"><span class="idiff left">pre_canon</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">false</span></span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC304" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC305" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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">

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<pre style="margin: 0;">+<span id="LC306" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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">

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<pre style="margin: 0;">+<span id="LC307" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pre_canon</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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">

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<pre style="margin: 0;">+<span id="LC308" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// It came in in a fully specified way.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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">

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<pre style="margin: 0;">+<span id="LC309" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// TODO: ideally, we'd check to make sure ref/alt lengths, svtypes, and ends line up right here.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC310" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC311" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC312" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC313" class="line" lang="cpp">    <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">svtype</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getSVTYPE</span><span class="p">();</span></span>

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC314" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC315" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">svtype</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()){</span></span>

</pre>

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC316" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// We have no SV type, so we can't interpret things.</span></span>

</pre>

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC317" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC318" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC319" class="line" lang="cpp">    </span>

</pre>

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<pre style="margin: 0;">+<span id="LC320" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Check the tags</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC321" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">has_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"SVLEN"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"SVLEN"</span><span class="p">).</span><span class="n" style="color: #333;">empty</span><span class="p">();</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC322" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">has_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"SEQ"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"SEQ"</span><span class="p">).</span><span class="n" style="color: #333;">empty</span><span class="p">();</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC323" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">has_span</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</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><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"SPAN"</span><span class="p">).</span><span class="n" style="color: #333;">empty</span><span class="p">();</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC324" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">has_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"END"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"END"</span><span class="p">).</span><span class="n" style="color: #333;">empty</span><span class="p">();</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC325" class="line" lang="cpp">    </span>

</pre>

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<pre style="margin: 0;">+<span id="LC326" class="line" lang="cpp">    </span>

</pre>

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<pre style="margin: 0;">+<span id="LC327" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">svtype</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"INS"</span><span class="p">){</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC328" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// Insertions need a SEQ, SVLEN, or SPAN</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC329" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">has_seq</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">has_len</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">has_span</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

330

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<pre style="margin: 0;">+<span id="LC330" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC331" class="line" lang="cpp">    <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;">svtype</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"DEL"</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

332

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<pre style="margin: 0;">+<span id="LC332" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// Deletions need an SVLEN, SPAN, or END</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

333

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<pre style="margin: 0;">+<span id="LC333" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">has_len</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">has_span</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">has_end</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC334" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

335

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<pre style="margin: 0;">+<span id="LC335" class="line" lang="cpp">    <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;">svtype</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"INV"</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

336

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<pre style="margin: 0;">+<span id="LC336" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// Inversions need a SPAN or END</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

337

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<pre style="margin: 0;">+<span id="LC337" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">has_span</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">has_end</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

338

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<pre style="margin: 0;">+<span id="LC338" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

220

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<td class="diff-line-num new_line" data-linenumber="339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

339

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<pre style="margin: 0;"> <span id="LC339" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

221

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<td class="diff-line-num new_line old" data-linenumber="340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC221" class="line" lang="cpp">        <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"VARIANT MUST BE SV"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

222

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<td class="diff-line-num new_line old" data-linenumber="340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC222" class="line" lang="cpp">        <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">99829</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC340" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// Other SV types are unsupported</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC341" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// TODO: DUP</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" 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="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

223

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<td class="diff-line-num new_line" data-linenumber="343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

343

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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="cpp">    <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

224

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<td class="diff-line-num new_line" data-linenumber="344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

344

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<pre style="margin: 0;"> <span id="LC344" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

225

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<td class="diff-line-num new_line" data-linenumber="345" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

345

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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="cpp"></span>

</pre>

</td>

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<pre style="margin: 0;">-<span id="LC226" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">canonicalize<span class="idiff left">_sv</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">FastaReference</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fasta_reference</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">vector</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">FastaReference</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">insertions</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">place_seq</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">max_interval</span></span><span class="p">){</span></span>

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<pre style="margin: 0;">+<span id="LC346" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">canonicalize</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">FastaReference</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fasta_reference</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">vector</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">FastaReference</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">insertions</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">place_seq</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">min_size</span></span><span class="p">){</span></span>

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<td class="diff-line-num old_line" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC347" class="line" lang="cpp">    </span>

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<pre style="margin: 0;">-<span id="LC228" class="line" lang="cpp">            <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">variant_acceptable</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

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<td class="diff-line-num old old_line" 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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<pre style="margin: 0;">-<span id="LC229" class="line" lang="cpp">            <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">do_external_insertions</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">insertions</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC230" class="line" lang="cpp">            <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">sv_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC231" class="line" lang="cpp">            <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">var_is_sv</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC232" class="line" lang="cpp"></span>

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<td class="diff-line-num old old_line" data-linenumber="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC233" class="line" lang="cpp">            <span class="n" style="color: #333;">FastaReference</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insertion_fasta</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC234" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC235" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef DEBUG</span></span>

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<pre style="margin: 0;">-<span id="LC236" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">do_external_insertions</span><span class="p">){</span></span>

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<pre style="margin: 0;">-<span id="LC237" class="line" lang="cpp">                <span class="n" style="color: #333;">insertion_fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">insertions</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC238" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">insertion_fasta</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sequenceNames</span><span class="p">){</span></span>

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<pre style="margin: 0;">-<span id="LC239" class="line" lang="cpp">                    <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC240" class="line" lang="cpp">                <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC348" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Nobody should call this without checking</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

349

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<pre style="margin: 0;">+<span id="LC349" class="line" lang="cpp">    <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">canonicalizable</span><span class="p">());</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

350

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<pre style="margin: 0;">+<span id="LC350" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC351" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Nobody should call this twice</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

352

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<pre style="margin: 0;">+<span id="LC352" class="line" lang="cpp">    <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">canonical</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC353" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="354" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC354" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Find where the inserted sequence can come from for insertions</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC355" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">do_external_insertions</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">insertions</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

356

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<pre style="margin: 0;">+<span id="LC356" class="line" lang="cpp">    <span class="n" style="color: #333;">FastaReference</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">insertion_fasta</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

357

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<pre style="margin: 0;">+<span id="LC357" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">do_external_insertions</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC358" class="line" lang="cpp">        <span class="n" style="color: #333;">insertion_fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">insertions</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC359" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

360

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<pre style="margin: 0;">+<span id="LC360" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC361" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">ref_valid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">allATGCN</span><span class="p">(</span><span class="n" style="color: #333;">ref</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC362" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="363" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

363

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<pre style="margin: 0;">+<span id="LC363" 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;">ref_valid</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">place_seq</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC364" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// If the reference is invalid, and we aren't allowed to change the ref sequence,</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC365" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// we can't canonicalize the variant.</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC366" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

367

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<pre style="margin: 0;">+<span id="LC367" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

368

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<pre style="margin: 0;">+<span id="LC368" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="369" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

369

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<pre style="margin: 0;">+<span id="LC369" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Check the alts to see if they are not symbolic</span></span>

</pre>

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC370" class="line" lang="cpp">    <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">alt_i_atgcn</span> <span class="p">(</span><span class="n" style="color: #333;">alt</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC371" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">alt</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

372

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<pre style="margin: 0;">+<span id="LC372" class="line" lang="cpp">        <span class="n" style="color: #333;">alt_i_atgcn</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;">allATGCN</span><span class="p">(</span><span class="n" style="color: #333;">alt</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC373" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC374" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC375" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Only allow single-alt variants</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC376" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">single_alt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alt</span><span class="p">.</span><span class="n" style="color: #333;">size</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>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC377" 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;">single_alt</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC378" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// TODO: this will need to be remove before supporting multiple alleles</span></span>

</pre>

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC379" class="line" lang="cpp">        <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Warning: multiple ALT alleles not yet allowed for SVs"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

380

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<pre style="margin: 0;">+<span id="LC380" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC381" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC382" class="line" lang="cpp">    </span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC383" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Fill in the SV tags</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC384" class="line" lang="cpp">    <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">svtype</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getSVTYPE</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC385" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">has_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"SVLEN"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"SVLEN"</span><span class="p">).</span><span class="n" style="color: #333;">empty</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC386" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">has_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"SEQ"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"SEQ"</span><span class="p">).</span><span class="n" style="color: #333;">empty</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC387" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">has_span</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</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><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"SPAN"</span><span class="p">).</span><span class="n" style="color: #333;">empty</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

388

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<pre style="margin: 0;">+<span id="LC388" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">has_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"END"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"END"</span><span class="p">).</span><span class="n" style="color: #333;">empty</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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

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<pre style="margin: 0;">+<span id="LC389" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC390" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Where is the end, or where should it be?</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC391" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">info_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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

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<pre style="margin: 0;">+<span id="LC392" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">has_end</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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

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<pre style="margin: 0;">+<span id="LC393" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// Get the END from the tag</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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

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<pre style="margin: 0;">+<span id="LC394" class="line" lang="cpp">        <span class="n" style="color: #333;">info_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stol</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"END"</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]);</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC395" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

396

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<pre style="margin: 0;">+<span id="LC396" class="line" lang="cpp">    <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;">ref_valid</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">place_seq</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

397

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<pre style="margin: 0;">+<span id="LC397" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// Get the END from the reference sequence, which is ready.</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC398" class="line" lang="cpp">        <span class="n" style="color: #333;">info_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</span> <span class="o" style="font-weight: 600;">+</span> <span class="k" style="font-weight: 600;">this</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;">length</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>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC399" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

400

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<pre style="margin: 0;">+<span id="LC400" class="line" lang="cpp">    <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;">svtype</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"DEL"</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">svtype</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"INV"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">has_span</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

401

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<pre style="margin: 0;">+<span id="LC401" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// For deletions and inversions, we can get the END from the SPAN</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

402

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC402" class="line" lang="cpp">        <span class="n" style="color: #333;">info_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</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;">stol</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"SPAN"</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]));</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

403

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<pre style="margin: 0;">+<span id="LC403" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

404

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<pre style="margin: 0;">+<span id="LC404" class="line" lang="cpp">    <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;">svtype</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"DEL"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">has_len</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

405

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<pre style="margin: 0;">+<span id="LC405" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// For deletions, we can get the END from the SVLEN</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

406

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<pre style="margin: 0;">+<span id="LC406" class="line" lang="cpp">        <span class="n" style="color: #333;">info_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</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;">stol</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"SVLEN"</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]));</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

407

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<pre style="margin: 0;">+<span id="LC407" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

408

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<pre style="margin: 0;">+<span id="LC408" class="line" lang="cpp">    <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;">svtype</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"INS"</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

409

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<pre style="margin: 0;">+<span id="LC409" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// For insertions, END is just POS if not specified</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

410

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC410" class="line" lang="cpp">        <span class="n" style="color: #333;">info_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

411

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC411" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" 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="cpp">    <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" 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="cpp">        <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Warning: could not set END info "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" 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="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" 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="cpp">    <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC416" class="line" lang="cpp">    </span>

</pre>

</td>

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC417" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Commit back the END</span></span>

</pre>

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC418" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"END"</span><span class="p">].</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

419

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<pre style="margin: 0;">+<span id="LC419" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"END"</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;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">info_end</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

420

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<pre style="margin: 0;">+<span id="LC420" class="line" lang="cpp">    <span class="n" style="color: #333;">has_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC421" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="422" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC422" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// What is the variant length change?</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC423" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// We store it as absolute value</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC424" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">info_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC425" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">has_len</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC426" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// Get the SVLEN from the tag</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC427" class="line" lang="cpp">        <span class="n" style="color: #333;">info_len</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;">stol</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"SVLEN"</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]));</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC428" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC429" class="line" lang="cpp">    <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;">svtype</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"INS"</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">svtype</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"DEL"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">has_span</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC430" class="line" lang="cpp">        <span class="n" style="color: #333;">info_len</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;">stol</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"SPAN"</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]));</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC431" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC432" class="line" lang="cpp">    <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;">svtype</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"DEL"</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC433" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// We always have the end by now</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC434" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// Deletion ends give you length change</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC435" class="line" lang="cpp">        <span class="n" style="color: #333;">info_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">info_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC436" class="line" lang="cpp">    <span class="p">}</span> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC437" class="line" lang="cpp">    <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;">svtype</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"INV"</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC438" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// Inversions have 0 length change unless otherwise specified.</span></span>

</pre>

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC439" class="line" lang="cpp">        <span class="n" style="color: #333;">info_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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440

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<pre style="margin: 0;">+<span id="LC440" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="441" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

441

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<pre style="margin: 0;">+<span id="LC441" class="line" lang="cpp">    <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;">svtype</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"INS"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">has_seq</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC442" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// Insertions can let us pick it up from the SEQ tag</span></span>

</pre>

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC443" class="line" lang="cpp">        <span class="n" style="color: #333;">info_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"SEQ"</span><span class="p">).</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">).</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC444" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC445" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC446" class="line" lang="cpp">        <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Warning: could not set SVLEN info "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC447" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC448" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC449" class="line" lang="cpp">    </span>

</pre>

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<pre style="margin: 0;">+<span id="LC450" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Commit the SVLEN back</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="451" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC451" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">svtype</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"DEL"</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="452" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

452

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<pre style="margin: 0;">+<span id="LC452" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// Should be saved as negative</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="453" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

453

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<pre style="margin: 0;">+<span id="LC453" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"SVLEN"</span><span class="p">].</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="454" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

454

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<pre style="margin: 0;">+<span id="LC454" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"SVLEN"</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;">to_string</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">info_len</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="455" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

455

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<pre style="margin: 0;">+<span id="LC455" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="456" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

456

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<pre style="margin: 0;">+<span id="LC456" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="457" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

457

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<pre style="margin: 0;">+<span id="LC457" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// Should be saved as positive</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="458" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

458

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<pre style="margin: 0;">+<span id="LC458" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"SVLEN"</span><span class="p">].</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

459

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<pre style="margin: 0;">+<span id="LC459" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"SVLEN"</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;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">info_len</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="460" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

460

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<pre style="margin: 0;">+<span id="LC460" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="461" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

461

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<pre style="margin: 0;">+<span id="LC461" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Now the length change is known</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="462" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

462

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<pre style="margin: 0;">+<span id="LC462" class="line" lang="cpp">    <span class="n" style="color: #333;">has_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

463

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<pre style="margin: 0;">+<span id="LC463" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="464" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC464" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// We also compute a span</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="465" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC465" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">info_span</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="466" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

466

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<pre style="margin: 0;">+<span id="LC466" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">has_span</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="467" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC467" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// Use the specified span</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="468" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC468" class="line" lang="cpp">        <span class="n" style="color: #333;">info_span</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;">stol</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"SVLEN"</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]));</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="469" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

469

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<pre style="margin: 0;">+<span id="LC469" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="470" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC470" class="line" lang="cpp">    <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;">svtype</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"INS"</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">svtype</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"DEL"</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="471" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

471

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<pre style="margin: 0;">+<span id="LC471" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// has_len is always true here</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="472" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

472

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<pre style="margin: 0;">+<span id="LC472" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// Insertions and deletions let us determine the span from the length change, unless they are complex.</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="473" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

473

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<pre style="margin: 0;">+<span id="LC473" class="line" lang="cpp">        <span class="n" style="color: #333;">info_span</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">info_len</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="474" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

474

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<pre style="margin: 0;">+<span id="LC474" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="475" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

475

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<pre style="margin: 0;">+<span id="LC475" class="line" lang="cpp">    <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;">svtype</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"INV"</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="476" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

476

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<pre style="margin: 0;">+<span id="LC476" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// has_end is always true here</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

477

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<pre style="margin: 0;">+<span id="LC477" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// Inversion span is start to end</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="478" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

478

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<pre style="margin: 0;">+<span id="LC478" class="line" lang="cpp">        <span class="n" style="color: #333;">info_span</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">info_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

479

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<pre style="margin: 0;">+<span id="LC479" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="480" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

480

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<pre style="margin: 0;">+<span id="LC480" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

481

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<pre style="margin: 0;">+<span id="LC481" class="line" lang="cpp">        <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Warning: could not set SPAN info "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="482" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

482

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC482" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

483

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<pre style="margin: 0;">+<span id="LC483" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

484

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC484" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

485

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<pre style="margin: 0;">+<span id="LC485" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Commit the SPAN back</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="486" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

486

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<pre style="margin: 0;">+<span id="LC486" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"SPAN"</span><span class="p">].</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

487

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC487" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"SPAN"</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;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">info_span</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

488

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<pre style="margin: 0;">+<span id="LC488" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Now the span change is known</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

489

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<pre style="margin: 0;">+<span id="LC489" class="line" lang="cpp">    <span class="n" style="color: #333;">has_span</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

490

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<pre style="margin: 0;">+<span id="LC490" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

491

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<pre style="margin: 0;">+<span id="LC491" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">info_end</span> <span class="o" style="font-weight: 600;"><</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

492

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<pre style="margin: 0;">+<span id="LC492" class="line" lang="cpp">        <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Warning: SV END is before POS [canonicalize] "</span> <span class="o" style="font-weight: 600;"><<</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

493

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<pre style="margin: 0;">+<span id="LC493" class="line" lang="cpp">        <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"END: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">info_end</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"  "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"POS: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

494

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<pre style="margin: 0;">+<span id="LC494" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

495

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<pre style="margin: 0;">+<span id="LC495" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

496

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<pre style="margin: 0;">+<span id="LC496" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

497

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<pre style="margin: 0;">+<span id="LC497" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">has_seq</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

498

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<pre style="margin: 0;">+<span id="LC498" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// Force the SEQ to upper case, if already present</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

499

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<pre style="margin: 0;">+<span id="LC499" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"SEQ"</span><span class="p">].</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

500

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<pre style="margin: 0;">+<span id="LC500" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"SEQ"</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;">toUpper</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"SEQ"</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

501

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<pre style="margin: 0;">+<span id="LC501" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="502" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

502

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<pre style="margin: 0;">+<span id="LC502" class="line" lang="cpp">     </span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

503

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<pre style="margin: 0;">+<span id="LC503" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Set the other necessary SV Tags (SVTYPE, SEQ (if insertion))</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

504

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<pre style="margin: 0;">+<span id="LC504" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Also check for agreement in the position tags</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

505

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<pre style="margin: 0;">+<span id="LC505" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">svtype</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"INS"</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

506

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<pre style="margin: 0;">+<span id="LC506" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">info_end</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

507

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<pre style="margin: 0;">+<span id="LC507" class="line" lang="cpp">            <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Warning: insertion END and POS do not agree (complex insertions not canonicalizeable) [canonicalize] "</span> <span class="o" style="font-weight: 600;"><<</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

508

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<pre style="margin: 0;">+<span id="LC508" class="line" lang="cpp">            <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"END: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">info_end</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"  "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"POS: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="509" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

509

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<pre style="margin: 0;">+<span id="LC509" class="line" lang="cpp">            </span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

510

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<pre style="margin: 0;">+<span id="LC510" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">info_end</span> <span class="o" style="font-weight: 600;">==</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">info_len</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

511

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<pre style="margin: 0;">+<span id="LC511" class="line" lang="cpp">                <span class="c1" style="color: #998; font-style: italic;">// We can probably guess what they meant here.</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

512

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<pre style="margin: 0;">+<span id="LC512" class="line" lang="cpp">                <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Warning: VCF writer incorrecty produced END = POS + SVLEN for an insertion. Fixing END to POS."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

513

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<pre style="margin: 0;">+<span id="LC513" class="line" lang="cpp">                <span class="n" style="color: #333;">info_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

514

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<pre style="margin: 0;">+<span id="LC514" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"END"</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;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">info_end</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

515

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<pre style="margin: 0;">+<span id="LC515" class="line" lang="cpp">            <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

516

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC516" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

517

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC517" class="line" lang="cpp">            <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

518

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<pre style="margin: 0;">+<span id="LC518" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

519

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC519" class="line" lang="cpp">        </span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

520

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC520" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">info_len</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">info_span</span><span class="p">){</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

521

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC521" class="line" lang="cpp">            <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Warning: insertion SVLEN and SPAN do not agree (complex insertions not canonicalizeable) [canonicalize] "</span> <span class="o" style="font-weight: 600;"><<</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

522

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<pre style="margin: 0;">+<span id="LC522" class="line" lang="cpp">            <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"SVLEN: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">info_len</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"  "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"SPAN: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">info_span</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

523

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<pre style="margin: 0;">+<span id="LC523" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

524

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<pre style="margin: 0;">+<span id="LC524" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

525

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<pre style="margin: 0;">+<span id="LC525" class="line" lang="cpp">       </span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

526

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<pre style="margin: 0;">+<span id="LC526" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">has_seq</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">allATGCN</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"SEQ"</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="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"SEQ"</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">info_len</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

527

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<pre style="margin: 0;">+<span id="LC527" class="line" lang="cpp">            <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Warning: insertion SVLEN and SEQ do not agree (complex insertions not canonicalizeable) [canonicalize] "</span> <span class="o" style="font-weight: 600;"><<</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

528

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<pre style="margin: 0;">+<span id="LC528" class="line" lang="cpp">            <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"SVLEN: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">info_len</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"  "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"SEQ length: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"SEQ"</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

529

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<pre style="margin: 0;">+<span id="LC529" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

530

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC530" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

531

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<pre style="margin: 0;">+<span id="LC531" class="line" lang="cpp">       </span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

532

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<pre style="margin: 0;">+<span id="LC532" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// Set REF</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

533

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<pre style="margin: 0;">+<span id="LC533" class="line" lang="cpp">        <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">ref_base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">toUpper</span><span class="p">(</span><span class="n" style="color: #333;">fasta_reference</span><span class="p">.</span><span class="n" style="color: #333;">getSubSequence</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sequenceName</span><span class="p">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">zeroBasedPosition</span><span class="p">(),</span> <span class="mi" style="color: #099;">1</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

534

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<pre style="margin: 0;">+<span id="LC534" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">place_seq</span><span class="p">){</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

535

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC535" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">this</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;">assign</span><span class="p">(</span><span class="n" style="color: #333;">ref_base</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

536

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC536" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

537

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC537" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

538

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<pre style="margin: 0;">+<span id="LC538" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">has_seq</span> <span class="o" style="font-weight: 600;">&&</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

539

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<pre style="margin: 0;">+<span id="LC539" class="line" lang="cpp">                 <span class="n" style="color: #333;">alt</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="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"SEQ"</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>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

540

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<pre style="margin: 0;">+<span id="LC540" class="line" lang="cpp">                 <span class="n" style="color: #333;">allATGCN</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"SEQ"</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">])){</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

541

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<pre style="margin: 0;">+<span id="LC541" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// Try to remove prepended ref sequence, assuming it's left-aligned</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

542

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<pre style="margin: 0;">+<span id="LC542" class="line" lang="cpp">            <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alt</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

543

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<pre style="margin: 0;">+<span id="LC543" class="line" lang="cpp">            <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">toUpper</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</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;">length</span><span class="p">()));</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

544

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<pre style="margin: 0;">+<span id="LC544" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"SEQ"</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="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">place_seq</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

545

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<pre style="margin: 0;">+<span id="LC545" class="line" lang="cpp">                <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Warning: INS sequence in alt field does not match SEQ tag"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span> <span class="o" style="font-weight: 600;"><<</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

546

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<pre style="margin: 0;">+<span id="LC546" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alt</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="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"SEQ"</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;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

547

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<pre style="margin: 0;">+<span id="LC547" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

241

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<td class="diff-line-num new_line" data-linenumber="548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

548

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC548" class="line" lang="cpp">            <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" 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="diff-line-num new_line 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">

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<pre style="margin: 0;">-<span id="LC242" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

549

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC549" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">place_seq</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

550

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC550" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alt</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">assign</span><span class="p">(</span> <span class="n" style="color: #333;">ref_base</span> <span class="o" style="font-weight: 600;">+</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"SEQ"</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

551

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<pre style="margin: 0;">+<span id="LC551" class="line" lang="cpp">            <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

552

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<pre style="margin: 0;">+<span id="LC552" class="line" lang="cpp">            </span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="553" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

553

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<pre style="margin: 0;">+<span id="LC553" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="554" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

554

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<pre style="margin: 0;">+<span id="LC554" class="line" lang="cpp">        <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;">alt_i_atgcn</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="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">has_seq</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

555

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC555" class="line" lang="cpp">            <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alt</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

556

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC556" class="line" lang="cpp">            <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">toUpper</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</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;">length</span><span class="p">()));</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

557

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC557" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"SEQ"</span><span class="p">].</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

558

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC558" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"SEQ"</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

559

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<pre style="margin: 0;">+<span id="LC559" class="line" lang="cpp">            </span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

560

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC560" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">info_len</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

561

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<pre style="margin: 0;">+<span id="LC561" class="line" lang="cpp">                <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Warning: insertion SVLEN and added bases do not agree (complex insertions not canonicalizeable) [canonicalize] "</span> <span class="o" style="font-weight: 600;"><<</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

562

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC562" class="line" lang="cpp">                <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"SVLEN: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">info_len</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"  "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"added bases: "</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;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

563

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC563" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

564

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC564" class="line" lang="cpp">            <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

565

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC565" class="line" lang="cpp">            </span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

566

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC566" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

567

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC567" class="line" lang="cpp">        <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;">alt</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="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'<'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">do_external_insertions</span><span class="p">){</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

243

</td>

<td class="diff-line-num new_line" data-linenumber="568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

568

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC568" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

569

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC569" class="line" lang="cpp">            <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">ins_seq</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

570

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<pre style="margin: 0;">+<span id="LC570" class="line" lang="cpp">            <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">seq_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alt</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">alt</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">size</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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

244

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<td class="diff-line-num new_line" data-linenumber="571" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

571

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<pre style="margin: 0;"> <span id="LC571" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" 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="diff-line-num new_line old" data-linenumber="572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC245" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">function</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</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;">allATGC</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[](</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">s</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

246

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<td class="diff-line-num new_line old" data-linenumber="572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC246" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">const_iterator</span> <span class="n" style="color: #333;">c</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;">begin</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;">s</span><span class="p">.</span><span class="n" style="color: #333;">end</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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

247

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<td class="diff-line-num new_line old" data-linenumber="572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC247" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">c</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

248

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<td class="diff-line-num new_line old" data-linenumber="572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC248" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'A'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'T'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'G'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'C'</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

572

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC572" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">insertion_fasta</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">seq_id</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">insertion_fasta</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">end</span><span class="p">()){</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

573

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<pre style="margin: 0;">+<span id="LC573" class="line" lang="cpp">                <span class="n" style="color: #333;">ins_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">toUpper</span><span class="p">(</span><span class="n" style="color: #333;">insertion_fasta</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getSequence</span><span class="p">(</span><span class="n" style="color: #333;">seq_id</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="574" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

574

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC574" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">allATGCN</span><span class="p">(</span><span class="n" style="color: #333;">ins_seq</span><span class="p">)){</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="575" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

575

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC575" class="line" lang="cpp">                    <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"SEQ"</span><span class="p">].</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

576

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC576" class="line" lang="cpp">                    <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"SEQ"</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">ins_seq</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

577

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC577" class="line" lang="cpp">                    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">place_seq</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

578

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC578" class="line" lang="cpp">                        <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alt</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">ref_base</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ins_seq</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

579

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<pre style="margin: 0;">+<span id="LC579" class="line" lang="cpp">                    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

580

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC580" class="line" lang="cpp">                <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

581

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC581" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

582

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC582" class="line" lang="cpp">                    <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Warning: Loaded invalid alt sequence for: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

583

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC583" class="line" lang="cpp">                    <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span>    </span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

584

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC584" class="line" lang="cpp">                <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

585

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC585" class="line" lang="cpp">                </span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

586

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC586" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ins_seq</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">info_len</span><span class="p">){</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

587

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC587" class="line" lang="cpp">                    <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Warning: insertion SVLEN and FASTA do not agree (complex insertions not canonicalizeable) [canonicalize] "</span> <span class="o" style="font-weight: 600;"><<</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

588

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC588" class="line" lang="cpp">                    <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"SVLEN: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">info_len</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"  "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"FASTA bases: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">ins_seq</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

589

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC589" class="line" lang="cpp">                    <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

590

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC590" class="line" lang="cpp">                <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

591

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC591" class="line" lang="cpp">            <span class="p">}</span> </span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

592

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC592" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

593

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC593" class="line" lang="cpp">                <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Warning: could not locate alt sequence for: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

594

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC594" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

595

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC595" class="line" lang="cpp">            <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

596

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC596" class="line" lang="cpp">            </span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

597

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC597" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

598

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC598" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

599

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<pre style="margin: 0;">+<span id="LC599" class="line" lang="cpp">            <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Warning: could not set SEQ [canonicalize]. "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

249

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<td class="diff-line-num new_line" data-linenumber="600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

600

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<pre style="margin: 0;"> <span id="LC600" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_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">

250

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<td class="diff-line-num new_line" data-linenumber="601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

601

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<pre style="margin: 0;"> <span id="LC601" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

251

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<td class="diff-line-num new_line" data-linenumber="602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

602

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<pre style="margin: 0;"> <span id="LC602" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

252

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<td class="diff-line-num new_line old" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC252" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" 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="diff-line-num new_line old" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC253" class="line" lang="cpp">    <span class="p">};</span></span>

</pre>

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<td class="diff-line-num old old_line" 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="diff-line-num new_line old" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC254" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" 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="LC255" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" 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">

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<pre style="margin: 0;">-<span id="LC256" class="line" lang="cpp">    <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">function</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</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;">revcomp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[](</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">s</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old old_line" 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">

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<pre style="margin: 0;">-<span id="LC257" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" 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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<pre style="margin: 0;">-<span id="LC258" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">len</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;">length</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

259

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<td class="diff-line-num new_line old" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC259" class="line" lang="cpp">        <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;">ret</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;">char</span><span class="p">[</span><span class="n" style="color: #333;">len</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old old_line" 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">

260

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<td class="diff-line-num new_line old" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC260" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">rev_arr</span> <span class="p">[</span><span class="mi" style="color: #099;">26</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="mi" style="color: #099;">84</span><span class="p">,</span> <span class="mi" style="color: #099;">66</span><span class="p">,</span> <span class="mi" style="color: #099;">71</span><span class="p">,</span> <span class="mi" style="color: #099;">68</span><span class="p">,</span> <span class="mi" style="color: #099;">69</span><span class="p">,</span> <span class="mi" style="color: #099;">70</span><span class="p">,</span> <span class="mi" style="color: #099;">67</span><span class="p">,</span> <span class="mi" style="color: #099;">72</span><span class="p">,</span> <span class="mi" style="color: #099;">73</span><span class="p">,</span> <span class="mi" style="color: #099;">74</span><span class="p">,</span> <span class="mi" style="color: #099;">75</span><span class="p">,</span> <span class="mi" style="color: #099;">76</span><span class="p">,</span> <span class="mi" style="color: #099;">77</span><span class="p">,</span> <span class="mi" style="color: #099;">78</span><span class="p">,</span> <span class="mi" style="color: #099;">79</span><span class="p">,</span> <span class="mi" style="color: #099;">80</span><span class="p">,</span> <span class="mi" style="color: #099;">81</span><span class="p">,</span> <span class="mi" style="color: #099;">82</span><span class="p">,</span> <span class="mi" style="color: #099;">83</span><span class="p">,</span> <span class="mi" style="color: #099;">65</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

261

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<td class="diff-line-num new_line old" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC261" class="line" lang="cpp">                        <span class="mi" style="color: #099;">85</span><span class="p">,</span> <span class="mi" style="color: #099;">86</span><span class="p">,</span> <span class="mi" style="color: #099;">87</span><span class="p">,</span> <span class="mi" style="color: #099;">88</span><span class="p">,</span> <span class="mi" style="color: #099;">89</span><span class="p">,</span> <span class="mi" style="color: #099;">90</span><span class="p">};</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); 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="diff-line-num new_line old" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC262" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="263" style="width: 35px; color: rgba(0,0,0,0.3); 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="cpp">        <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">>=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">--</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

264

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<td class="diff-line-num new_line old" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<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="cpp">            <span class="n" style="color: #333;">ret</span><span class="p">[</span> <span class="n" style="color: #333;">len</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;">i</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;">char</span><span class="p">)</span> <span class="n" style="color: #333;">rev_arr</span><span class="p">[</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;">s</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">65</span><span class="p">];</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

603

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC603" class="line" lang="cpp">    <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;">svtype</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"DEL"</span><span class="p">){</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

604

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC604" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">info_span</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">info_end</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

605

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC605" class="line" lang="cpp">            <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Warning: deletion END and SVLEN do not agree [canonicalize] "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span> <span class="o" style="font-weight: 600;"><<</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" 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

</td>

<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="cpp">            <span class="s" style="color: #d14;">"END: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">info_end</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"  "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"SVLEN: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">info_len</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

607

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC607" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

265

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<td class="diff-line-num new_line" 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

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC608" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

266

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<td class="diff-line-num new_line old" data-linenumber="609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<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="cpp"></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

267

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<td class="diff-line-num new_line old" data-linenumber="609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<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="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">ret</span><span class="p">,</span> <span class="n" style="color: #333;">len</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

268

</td>

<td class="diff-line-num new_line old" data-linenumber="609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC268" class="line" lang="cpp">        </span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

269

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<td class="diff-line-num new_line old" data-linenumber="609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC269" class="line" lang="cpp"></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

270

</td>

<td class="diff-line-num new_line old" data-linenumber="609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC270" class="line" lang="cpp">    <span class="p">};</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

271

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<td class="diff-line-num new_line old" data-linenumber="609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<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="cpp"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

272

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<td class="diff-line-num new_line old" data-linenumber="609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<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="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_sv</span><span class="p">()){</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

609

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC609" class="line" lang="cpp">    </span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

610

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC610" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">info_span</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">info_end</span><span class="p">){</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

611

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC611" class="line" lang="cpp">            <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Warning: deletion END and SPAN do not agree [canonicalize] "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span> <span class="o" style="font-weight: 600;"><<</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

612

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<pre style="margin: 0;">+<span id="LC612" class="line" lang="cpp">            <span class="s" style="color: #d14;">"END: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">info_end</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"  "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"SPAN: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">info_span</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_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">

273

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<td class="diff-line-num new_line" data-linenumber="613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

613

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<pre style="margin: 0;"> <span id="LC613" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" 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

</td>

<td class="diff-line-num new_line" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

614

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC614" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

615

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC615" class="line" lang="cpp">    </span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

616

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<pre style="margin: 0;">+<span id="LC616" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// Set REF</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

617

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC617" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">place_seq</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

618

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC618" class="line" lang="cpp">            <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">del_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">toUpper</span><span class="p">(</span><span class="n" style="color: #333;">fasta_reference</span><span class="p">.</span><span class="n" style="color: #333;">getSubSequence</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sequenceName</span><span class="p">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">zeroBasedPosition</span><span class="p">(),</span> <span class="n" style="color: #333;">info_len</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

619

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC619" class="line" lang="cpp">            <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">ref_base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">toUpper</span><span class="p">(</span><span class="n" style="color: #333;">fasta_reference</span><span class="p">.</span><span class="n" style="color: #333;">getSubSequence</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sequenceName</span><span class="p">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">zeroBasedPosition</span><span class="p">(),</span> <span class="mi" style="color: #099;">1</span><span class="p">));</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

620

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC620" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">this</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;">assign</span><span class="p">(</span> <span class="n" style="color: #333;">del_seq</span> <span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

621

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC621" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alt</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">assign</span><span class="p">(</span> <span class="n" style="color: #333;">ref_base</span> <span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" 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

</td>

<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="cpp">        <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

623

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC623" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

624

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC624" class="line" lang="cpp">    <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;">svtype</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"INV"</span><span class="p">){</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

625

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC625" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">info_span</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">info_end</span><span class="p">){</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

626

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC626" class="line" lang="cpp">            <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Warning: inversion END and SPAN do not agree [canonicalize] "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span> <span class="o" style="font-weight: 600;"><<</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

627

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC627" class="line" lang="cpp">            <span class="s" style="color: #d14;">"END: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">info_end</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"  "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"SPAN: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">info_span</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

628

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<pre style="margin: 0;">+<span id="LC628" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

629

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC629" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

630

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC630" class="line" lang="cpp">        </span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

631

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<pre style="margin: 0;">+<span id="LC631" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">info_len</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">){</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

632

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC632" class="line" lang="cpp">            <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Warning: inversion SVLEN specifies nonzero length change (complex inversions not canonicalizeable) [canonicalize] "</span> <span class="o" style="font-weight: 600;"><<</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

633

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<pre style="margin: 0;">+<span id="LC633" class="line" lang="cpp">            <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"SVLEN: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">info_len</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

634

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<pre style="margin: 0;">+<span id="LC634" class="line" lang="cpp">            </span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

635

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<pre style="margin: 0;">+<span id="LC635" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">info_end</span> <span class="o" style="font-weight: 600;">==</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">info_len</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

636

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<pre style="margin: 0;">+<span id="LC636" class="line" lang="cpp">                <span class="c1" style="color: #998; font-style: italic;">// We can probably guess what they meant here.</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

637

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<pre style="margin: 0;">+<span id="LC637" class="line" lang="cpp">                <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Warning: VCF writer incorrecty produced END = POS + SVLEN for an inversion. Fixing SVLEN to 0."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

638

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<pre style="margin: 0;">+<span id="LC638" class="line" lang="cpp">                <span class="n" style="color: #333;">info_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

639

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC639" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"SVLEN"</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;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">info_len</span><span class="p">);</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

640

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC640" class="line" lang="cpp">            <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

641

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC641" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

642

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC642" class="line" lang="cpp">            <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

643

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC643" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

644

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC644" class="line" lang="cpp">    </span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

645

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC645" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">place_seq</span><span class="p">){</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

646

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<pre style="margin: 0;">+<span id="LC646" class="line" lang="cpp">            <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">ref_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">toUpper</span><span class="p">(</span><span class="n" style="color: #333;">fasta_reference</span><span class="p">.</span><span class="n" style="color: #333;">getSubSequence</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sequenceName</span><span class="p">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">zeroBasedPosition</span><span class="p">(),</span> <span class="n" style="color: #333;">info_span</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC647" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// Note that inversions still need an anchoring left base at POS</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

648

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<pre style="margin: 0;">+<span id="LC648" class="line" lang="cpp">            <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">inv_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ref_seq</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">reverse_complement</span><span class="p">(</span><span class="n" style="color: #333;">ref_seq</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

649

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<pre style="margin: 0;">+<span id="LC649" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">this</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;">assign</span><span class="p">(</span><span class="n" style="color: #333;">ref_seq</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

650

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<pre style="margin: 0;">+<span id="LC650" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alt</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">inv_seq</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

651

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<pre style="margin: 0;">+<span id="LC651" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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652

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<pre style="margin: 0;"> <span id="LC652" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

653

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<pre style="margin: 0;">+<span id="LC653" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

654

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<pre style="margin: 0;">+<span id="LC654" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC655" class="line" lang="cpp">        <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Warning: invalid SV type [canonicalize]:"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC656" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="657" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC657" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="658" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

658

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<pre style="margin: 0;"> <span id="LC658" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC277" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="s" style="color: #d14;">"SVTYPE"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC278" class="line" lang="cpp">                        <span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"SVTYPE"</span><span class="p">].</span><span class="n" style="color: #333;">empty</span><span class="p">())){</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC279" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC280" class="line" lang="cpp">                    <span class="n" style="color: #333;">var_is_sv</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC281" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC282" class="line" lang="cpp">                    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alt_pos</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;">alt_pos</span> <span class="o" style="font-weight: 600;"><</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alt</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">alt_pos</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num old old_line" 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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<pre style="margin: 0;">-<span id="LC283" class="line" lang="cpp">                        <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alt</span><span class="p">[</span><span class="n" style="color: #333;">alt_pos</span><span class="p">];</span></span>

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<td class="diff-line-num old old_line" data-linenumber="284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC284" class="line" lang="cpp">                            <span class="c1" style="color: #998; font-style: italic;">// These should be normalized-ish</span></span>

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<td class="diff-line-num old old_line" 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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<pre style="margin: 0;">-<span id="LC285" class="line" lang="cpp">                            <span class="c1" style="color: #998; font-style: italic;">// Ref field might be "N"</span></span>

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<td class="diff-line-num old old_line" data-linenumber="286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC286" class="line" lang="cpp">                            <span class="c1" style="color: #998; font-style: italic;">// Alt field could be <INS>, but it *should* be the inserted sequence,</span></span>

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<pre style="margin: 0;">-<span id="LC287" class="line" lang="cpp">                            <span class="c1" style="color: #998; font-style: italic;">// but that might be tucked away in an info field</span></span>

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<pre style="margin: 0;">-<span id="LC288" class="line" lang="cpp">                            <span class="c1" style="color: #998; font-style: italic;">//</span></span>

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<pre style="margin: 0;">-<span id="LC289" class="line" lang="cpp">                            <span class="c1" style="color: #998; font-style: italic;">//</span></span>

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<pre style="margin: 0;">-<span id="LC290" class="line" lang="cpp">                            <span class="c1" style="color: #998; font-style: italic;">// From the VCF4.2 Specs:</span></span>

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<pre style="margin: 0;">-<span id="LC291" class="line" lang="cpp">                            <span class="c1" style="color: #998; font-style: italic;">// END is POS + LEN(REF) - 1</span></span>

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<td class="diff-line-num old old_line" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC292" class="line" lang="cpp">                            <span class="c1" style="color: #998; font-style: italic;">// SVLEN is the difference in length between REF and ALT alleles.</span></span>

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<pre style="margin: 0;">-<span id="LC293" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" 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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<pre style="margin: 0;">-<span id="LC294" class="line" lang="cpp"></span>

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<td class="diff-line-num old old_line" 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">

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<pre style="margin: 0;">-<span id="LC295" 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="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"SVTYPE"</span><span class="p">][</span><span class="n" style="color: #333;">alt_pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"INV"</span> <span class="o" style="font-weight: 600;">||</span></span>

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<pre style="margin: 0;">-<span id="LC296" class="line" lang="cpp">                                        <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"SVTYPE"</span><span class="p">][</span><span class="n" style="color: #333;">alt_pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"DEL"</span> <span class="o" style="font-weight: 600;">||</span></span>

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<pre style="margin: 0;">-<span id="LC297" class="line" lang="cpp">                                        <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"SVTYPE"</span><span class="p">][</span><span class="n" style="color: #333;">alt_pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"INS"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alt</span><span class="p">.</span><span class="n" style="color: #333;">size</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="diff-line-num old old_line" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC298" class="line" lang="cpp">                                <span class="n" style="color: #333;">variant_acceptable</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC299" class="line" lang="cpp">                                <span class="k" style="font-weight: 600;">break</span><span class="p">;</span>                                                                                                                                  </span>

</pre>

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<pre style="margin: 0;">-<span id="LC300" class="line" lang="cpp">                        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" 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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<pre style="margin: 0;">-<span id="LC301" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC302" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC303" class="line" lang="cpp">                        <span class="n" style="color: #333;">sv_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_sv_len</span><span class="p">(</span><span class="n" style="color: #333;">alt_pos</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC304" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC305" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC306" class="line" lang="cpp">                        <span class="cm" style="color: #998; font-style: italic;">/**if (this->info.find("SVLEN") != this->info.end()){</span></span>

</pre>

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<td class="diff-line-num old old_line" 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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<pre style="margin: 0;">-<span id="LC307" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                            int32_t pre_abs = stoi(this->info["SVLEN"][alt_pos]); </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC308" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                            sv_len = abs(pre_abs);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC309" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                            this->info["END"][alt_pos] = this->position + sv_len;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC310" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                        }</span></span>

</pre>

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<td class="diff-line-num old old_line" 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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<pre style="margin: 0;">-<span id="LC311" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                        else if (this->info.find("END") != this->info.end()){</span></span>

</pre>

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<td class="diff-line-num old old_line" 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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<pre style="margin: 0;">-<span id="LC312" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                            int32_t pre_abs = stoi(this->info["END"][alt_pos]) - (this->position);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC313" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                            sv_len = abs( pre_abs );</span></span>

</pre>

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<td class="diff-line-num old old_line" 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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<pre style="margin: 0;">-<span id="LC314" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                            this->info["SVLEN"][alt_pos] = sv_len;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC315" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC316" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                        }</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC317" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                        else{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC318" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                            // If we have neither, we'll ignore it.</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC319" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                            variant_acceptable = false;</span></span>

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<pre style="margin: 0;">-<span id="LC320" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                            break;</span></span>

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<pre style="margin: 0;">-<span id="LC321" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                        }</span></span>

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<pre style="margin: 0;">-<span id="LC322" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                        **/</span></span>

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<pre style="margin: 0;">-<span id="LC323" class="line" lang="cpp">                        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">place_seq</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"SVTYPE"</span><span class="p">][</span><span class="n" style="color: #333;">alt_pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"INS"</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="s" style="color: #d14;">"<INS>"</span><span class="p">)){</span></span>

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<pre style="margin: 0;">-<span id="LC324" class="line" lang="cpp">                            <span class="k" style="font-weight: 600;">this</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;">assign</span><span class="p">(</span><span class="n" style="color: #333;">fasta_reference</span><span class="p">.</span><span class="n" style="color: #333;">getSubSequence</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sequenceName</span><span class="p">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">));</span></span>

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<pre style="margin: 0;">-<span id="LC325" class="line" lang="cpp">                            <span class="c1" style="color: #998; font-style: italic;">//if (this->alt[alt_pos] == "<INS>"){</span></span>

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<pre style="margin: 0;">-<span id="LC326" class="line" lang="cpp">                            <span class="c1" style="color: #998; font-style: italic;">//    variant_acceptable = false;</span></span>

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<pre style="margin: 0;">-<span id="LC327" class="line" lang="cpp">                            <span class="c1" style="color: #998; font-style: italic;">//}</span></span>

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<pre style="margin: 0;">-<span id="LC328" class="line" lang="cpp">                            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">do_external_insertions</span><span class="p">){</span></span>

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<pre style="margin: 0;">-<span id="LC329" class="line" lang="cpp">                                <span class="n" style="color: #333;">insertion_fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">insertions</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>

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<pre style="margin: 0;">-<span id="LC330" class="line" lang="cpp">                                <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">var_name</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC331" class="line" lang="cpp">                                <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">alt</span><span class="p">[</span><span class="n" style="color: #333;">alt_pos</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;">'<'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">alt</span><span class="p">[</span><span class="n" style="color: #333;">alt_pos</span><span class="p">][</span> <span class="n" style="color: #333;">alt</span><span class="p">[</span><span class="n" style="color: #333;">alt_pos</span><span class="p">].</span><span class="n" style="color: #333;">size</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="sc" style="color: #d14;">'>'</span><span class="p">){</span></span>

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<pre style="margin: 0;">-<span id="LC332" class="line" lang="cpp">                                    <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">shortname</span> <span class="p">(</span><span class="n" style="color: #333;">alt</span><span class="p">[</span><span class="n" style="color: #333;">alt_pos</span><span class="p">],</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">alt</span><span class="p">[</span><span class="n" style="color: #333;">alt_pos</span><span class="p">].</span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">2</span> <span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC333" class="line" lang="cpp">                                    <span class="n" style="color: #333;">var_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">shortname</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC334" class="line" lang="cpp">                                <span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC335" class="line" lang="cpp">                                <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC336" class="line" lang="cpp">                                    <span class="n" style="color: #333;">var_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alt</span><span class="p">[</span><span class="n" style="color: #333;">alt_pos</span><span class="p">];</span> </span>

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<pre style="margin: 0;">-<span id="LC337" class="line" lang="cpp">                                <span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC338" class="line" lang="cpp">                                <span class="cp" style="color: #999; font-weight: 600;">#ifdef DEBUG</span></span>

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<td class="diff-line-num old old_line" data-linenumber="339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC339" class="line" lang="cpp">                                    <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"My variant name is: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">var_name</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC340" class="line" lang="cpp">                                <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>

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<td class="diff-line-num old old_line" data-linenumber="341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC341" class="line" lang="cpp">                                <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">insertion_fasta</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">var_name</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">insertion_fasta</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">end</span><span class="p">()){</span></span>

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<pre style="margin: 0;">-<span id="LC342" class="line" lang="cpp">                                    <span class="k" style="font-weight: 600;">this</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;">assign</span><span class="p">(</span><span class="n" style="color: #333;">fasta_reference</span><span class="p">.</span><span class="n" style="color: #333;">getSubSequence</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sequenceName</span><span class="p">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span> <span class="p">));</span></span>

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<pre style="margin: 0;">-<span id="LC343" class="line" lang="cpp">                                    <span class="cp" style="color: #999; font-weight: 600;">#ifdef DEBUG</span></span>

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<pre style="margin: 0;">-<span id="LC344" class="line" lang="cpp">                                        <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Replacing insertion with sequence of "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">var_name</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC345" class="line" lang="cpp">                                    <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>

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<pre style="margin: 0;">-<span id="LC346" class="line" lang="cpp">                                    <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alt</span><span class="p">[</span><span class="n" style="color: #333;">alt_pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fasta_reference</span><span class="p">.</span><span class="n" style="color: #333;">getSubSequence</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sequenceName</span><span class="p">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">insertion_fasta</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getSequence</span><span class="p">(</span><span class="n" style="color: #333;">var_name</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC347" class="line" lang="cpp">                                    <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">updateAlleleIndexes</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC348" class="line" lang="cpp">                                <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC349" class="line" lang="cpp">                            <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC350" class="line" lang="cpp">                            <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;">allATGC</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">)){</span></span>

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<td class="diff-line-num old old_line" data-linenumber="351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC351" class="line" lang="cpp">                                <span class="c1" style="color: #998; font-style: italic;">// we don't have to do anything - our INS is already in the correct format!</span></span>

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<pre style="margin: 0;">-<span id="LC352" class="line" lang="cpp">                            <span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC353" class="line" lang="cpp">                            <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC354" class="line" lang="cpp">                                <span class="n" style="color: #333;">variant_acceptable</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC355" class="line" lang="cpp">                            <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC356" class="line" lang="cpp">                        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC357" class="line" lang="cpp">                        <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;">place_seq</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"<DEL>"</span> <span class="o" style="font-weight: 600;">||</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"SVTYPE"</span><span class="p">][</span><span class="n" style="color: #333;">alt_pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"DEL"</span><span class="p">)){</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC358" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC359" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC360" class="line" lang="cpp">                            <span class="k" style="font-weight: 600;">this</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;">assign</span><span class="p">(</span><span class="n" style="color: #333;">fasta_reference</span><span class="p">.</span><span class="n" style="color: #333;">getSubSequence</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sequenceName</span><span class="p">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</span><span class="p">,</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sv_len</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>

</pre>

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<pre style="margin: 0;">-<span id="LC361" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC362" class="line" lang="cpp">                            <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alt</span><span class="p">[</span><span class="n" style="color: #333;">alt_pos</span><span class="p">].</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="n" style="color: #333;">fasta_reference</span><span class="p">.</span><span class="n" style="color: #333;">getSubSequence</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sequenceName</span><span class="p">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">));</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC363" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC364" class="line" lang="cpp">                            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="k" style="font-weight: 600;">this</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;">size</span><span class="p">()</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;">1</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sv_len</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>

</pre>

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<pre style="margin: 0;">-<span id="LC365" class="line" lang="cpp">                                <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Variant made is incorrect size"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="366" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC366" class="line" lang="cpp">                                <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="k" style="font-weight: 600;">this</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;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">sv_len</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC367" class="line" lang="cpp">                                <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="k" style="font-weight: 600;">this</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;">this</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;">size</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="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC368" class="line" lang="cpp">                                <span class="n" style="color: #333;">variant_acceptable</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC369" class="line" lang="cpp">                            <span class="p">}</span></span>

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<td class="diff-line-num old old_line" data-linenumber="370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC370" class="line" lang="cpp">                            <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">updateAlleleIndexes</span><span class="p">();</span></span>

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371

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<pre style="margin: 0;">-<span id="LC371" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC372" class="line" lang="cpp">                        <span class="p">}</span></span>

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<td class="diff-line-num old old_line" data-linenumber="373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC373" class="line" lang="cpp">                        <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;">place_seq</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"<INV>"</span> <span class="o" style="font-weight: 600;">||</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">[</span><span class="s" style="color: #d14;">"SVTYPE"</span><span class="p">][</span><span class="n" style="color: #333;">alt_pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"INV"</span><span class="p">)){</span></span>

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<pre style="margin: 0;">-<span id="LC374" class="line" lang="cpp">                            <span class="k" style="font-weight: 600;">this</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="n" style="color: #333;">fasta_reference</span><span class="p">.</span><span class="n" style="color: #333;">getSubSequence</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sequenceName</span><span class="p">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</span><span class="p">,</span> <span class="n" style="color: #333;">sv_len</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC375" class="line" lang="cpp">                            <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">alt_str</span><span class="p">(</span><span class="n" style="color: #333;">fasta_reference</span><span class="p">.</span><span class="n" style="color: #333;">getSubSequence</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sequenceName</span><span class="p">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</span><span class="p">,</span> <span class="n" style="color: #333;">sv_len</span><span class="p">));</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC376" class="line" lang="cpp">                            <span class="n" style="color: #333;">alt_str</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">revcomp</span><span class="p">(</span><span class="n" style="color: #333;">alt_str</span><span class="p">);</span></span>

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<td class="diff-line-num old old_line" data-linenumber="377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC377" class="line" lang="cpp">                            <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alt</span><span class="p">[</span><span class="n" style="color: #333;">alt_pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alt_str</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC378" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC379" class="line" lang="cpp">                            <span class="c1" style="color: #998; font-style: italic;">// add 3 bases padding to right side </span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC380" class="line" lang="cpp">                            <span class="c1" style="color: #998; font-style: italic;">//this->ref.insert(0, reference.getSubSequence(this->sequenceName, this->position - 3, 3));</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC381" class="line" lang="cpp">                            <span class="c1" style="color: #998; font-style: italic;">//this->alt[alt_pos].insert(0, reference.getSubSequence(this->sequenceName, this->position - 3, 3));</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC382" class="line" lang="cpp">                            <span class="c1" style="color: #998; font-style: italic;">//this->position = this->position - 3;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC383" class="line" lang="cpp">                            <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">updateAlleleIndexes</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC384" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC385" class="line" lang="cpp">                            <span class="c1" style="color: #998; font-style: italic;">//variant_acceptable = false;</span></span>

</pre>

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<td class="diff-line-num old_line" 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

</td>

<td class="diff-line-num new_line" data-linenumber="659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

659

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC659" class="line" lang="cpp"></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

387

</td>

<td class="diff-line-num new_line old" data-linenumber="660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC387" class="line" lang="cpp">                        <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

388

</td>

<td class="diff-line-num new_line old" data-linenumber="660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC388" class="line" lang="cpp">                        <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

389

</td>

<td class="diff-line-num new_line old" data-linenumber="660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<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;">variant_acceptable</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

390

</td>

<td class="diff-line-num new_line old" data-linenumber="660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC390" class="line" lang="cpp">                        <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

391

</td>

<td class="diff-line-num new_line old" data-linenumber="660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC391" class="line" lang="cpp">                    <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

660

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC660" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">updateAlleleIndexes</span><span class="p">();</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

392

</td>

<td class="diff-line-num new_line" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

661

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC661" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

393

</td>

<td class="diff-line-num new_line old" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC393" class="line" lang="cpp">                <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

662

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC662" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Check for harmony between ref / alt / tags</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

663

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC663" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">stol</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"END"</span><span class="p">).</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">))){</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

664

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC664" class="line" lang="cpp">        <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Warning: position > END. Possible reference genome mismatch."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

665

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC665" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

666

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC666" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

394

</td>

<td class="diff-line-num new_line" data-linenumber="667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

667

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC667" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

668

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC668" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">svtype</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"INS"</span><span class="p">){</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

669

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC669" class="line" lang="cpp">        <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"SEQ"</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">empty</span><span class="p">());</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="670" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

670

</td>

<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="cpp">    <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

395

</td>

<td class="diff-line-num new_line" data-linenumber="671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

671

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC671" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

396

</td>

<td class="diff-line-num new_line old" data-linenumber="672" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC396" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">variant_acceptable</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="672" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

672

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC672" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">canonical</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

673

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC673" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

397

</td>

<td class="diff-line-num new_line" data-linenumber="674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

674

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC674" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

398

</td>

<td class="diff-line-num new_line" data-linenumber="675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

675

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC675" class="line" lang="cpp"></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

399

</td>

<td class="diff-line-num new_line" data-linenumber="676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

676

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC676" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setVariantCallFile</span><span class="p">(</span><span class="n" style="color: #333;">VariantCallFile</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">v</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="443" style="width: 35px; color: rgba(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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -443,7 +720,7 @@ VariantFieldType typeStrToVariantFieldType(string& typeStr) {</td>

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<td class="diff-line-num old_line" data-linenumber="443" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

443

</td>

<td class="diff-line-num new_line" 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="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="444" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

444

</td>

<td class="diff-line-num new_line" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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="cpp"><span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="445" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

445

</td>

<td class="diff-line-num new_line" data-linenumber="722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

722

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC722" class="line" lang="cpp"></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

446

</td>

<td class="diff-line-num new_line old" data-linenumber="723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC446" class="line" lang="cpp"><span class="n" style="color: #333;">VariantFieldType</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">infoType</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

723

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC723" class="line" lang="cpp"><span class="n" style="color: #333;">VariantFieldType</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">infoType</span><span class="p">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="447" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

447

</td>

<td class="diff-line-num new_line" data-linenumber="724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

724

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC724" class="line" lang="cpp">    <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">VariantFieldType</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vcf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">infoTypes</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

448

</td>

<td class="diff-line-num new_line" data-linenumber="725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

725

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC725" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</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;">vcf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">infoTypes</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" 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

</td>

<td class="diff-line-num new_line" data-linenumber="726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

726

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC726" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"FILTER"</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// hack to use FILTER as an "info" field (why the hack?)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="459" style="width: 35px; color: rgba(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="736" style="width: 35px; color: rgba(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">@@ -459,7 +736,7 @@ VariantFieldType Variant::infoType(string& key) {</td>

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<td class="diff-line-num old_line" data-linenumber="459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

459

</td>

<td class="diff-line-num new_line" data-linenumber="736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

736

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC736" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="460" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

460

</td>

<td class="diff-line-num new_line" data-linenumber="737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

737

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC737" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="461" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

461

</td>

<td class="diff-line-num new_line" data-linenumber="738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

738

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC738" class="line" lang="cpp"></span>

</pre>

</td>

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462

</td>

<td class="diff-line-num new_line old" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC462" class="line" lang="cpp">    <span class="n" style="color: #333;">VariantFieldType</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">formatType</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

739

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<pre style="margin: 0;">+<span id="LC739" class="line" lang="cpp">    <span class="n" style="color: #333;">VariantFieldType</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">formatType</span><span class="p">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

463

</td>

<td class="diff-line-num new_line" data-linenumber="740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

740

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<pre style="margin: 0;"> <span id="LC740" class="line" lang="cpp">        <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">VariantFieldType</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vcf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">formatTypes</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="464" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

464

</td>

<td class="diff-line-num new_line" data-linenumber="741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

741

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<pre style="margin: 0;"> <span id="LC741" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</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;">vcf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">formatTypes</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="465" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

465

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<td class="diff-line-num new_line" data-linenumber="742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

742

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<pre style="margin: 0;"> <span id="LC742" class="line" lang="cpp">            <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"no format field "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="469" style="width: 35px; color: rgba(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="746" style="width: 35px; color: rgba(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">@@ -469,7 +746,7 @@ VariantFieldType Variant::infoType(string& key) {</td>

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<td class="diff-line-num old_line" data-linenumber="469" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

469

</td>

<td class="diff-line-num new_line" data-linenumber="746" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

746

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC746" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="470" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

470

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<td class="diff-line-num new_line" data-linenumber="747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

747

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<pre style="margin: 0;"> <span id="LC747" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="471" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

471

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<td class="diff-line-num new_line" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

748

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC748" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="472" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

472

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<td class="diff-line-num new_line old" data-linenumber="749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC472" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getInfoValueBool</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="473" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

749

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<pre style="margin: 0;">+<span id="LC749" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getInfoValueBool</span><span class="p">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="473" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

473

</td>

<td class="diff-line-num new_line" data-linenumber="750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

750

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC750" class="line" lang="cpp">        <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">VariantFieldType</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vcf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">infoTypes</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="474" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

474

</td>

<td class="diff-line-num new_line" data-linenumber="751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

751

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC751" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</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;">vcf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">infoTypes</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="475" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

475

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<td class="diff-line-num new_line" data-linenumber="752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

752

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<pre style="margin: 0;"> <span id="LC752" class="line" lang="cpp">            <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"no info field "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="497" style="width: 35px; color: rgba(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="774" style="width: 35px; color: rgba(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">@@ -497,11 +774,12 @@ VariantFieldType Variant::infoType(string& key) {</td>

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<td class="diff-line-num old_line" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

497

</td>

<td class="diff-line-num new_line" data-linenumber="774" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

774

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<pre style="margin: 0;"> <span id="LC774" class="line" lang="cpp">                    <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

498

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775

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<pre style="margin: 0;"> <span id="LC775" class="line" lang="cpp">            <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

499

</td>

<td class="diff-line-num new_line" data-linenumber="776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

776

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<pre style="margin: 0;"> <span id="LC776" class="line" lang="cpp">                <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"not flag type "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="777" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

777

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<pre style="margin: 0;">+<span id="LC777" class="line" lang="cpp">                <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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

500

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<td class="diff-line-num new_line" data-linenumber="778" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

778

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<pre style="margin: 0;"> <span id="LC778" class="line" lang="cpp">            <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

501

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<td class="diff-line-num new_line" data-linenumber="779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

779

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<pre style="margin: 0;"> <span id="LC779" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="502" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

502

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<td class="diff-line-num new_line" data-linenumber="780" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

780

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<pre style="margin: 0;"> <span id="LC780" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

503

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<td class="diff-line-num new_line" data-linenumber="781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

781

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC781" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

504

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<td class="diff-line-num new_line old" data-linenumber="782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC504" class="line" lang="cpp">    <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getInfoValueString</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

782

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<pre style="margin: 0;">+<span id="LC782" class="line" lang="cpp">    <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getInfoValueString</span><span class="p">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

505

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<td class="diff-line-num new_line" data-linenumber="783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

783

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC783" class="line" lang="cpp">        <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">VariantFieldType</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vcf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">infoTypes</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

506

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<td class="diff-line-num new_line" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

784

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<pre style="margin: 0;"> <span id="LC784" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</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;">vcf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">infoTypes</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

507

</td>

<td class="diff-line-num new_line" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

785

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC785" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"FILTER"</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="536" style="width: 35px; color: rgba(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="814" style="width: 35px; color: rgba(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">@@ -536,7 +814,7 @@ VariantFieldType Variant::infoType(string& key) {</td>

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<td class="diff-line-num old_line" data-linenumber="536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

536

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<td class="diff-line-num new_line" data-linenumber="814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

814

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC814" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

537

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<td class="diff-line-num new_line" data-linenumber="815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

815

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC815" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

538

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<td class="diff-line-num new_line" data-linenumber="816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

816

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC816" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

539

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<td class="diff-line-num new_line old" data-linenumber="817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC539" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getInfoValueFloat</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

817

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<pre style="margin: 0;">+<span id="LC817" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getInfoValueFloat</span><span class="p">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

540

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<td class="diff-line-num new_line" data-linenumber="818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

818

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<pre style="margin: 0;"> <span id="LC818" class="line" lang="cpp">        <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">VariantFieldType</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vcf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">infoTypes</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

541

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<td class="diff-line-num new_line" data-linenumber="819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

819

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<pre style="margin: 0;"> <span id="LC819" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</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;">vcf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">infoTypes</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

542

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<td class="diff-line-num new_line" data-linenumber="820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

820

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<pre style="margin: 0;"> <span id="LC820" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"QUAL"</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="593" style="width: 35px; color: rgba(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="871" style="width: 35px; color: rgba(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">@@ -593,7 +871,7 @@ VariantFieldType Variant::infoType(string& key) {</td>

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<td class="diff-line-num old_line" data-linenumber="593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

593

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<td class="diff-line-num new_line" data-linenumber="871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

871

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<pre style="margin: 0;"> <span id="LC871" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">valid_genotypes</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

594

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<td class="diff-line-num new_line" data-linenumber="872" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

872

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<pre style="margin: 0;"> <span id="LC872" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

595

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<td class="diff-line-num new_line" data-linenumber="873" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

873

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<pre style="margin: 0;"> <span id="LC873" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

596

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<td class="diff-line-num new_line old" data-linenumber="874" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC596" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getSampleValueBool</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="874" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

874

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<pre style="margin: 0;">+<span id="LC874" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getSampleValueBool</span><span class="p">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

597

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<td class="diff-line-num new_line" data-linenumber="875" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

875

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<pre style="margin: 0;"> <span id="LC875" class="line" lang="cpp">        <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">VariantFieldType</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vcf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">formatTypes</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_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">

598

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<td class="diff-line-num new_line" data-linenumber="876" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

876

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<pre style="margin: 0;"> <span id="LC876" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</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;">vcf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">infoTypes</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

599

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<td class="diff-line-num new_line" data-linenumber="877" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

877

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<pre style="margin: 0;"> <span id="LC877" class="line" lang="cpp">            <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"no info field "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="900" style="width: 35px; color: rgba(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">@@ -622,11 +900,12 @@ VariantFieldType Variant::infoType(string& key) {</td>

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<td class="diff-line-num old_line" data-linenumber="622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

622

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<td class="diff-line-num new_line" data-linenumber="900" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

900

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<pre style="margin: 0;"> <span id="LC900" class="line" lang="cpp">                    <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

623

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<td class="diff-line-num new_line" data-linenumber="901" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

901

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<pre style="margin: 0;"> <span id="LC901" class="line" lang="cpp">            <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

624

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<td class="diff-line-num new_line" data-linenumber="902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

902

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<pre style="margin: 0;"> <span id="LC902" class="line" lang="cpp">                <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"not bool type "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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="cpp">                <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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

625

</td>

<td class="diff-line-num new_line" data-linenumber="904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

904

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC904" class="line" lang="cpp">            <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

626

</td>

<td class="diff-line-num new_line" data-linenumber="905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

905

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC905" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

627

</td>

<td class="diff-line-num new_line" data-linenumber="906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

906

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC906" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

628

</td>

<td class="diff-line-num new_line" data-linenumber="907" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

907

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC907" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

629

</td>

<td class="diff-line-num new_line old" data-linenumber="908" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC629" class="line" lang="cpp">    <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getSampleValueString</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="908" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

908

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<pre style="margin: 0;">+<span id="LC908" class="line" lang="cpp">    <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getSampleValueString</span><span class="p">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

630

</td>

<td class="diff-line-num new_line" data-linenumber="909" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

909

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<pre style="margin: 0;"> <span id="LC909" class="line" lang="cpp">        <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">VariantFieldType</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vcf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">formatTypes</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

631

</td>

<td class="diff-line-num new_line" data-linenumber="910" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

910

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC910" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</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;">vcf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">infoTypes</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

632

</td>

<td class="diff-line-num new_line" data-linenumber="911" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

911

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC911" class="line" lang="cpp">            <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"no info field "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="656" style="width: 35px; color: rgba(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="935" style="width: 35px; color: rgba(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">@@ -656,11 +935,12 @@ VariantFieldType Variant::infoType(string& key) {</td>

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<td class="diff-line-num old_line" data-linenumber="656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

656

</td>

<td class="diff-line-num new_line" data-linenumber="935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

935

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC935" class="line" lang="cpp">                <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="657" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

657

</td>

<td class="diff-line-num new_line" data-linenumber="936" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

936

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC936" class="line" lang="cpp">            <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="658" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

658

</td>

<td class="diff-line-num new_line" data-linenumber="937" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

937

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC937" class="line" lang="cpp">                <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"not string type "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

938

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC938" class="line" lang="cpp">                <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>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

659

</td>

<td class="diff-line-num new_line" data-linenumber="939" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

939

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC939" class="line" lang="cpp">            <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

660

</td>

<td class="diff-line-num new_line" data-linenumber="940" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

940

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC940" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

661

</td>

<td class="diff-line-num new_line" data-linenumber="941" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

941

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC941" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

662

</td>

<td class="diff-line-num new_line" data-linenumber="942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

942

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC942" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

663

</td>

<td class="diff-line-num new_line old" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC663" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getSampleValueFloat</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

943

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC943" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getSampleValueFloat</span><span class="p">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

664

</td>

<td class="diff-line-num new_line" 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

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC944" class="line" lang="cpp">        <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">VariantFieldType</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vcf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">formatTypes</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

665

</td>

<td class="diff-line-num new_line" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC945" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</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;">vcf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">infoTypes</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

666

</td>

<td class="diff-line-num new_line" data-linenumber="946" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

946

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC946" class="line" lang="cpp">            <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"no info field "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="694" style="width: 35px; color: rgba(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="974" style="width: 35px; color: rgba(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">@@ -694,11 +974,12 @@ VariantFieldType Variant::infoType(string& key) {</td>

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<td class="diff-line-num old_line" data-linenumber="694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

694

</td>

<td class="diff-line-num new_line" data-linenumber="974" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

974

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC974" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">r</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

695

</td>

<td class="diff-line-num new_line" data-linenumber="975" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

975

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC975" class="line" lang="cpp">            <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

696

</td>

<td class="diff-line-num new_line" data-linenumber="976" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

976

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC976" class="line" lang="cpp">                <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"unsupported type for sample "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">type</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="977" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

977

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC977" class="line" lang="cpp">                <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>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" 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

</td>

<td class="diff-line-num new_line" data-linenumber="978" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

978

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC978" class="line" lang="cpp">            <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

698

</td>

<td class="diff-line-num new_line" data-linenumber="979" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

979

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC979" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

699

</td>

<td class="diff-line-num new_line" data-linenumber="980" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

980

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC980" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

700

</td>

<td class="diff-line-num 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">

981

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC981" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

701

</td>

<td class="diff-line-num new_line old" data-linenumber="982" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC701" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getValueBool</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="982" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

982

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<pre style="margin: 0;">+<span id="LC982" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getValueBool</span><span class="p">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

702

</td>

<td class="diff-line-num new_line" 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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<pre style="margin: 0;"> <span id="LC983" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sample</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// an empty sample name means</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

703

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<td class="diff-line-num new_line" 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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<pre style="margin: 0;"> <span id="LC984" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">getInfoValueBool</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

704

</td>

<td class="diff-line-num new_line" 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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<pre style="margin: 0;"> <span id="LC985" class="line" lang="cpp">        <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="706" style="width: 35px; color: rgba(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="987" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -706,7 +987,7 @@ VariantFieldType Variant::infoType(string& key) {</td>

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<td class="diff-line-num old_line" data-linenumber="706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

706

</td>

<td class="diff-line-num new_line" data-linenumber="987" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

987

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<pre style="margin: 0;"> <span id="LC987" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

707

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<td class="diff-line-num new_line" data-linenumber="988" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

988

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<pre style="margin: 0;"> <span id="LC988" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

708

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<td class="diff-line-num new_line" data-linenumber="989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

989

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<pre style="margin: 0;"> <span id="LC989" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

709

</td>

<td class="diff-line-num new_line old" data-linenumber="990" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC709" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getValueFloat</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="990" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

990

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<pre style="margin: 0;">+<span id="LC990" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getValueFloat</span><span class="p">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

710

</td>

<td class="diff-line-num new_line" data-linenumber="991" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

991

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<pre style="margin: 0;"> <span id="LC991" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sample</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// an empty sample name means</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

711

</td>

<td class="diff-line-num new_line" data-linenumber="992" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

992

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<pre style="margin: 0;"> <span id="LC992" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">getInfoValueFloat</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

712

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<td class="diff-line-num new_line" data-linenumber="993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

993

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<pre style="margin: 0;"> <span id="LC993" class="line" lang="cpp">        <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="714" style="width: 35px; color: rgba(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="995" style="width: 35px; color: rgba(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">@@ -714,7 +995,7 @@ VariantFieldType Variant::infoType(string& key) {</td>

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<td class="diff-line-num old_line" data-linenumber="714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

714

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<td class="diff-line-num new_line" data-linenumber="995" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

995

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<pre style="margin: 0;"> <span id="LC995" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

715

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<td class="diff-line-num new_line" data-linenumber="996" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

996

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC996" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_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">

716

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<td class="diff-line-num new_line" data-linenumber="997" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

997

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC997" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

717

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<td class="diff-line-num new_line old" data-linenumber="998" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC717" class="line" lang="cpp">    <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getValueString</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="998" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

998

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<pre style="margin: 0;">+<span id="LC998" class="line" lang="cpp">    <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getValueString</span><span class="p">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

718

</td>

<td class="diff-line-num new_line" data-linenumber="999" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

999

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<pre style="margin: 0;"> <span id="LC999" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sample</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// an empty sample name means</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

719

</td>

<td class="diff-line-num new_line" data-linenumber="1000" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1000

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<pre style="margin: 0;"> <span id="LC1000" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">getInfoValueString</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" 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

</td>

<td class="diff-line-num new_line" data-linenumber="1001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1001

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<pre style="margin: 0;"> <span id="LC1001" class="line" lang="cpp">        <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="722" style="width: 35px; color: rgba(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="1003" style="width: 35px; color: rgba(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">@@ -722,7 +1003,7 @@ VariantFieldType Variant::infoType(string& key) {</td>

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<td class="diff-line-num old_line" data-linenumber="722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

722

</td>

<td class="diff-line-num new_line" data-linenumber="1003" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1003

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1003" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

723

</td>

<td class="diff-line-num new_line" data-linenumber="1004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1004

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<pre style="margin: 0;"> <span id="LC1004" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

724

</td>

<td class="diff-line-num new_line" data-linenumber="1005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1005

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1005" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

725

</td>

<td class="diff-line-num new_line old" data-linenumber="1006" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC725" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getAltAlleleIndex</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">allele</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1006" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1006

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<pre style="margin: 0;">+<span id="LC1006" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getAltAlleleIndex</span><span class="p">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">allele</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

726

</td>

<td class="diff-line-num new_line" data-linenumber="1007" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1007

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1007" class="line" lang="cpp">        <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</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;">iterator</span> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">altAlleleIndexes</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">allele</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

727

</td>

<td class="diff-line-num new_line" data-linenumber="1008" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1008

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1008" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">altAlleleIndexes</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

728

</td>

<td class="diff-line-num new_line" data-linenumber="1009" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1009

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1009" class="line" lang="cpp">            <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"no such allele </span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">allele</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;"> in record "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">sequenceName</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;">position</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="732" style="width: 35px; color: rgba(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="1013" style="width: 35px; color: rgba(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">@@ -732,14 +1013,14 @@ VariantFieldType Variant::infoType(string& key) {</td>

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<td class="diff-line-num old_line" data-linenumber="732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

732

</td>

<td class="diff-line-num new_line" data-linenumber="1013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1013

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1013" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

733

</td>

<td class="diff-line-num new_line" data-linenumber="1014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1014

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1014" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

734

</td>

<td class="diff-line-num new_line" data-linenumber="1015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1015

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1015" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

735

</td>

<td class="diff-line-num new_line old" data-linenumber="1016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC735" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">addFilter</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">tag</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1016

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1016" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">addFilter</span><span class="p">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">tag</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

736

</td>

<td class="diff-line-num new_line" data-linenumber="1017" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1017

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1017" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">filter</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;">filter</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"."</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

737

</td>

<td class="diff-line-num new_line" data-linenumber="1018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1018

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1018" class="line" lang="cpp">            <span class="n" style="color: #333;">filter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tag</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

738

</td>

<td class="diff-line-num new_line" data-linenumber="1019" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1019

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1019" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">else</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

739

</td>

<td class="diff-line-num new_line" data-linenumber="1020" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1020

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1020" class="line" lang="cpp">            <span class="n" style="color: #333;">filter</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;">tag</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

740

</td>

<td class="diff-line-num new_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1021

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1021" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

741

</td>

<td class="diff-line-num new_line" data-linenumber="1022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1022

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1022" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

742

</td>

<td class="diff-line-num new_line old" data-linenumber="1023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC742" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">addFormatField</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1023

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1023" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">addFormatField</span><span class="p">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

743

</td>

<td class="diff-line-num new_line" data-linenumber="1024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1024

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1024" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">hasTag</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="744" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

744

</td>

<td class="diff-line-num new_line" data-linenumber="1025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1025

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1025" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">format</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">format</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">t</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

745

</td>

<td class="diff-line-num new_line" data-linenumber="1026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1026

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1026" 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;">t</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">key</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1791" style="width: 35px; color: rgba(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="2072" style="width: 35px; color: rgba(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">@@ -1791,6 +2072,10 @@ map<string, vector<VariantAllele> > Variant::parsedAlternates(bool includePrevio</td>

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<td class="diff-line-num old_line" data-linenumber="1791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1791

</td>

<td class="diff-line-num new_line" data-linenumber="2072" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2072

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2072" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1792

</td>

<td class="diff-line-num new_line" data-linenumber="2073" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2073

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2073" class="line" lang="cpp">    <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">VariantAllele</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">variantAlleles</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1793

</td>

<td class="diff-line-num new_line" data-linenumber="2074" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2074

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2074" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="1794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2075" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2075

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2075" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isSymbolicSV</span><span class="p">()){</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2076" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2076

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<pre style="margin: 0;">+<span id="LC2076" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// Don't ever align SVs. It just wrecks things.</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2077

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2077" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">flatAlternates</span><span class="p">();</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2078" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2078

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<pre style="margin: 0;">+<span id="LC2078" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1794

</td>

<td class="diff-line-num new_line" data-linenumber="2079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2079

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<pre style="margin: 0;"> <span id="LC2079" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// add the reference allele</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1795

</td>

<td class="diff-line-num new_line" data-linenumber="2080" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2080

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<pre style="margin: 0;"> <span id="LC2080" class="line" lang="cpp">    <span class="n" style="color: #333;">variantAlleles</span><span class="p">[</span><span class="n" style="color: #333;">ref</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">VariantAllele</span><span class="p">(</span><span class="n" style="color: #333;">ref</span><span class="p">,</span> <span class="n" style="color: #333;">ref</span><span class="p">,</span> <span class="n" style="color: #333;">position</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1796

</td>

<td class="diff-line-num new_line" data-linenumber="2081" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2081

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2081" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2035" style="width: 35px; color: rgba(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="2320" style="width: 35px; color: rgba(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">@@ -2035,7 +2320,7 @@ void Variant::updateAlleleIndexes(void) {</td>

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<td class="diff-line-num old_line" data-linenumber="2035" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2035

</td>

<td class="diff-line-num new_line" data-linenumber="2320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2320

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<pre style="margin: 0;"> <span id="LC2320" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2036" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2036

</td>

<td class="diff-line-num new_line" data-linenumber="2321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2321

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2321" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2037" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2037

</td>

<td class="diff-line-num new_line" data-linenumber="2322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2322

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<pre style="margin: 0;"> <span id="LC2322" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// TODO only works on "A"llele variant fields</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="2038" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2038

</td>

<td class="diff-line-num new_line old" data-linenumber="2323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2038" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">removeAlt</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">altAllele</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2039" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2323

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<pre style="margin: 0;">+<span id="LC2323" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">removeAlt</span><span class="p">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">altAllele</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2039" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2039

</td>

<td class="diff-line-num new_line" data-linenumber="2324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2324

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2324" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2040" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2040

</td>

<td class="diff-line-num new_line" data-linenumber="2325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2325

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<pre style="margin: 0;"> <span id="LC2325" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">altIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getAltAlleleIndex</span><span class="p">(</span><span class="n" style="color: #333;">altAllele</span><span class="p">);</span>  <span class="c1" style="color: #998; font-style: italic;">// this is the alt-relative index, 0-based</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2041

</td>

<td class="diff-line-num new_line" data-linenumber="2326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2326

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2326" class="line" lang="cpp">    </span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2431" style="width: 35px; color: rgba(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="2716" style="width: 35px; color: rgba(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">@@ -2431,7 +2716,7 @@ map<int, int> glReorder(int ploidy, int numalts, map<int, int>& alleleIndexMappi</td>

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<td class="diff-line-num old_line" data-linenumber="2431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2431

</td>

<td class="diff-line-num new_line" data-linenumber="2716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2716

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<pre style="margin: 0;"> <span id="LC2716" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">mapping</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2432

</td>

<td class="diff-line-num new_line" data-linenumber="2717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2717

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2717" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2433

</td>

<td class="diff-line-num new_line" data-linenumber="2718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2718

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2718" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="2434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2434

</td>

<td class="diff-line-num new_line old" data-linenumber="2719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2434" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getGenotype</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sample</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2719

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2719" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getGenotype</span><span class="p">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sample</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2435

</td>

<td class="diff-line-num new_line" data-linenumber="2720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2720

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<pre style="margin: 0;"> <span id="LC2720" class="line" lang="cpp">    <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">samples</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">sample</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2436" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2436

</td>

<td class="diff-line-num new_line" data-linenumber="2721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2721

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2721" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</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;">samples</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2437" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2437

</td>

<td class="diff-line-num new_line" data-linenumber="2722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2722

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2722" class="line" lang="cpp">        <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="s" style="color: #d14;">"GT"</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2456" style="width: 35px; color: rgba(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="2741" style="width: 35px; color: rgba(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">@@ -2456,7 +2741,7 @@ bool Variant::isPhased(void) {</td>

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<td class="diff-line-num old_line" data-linenumber="2456" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2456

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<td class="diff-line-num new_line" data-linenumber="2741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2741

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2741" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2457" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2457

</td>

<td class="diff-line-num new_line" data-linenumber="2742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2742

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2742" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2458" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2458

</td>

<td class="diff-line-num new_line" data-linenumber="2743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2743

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2743" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="2459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2459

</td>

<td class="diff-line-num new_line old" data-linenumber="2744" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC2459" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">zeroBasedPosition</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2460" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2744" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2744

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2744" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">zeroBasedPosition</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span> <span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2460" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2460

</td>

<td class="diff-line-num new_line" data-linenumber="2745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2745

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<pre style="margin: 0;"> <span id="LC2745" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">position</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2461" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2461

</td>

<td class="diff-line-num new_line" data-linenumber="2746" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2746

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2746" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2462" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2462

</td>

<td class="diff-line-num new_line" data-linenumber="2747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2747

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2747" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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<br>

</li>

<li id="652b96bba65afc5f190351f4ffa54108321ad32e">

<a href="https://salsa.debian.org/med-team/libvcflib/commit/18f9a56680d84676eadf8905cf2bd95b76fc9841#652b96bba65afc5f190351f4ffa54108321ad32e"><strong>src/Variant.h</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="54" style="width: 35px; color: rgba(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="54" style="width: 35px; color: rgba(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">@@ -54,6 +54,12 @@ ostream& operator<<(ostream& out, VariantFieldType type);</td>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="c"><span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">Samples</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="c"><span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></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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<pre style="margin: 0;"> <span id="LC56" class="line" lang="c"></span>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">/// Compute a reverse complement. Supports both upper-case and lower-case input characters.</span></span>

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="c"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">reverse_complement</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</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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<pre style="margin: 0;">+<span id="LC59" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">/// Convert a sequence to upper-case</span></span>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="c"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">toUpper</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</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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<pre style="margin: 0;">+<span id="LC61" class="line" lang="c"><span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">allATGCN</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</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;">bool</span> <span class="n" style="color: #333;">allowLowerCase</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="c"><span class="n" style="color: #333;">class</span> <span class="n" style="color: #333;">VariantCallFile</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="c"><span class="nl">public:</span></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>

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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">@@ -193,7 +199,7 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC199" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC200" class="line" lang="c">    <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">sequenceName</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC201" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">position</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC196" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">zeroBasedPosition</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC202" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">zeroBasedPosition</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff right">const</span></span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC203" class="line" lang="c">    <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">id</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC204" class="line" lang="c">    <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">ref</span><span class="p">;</span></span>

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<td class="diff-line-num new_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC205" class="line" lang="c">    <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">alt</span><span class="p">;</span>      <span class="c1" style="color: #998; font-style: italic;">// a list of all the alternate alleles present at this locus</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="201" style="width: 35px; color: rgba(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="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -201,6 +207,7 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC207" class="line" lang="c">                             <span class="c1" style="color: #998; font-style: italic;">// the indicies are organized such that the genotype codes (0,1,2,.etc.)</span></span>

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<pre style="margin: 0;"> <span id="LC208" class="line" lang="c">                             <span class="c1" style="color: #998; font-style: italic;">// correspond to the correct offest into the allelese vector.</span></span>

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<pre style="margin: 0;"> <span id="LC209" class="line" lang="c">                             <span class="c1" style="color: #998; font-style: italic;">// that is, alleles[0] = ref, alleles[1] = first alternate allele, etc.</span></span>

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<pre style="margin: 0;">+<span id="LC210" class="line" lang="c"></span>

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<td class="diff-line-num old_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC211" class="line" lang="c">    <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">vrepr</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">);</span>  <span class="c1" style="color: #998; font-style: italic;">// a comparable record of the variantion described by the record</span></span>

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<td class="diff-line-num new_line" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC212" class="line" lang="c">    <span class="n" style="color: #333;">set</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">altSet</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">);</span>  <span class="c1" style="color: #998; font-style: italic;">// set of alleles, rather than vector of them</span></span>

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<pre style="margin: 0;"> <span id="LC213" class="line" lang="c">    <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</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;">altAlleleIndexes</span><span class="p">;</span>  <span class="c1" style="color: #998; font-style: italic;">// reverse lookup for alleles</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="219" style="width: 35px; color: rgba(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="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -219,14 +226,67 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC226" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC227" class="line" lang="c">    <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">extendedAlternates</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">newPosition</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">length</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC228" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new_line 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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<pre style="margin: 0;">-<span id="LC222" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">// Convert a structural variant the canonical VCF4.2 format using a reference.</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC223" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">// returns true if the variant is canonicalized, false otherwise.</span></span>

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<pre style="margin: 0;">-<span id="LC224" class="line" lang="c">    <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">canonicalize_sv</span><span class="p">(</span><span class="n" style="color: #333;">FastaReference</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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">FastaReference</span><span class="o" style="font-weight: 600;">*></span> <span class="n" style="color: #333;">insertions</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">place_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">interval_sz</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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<pre style="margin: 0;">+<span id="LC229" class="line" lang="c">    <span class="cm" style="color: #998; font-style: italic;">/** </span></span>

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<pre style="margin: 0;">+<span id="LC230" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     * Convert a structural variant to the canonical VCF4.3 format using a reference.</span></span>

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<pre style="margin: 0;">+<span id="LC231" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     *   Meturns true if the variant is canonicalized, false otherwise.</span></span>

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<pre style="margin: 0;">+<span id="LC232" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     *   May NOT be called twice on the same variant; it will fail an assert.</span></span>

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<pre style="margin: 0;">+<span id="LC233" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     *   Returns false for non-SVs</span></span>

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<pre style="margin: 0;">+<span id="LC234" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     *   place_seq: if true, the ref/alt fields are</span></span>

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<pre style="margin: 0;">+<span id="LC235" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     *       filled in with the corresponding sequences</span></span>

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<pre style="margin: 0;">+<span id="LC236" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     *     from the reference (and optionally insertion FASTA)</span></span>

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<pre style="margin: 0;">+<span id="LC237" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     * min_size_override: If a variant is less than this size,</span></span>

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<pre style="margin: 0;">+<span id="LC238" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     *     and it has a valid REF and ALT, consider it canonicalized</span></span>

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<pre style="margin: 0;">+<span id="LC239" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     *     even if the below conditions are not true.</span></span>

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<pre style="margin: 0;">+<span id="LC240" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     * Fully canonicalized variants (which are greater than min_size_override)</span></span>

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<pre style="margin: 0;">+<span id="LC241" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     * guarantee the following:</span></span>

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<pre style="margin: 0;">+<span id="LC242" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     *  - POS <= END and corresponds to the anchoring base for symbolic alleles</span></span>

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<pre style="margin: 0;">+<span id="LC243" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     *  - SVLEN info field is set and is positive for all variants except DELs</span></span>

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<pre style="margin: 0;">+<span id="LC244" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     *  - SVTYPE info field is set and is in {DEL, INS, INV, DUP}</span></span>

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<pre style="margin: 0;">+<span id="LC245" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     *  - END info field is set to the POS + len(REF allele) - 1 and corresponds to the final affected reference base</span></span>

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<pre style="margin: 0;">+<span id="LC246" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     *  - Insertions get an upper-case SEQ info field</span></span>

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC247" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     *  - REF and ALT are upper-case if filled in by this function</span></span>

</pre>

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC248" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     *  - canonical = true;</span></span>

</pre>

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC249" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     * TODO: CURRENTLY: canonical requires there be only one alt allele</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC250" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">    **/</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC251" class="line" lang="c">    <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">canonicalize</span><span class="p">(</span><span class="n" style="color: #333;">FastaReference</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ref</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC252" class="line" lang="c">         <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">FastaReference</span><span class="o" style="font-weight: 600;">*></span> <span class="n" style="color: #333;">insertions</span><span class="p">,</span> </span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC253" class="line" lang="c">         <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">place_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> </span>

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC254" class="line" lang="c">         <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_size_override</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC255" class="line" lang="c">         </span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<pre style="margin: 0;">+<span id="LC256" class="line" lang="c">    <span class="cm" style="color: #998; font-style: italic;">/** </span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC257" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     * Returns true if the variant's ALT contains a symbolic allele like <INV></span></span>

</pre>

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC258" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     * instead of sequence, and the variant has an SVTYPE INFO tag.</span></span>

</pre>

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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC259" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     */</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC260" class="line" lang="c">    <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">isSymbolicSV</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC261" class="line" lang="c">    </span>

</pre>

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<pre style="margin: 0;">-<span id="LC226" class="line" lang="c">    <span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Variant</span><span class="p">,</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">convert_to_breakends</span><span class="p">(</span><span class="n" style="color: #333;">FastaReference</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ref</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC227" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">get_sv_end</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC228" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">get_sv_len</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC229" class="line" lang="c">    <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">is_sv</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC262" class="line" lang="c">    <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

</pre>

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC263" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     * Returns true if the variant has an SVTYPE INFO tag and either an SVLEN or END INFO tag.</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC264" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     */</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC265" class="line" lang="c">    <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">hasSVTags</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC266" class="line" lang="c">    </span>

</pre>

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC267" class="line" lang="c">    <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC268" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     * This returns true if the variant appears able to be handled by</span></span>

</pre>

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<td class="diff-line-num new new_line" 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">

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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="c"><span class="cm" style="color: #998; font-style: italic;">     * canonicalize(). It checks if it has fully specified sequence, or if it</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC270" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     * has a defined SV type and length/endpoint. </span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC271" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     */</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC272" class="line" lang="c">    <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">canonicalizable</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC273" class="line" lang="c">    </span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC274" class="line" lang="c">    <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC275" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     * This gets set to true after canonicalize() has been called on the variant, if it succeeded.</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC276" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     */</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC277" class="line" lang="c">    <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">canonical</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC278" class="line" lang="c">    </span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC279" class="line" lang="c">    <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC280" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     * Get the maximum zero-based position of the reference affected by this variant.</span></span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC281" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     * Only works reliably for variants that are not SVs or for SVs that have been canonicalize()'d.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC282" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     */</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC283" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">getMaxReferencePos</span><span class="p">();</span></span>

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<pre style="margin: 0;">+<span id="LC284" class="line" lang="c">   </span>

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<pre style="margin: 0;">+<span id="LC285" class="line" lang="c">    <span class="cm" style="color: #998; font-style: italic;">/**</span></span>

</pre>

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC286" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     * Return the SV type of the given alt, or "" if there is no SV type set for that alt.</span></span>

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<pre style="margin: 0;">+<span id="LC287" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     * This is the One True Way to get the SVTYPE of a variant; we should not touch the SVTYPE tag anywhere else.</span></span>

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<pre style="margin: 0;">+<span id="LC288" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">     */</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC289" class="line" lang="c">    <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">getSVTYPE</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">altpos</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;">const</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC290" class="line" lang="c"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC291" class="line" lang="c">    <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">originalLine</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// the literal of the record, as read</span></span>

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<pre style="margin: 0;"> <span id="LC292" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">// TODO</span></span>

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<td class="diff-line-num unfold js-unfold old_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>

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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">@@ -234,10 +294,10 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC294" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">// vector<pair<int, int> > genotypes;  // indexes into the alleles, ordered as per the spec</span></span>

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<pre style="margin: 0;"> <span id="LC295" class="line" lang="c">    <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">filter</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC296" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">quality</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC237" class="line" lang="c">    <span class="n" style="color: #333;">VariantFieldType</span> <span class="n" style="color: #333;">infoType</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC297" class="line" lang="c">    <span class="n" style="color: #333;">VariantFieldType</span> <span class="n" style="color: #333;">infoType</span><span class="p">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC298" class="line" lang="c">    <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">info</span><span class="p">;</span>  <span class="c1" style="color: #998; font-style: italic;">// vector<string> allows for lists by Genotypes or Alternates</span></span>

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<pre style="margin: 0;"> <span id="LC299" class="line" lang="c">    <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">infoFlags</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC240" class="line" lang="c">    <span class="n" style="color: #333;">VariantFieldType</span> <span class="n" style="color: #333;">formatType</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC300" class="line" lang="c">    <span class="n" style="color: #333;">VariantFieldType</span> <span class="n" style="color: #333;">formatType</span><span class="p">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC301" class="line" lang="c">    <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">format</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC302" class="line" lang="c">    <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">samples</span><span class="p">;</span>  <span class="c1" style="color: #998; font-style: italic;">// vector<string> allows for lists by Genotypes or Alternates</span></span>

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<pre style="margin: 0;"> <span id="LC303" class="line" lang="c">    <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">sampleNames</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold new_line" 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">...</td>

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<pre style="margin: 0;"> <span id="LC308" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">//void addInfoFloat(string& tag, double value);</span></span>

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<pre style="margin: 0;"> <span id="LC309" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">//void addInfoString(string& tag, string& value);</span></span>

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<pre style="margin: 0;"> <span id="LC310" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC251" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">removeAlt</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">altallele</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC311" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">removeAlt</span><span class="p">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">altallele</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC312" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC313" class="line" lang="c"><span class="nl">public:</span></span>

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<pre style="margin: 0;"> <span id="LC314" class="line" lang="c"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="264" style="width: 35px; color: rgba(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="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">...</td>

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<pre style="margin: 0;"> <span id="LC324" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">setVariantCallFile</span><span class="p">(</span><span class="n" style="color: #333;">VariantCallFile</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">v</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC325" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC326" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">line</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">parseSamples</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC267" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">addFilter</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">tag</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC268" class="line" lang="c">    <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">getValueBool</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">INDEX_NONE</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC269" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">getValueFloat</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">INDEX_NONE</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC270" class="line" lang="c">    <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">getValueString</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">INDEX_NONE</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC271" class="line" lang="c">    <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">getSampleValueBool</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">INDEX_NONE</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC272" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">getSampleValueFloat</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">INDEX_NONE</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC273" class="line" lang="c">    <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">getSampleValueString</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">INDEX_NONE</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC274" class="line" lang="c">    <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">getInfoValueBool</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">INDEX_NONE</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC275" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">getInfoValueFloat</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">INDEX_NONE</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC276" class="line" lang="c">    <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">getInfoValueString</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">INDEX_NONE</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC327" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">addFilter</span><span class="p">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">tag</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC328" class="line" lang="c">    <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">getValueBool</span><span class="p">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">INDEX_NONE</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC329" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">getValueFloat</span><span class="p">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">INDEX_NONE</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC330" class="line" lang="c">    <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">getValueString</span><span class="p">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">INDEX_NONE</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC331" class="line" lang="c">    <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">getSampleValueBool</span><span class="p">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">INDEX_NONE</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC332" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">getSampleValueFloat</span><span class="p">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">INDEX_NONE</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC333" class="line" lang="c">    <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">getSampleValueString</span><span class="p">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sample</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">INDEX_NONE</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC334" class="line" lang="c">    <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">getInfoValueBool</span><span class="p">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">INDEX_NONE</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC335" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">getInfoValueFloat</span><span class="p">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">INDEX_NONE</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC336" class="line" lang="c">    <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">getInfoValueString</span><span class="p">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">INDEX_NONE</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC337" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">printAlt</span><span class="p">(</span><span class="n" style="color: #333;">ostream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">out</span><span class="p">);</span>      <span class="c1" style="color: #998; font-style: italic;">// print a comma-sep list of alternate alleles to an ostream</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC338" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">printAlleles</span><span class="p">(</span><span class="n" style="color: #333;">ostream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">out</span><span class="p">);</span>  <span class="c1" style="color: #998; font-style: italic;">// print a comma-sep list of *all* alleles to an ostream</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC279" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">getAltAlleleIndex</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">allele</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC339" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">getAltAlleleIndex</span><span class="p">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">allele</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC340" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">updateAlleleIndexes</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC281" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">addFormatField</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC341" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">addFormatField</span><span class="p">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">key</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC342" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">setOutputSampleNames</span><span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">outputSamples</span><span class="p">);</span></span>

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<td class="diff-line-num old_line" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC343" class="line" lang="c">    <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</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="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">getGenotypeIndexesDiploid</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC344" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">getNumSamples</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC345" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">getNumValidGenotypes</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">);</span></span>

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<td class="diff-line-num old old_line" data-linenumber="286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC286" class="line" lang="c">    <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">getGenotype</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sample</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<pre style="margin: 0;">+<span id="LC346" class="line" lang="c">    <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">getGenotype</span><span class="p">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sample</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC347" class="line" lang="c">    <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">isPhased</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC348" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">// TODO</span></span>

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<pre style="margin: 0;">-<span id="LC289" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">//void setInfoField(string& key, string& val);</span></span>

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<pre style="margin: 0;">+<span id="LC349" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;">//void setInfoField(<span class="idiff left right">const </span>string& key, string& val);</span></span>

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<pre style="margin: 0;"> <span id="LC350" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC351" class="line" lang="c"><span class="nl">private:</span></span>

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<pre style="margin: 0;"> <span id="LC352" class="line" lang="c"></span>

</pre>

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<br>

</li>

<li id="9189853d8f456e526b136ecd561456f45ecc315b">

<a href="https://salsa.debian.org/med-team/libvcflib/commit/18f9a56680d84676eadf8905cf2bd95b76fc9841#9189853d8f456e526b136ecd561456f45ecc315b"><strong>src/cdflib.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">@@ -10040,7 +10040,7 @@ void negative_binomial_cdf_values ( int *n_data, int *f, int *s, double *p,</td>

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<pre style="margin: 0;"> <span id="LC10040" class="line" lang="cpp">    <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC10041" class="line" lang="cpp">    <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span> <span class="p">};</span></span>

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10042

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<pre style="margin: 0;"> <span id="LC10042" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="10043" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

10043

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<td class="diff-line-num new_line old" data-linenumber="10043" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC10043" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">n_data</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 new old_line" data-linenumber="10044" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC10043" 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 class="idiff left right">*</span></span><span class="n" style="color: #333;">n_data</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC10044" class="line" lang="cpp">  <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="10045" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC10045" class="line" lang="cpp">    <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">n_data</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 old_line" data-linenumber="10046" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC10046" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<br>

</li>

<li id="de10b670208808941807d0db7069159f2749af37">

<a href="https://salsa.debian.org/med-team/libvcflib/commit/18f9a56680d84676eadf8905cf2bd95b76fc9841#de10b670208808941807d0db7069159f2749af37"><strong>src/split.h</strong></a>

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<td class="diff-line-num unfold js-unfold old_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="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">@@ -47,7 +47,7 @@ void tokenize(const std::string& str, ContainerT& tokens,</td>

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47

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47

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="c"></span>

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<td class="diff-line-num old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="c">     <span class="n" style="color: #333;">lastPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="49" style="width: 35px; color: rgba(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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49

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="c">    <span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC50" class="line" lang="c"><span class="p">}<span class="idiff left right">;</span></span></span>

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<td class="diff-line-num new old_line" 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">

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="c"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span></pre>

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</li>

<li id="3dc965d7809a4f1703d452c230376064628bf793">

<a href="https://salsa.debian.org/med-team/libvcflib/commit/18f9a56680d84676eadf8905cf2bd95b76fc9841#3dc965d7809a4f1703d452c230376064628bf793"><strong>src/vcfintersect.cpp</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -290,9 +290,9 @@ int main(int argc, char** argv) {</td>

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<td class="diff-line-num old_line" data-linenumber="290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC290" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// read the VCF file for union or intersection into an interval tree</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC291" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// indexed using some proximity window</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC292" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" 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">

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<pre style="margin: 0;">-<span id="LC293" class="line" lang="cpp">    <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">IntervalTree</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">variantIntervals</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC293" class="line" lang="cpp">    <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">IntervalTree</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">size_t</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">variantIntervals</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC294" class="line" lang="cpp">    <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">otherVariants</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC295" class="line" lang="cpp">    <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">otherVariantIntervals</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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">

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<pre style="margin: 0;">+<span id="LC295" class="line" lang="cpp">    <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">size_t</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">otherVariantIntervals</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC296" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC297" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unioning</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">intersecting</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC298" class="line" lang="cpp"></span>

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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -302,11 +302,10 @@ int main(int argc, char** argv) {</td>

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<pre style="margin: 0;"> <span id="LC302" class="line" lang="cpp">            <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">right</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ovar</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="c1" style="color: #998; font-style: italic;">// this should be 1-past the end</span></span>

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<pre style="margin: 0;"> <span id="LC303" class="line" lang="cpp">            <span class="n" style="color: #333;">otherVariants</span><span class="p">[</span><span class="n" style="color: #333;">ovar</span><span class="p">.</span><span class="n" style="color: #333;">sequenceName</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">ovar</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC304" class="line" lang="cpp">            <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">otherVariants</span><span class="p">[</span><span class="n" style="color: #333;">ovar</span><span class="p">.</span><span class="n" style="color: #333;">sequenceName</span><span class="p">].</span><span class="n" style="color: #333;">back</span><span class="p">();</span></span>

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<pre style="margin: 0;">-<span id="LC305" class="line" lang="cpp">            <span class="n" style="color: #333;">otherVariantIntervals</span><span class="p">[</span><span class="n" style="color: #333;">ovar</span><span class="p">.</span><span class="n" style="color: #333;">sequenceName</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*></span><span class="p">(</span><span class="n" style="color: #333;">left</span><span class="p">,</span> <span class="n" style="color: #333;">right</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="p">));</span></span>

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<td class="diff-line-num new old_line" 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">

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<pre style="margin: 0;">+<span id="LC305" class="line" lang="cpp">            <span class="n" style="color: #333;">otherVariantIntervals</span><span class="p">[</span><span class="n" style="color: #333;">ovar</span><span class="p">.</span><span class="n" style="color: #333;">sequenceName</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">size_t</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*></span><span class="p">(</span><span class="n" style="color: #333;">left</span><span class="p">,</span> <span class="n" style="color: #333;">right</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="p">));</span></span>

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<pre style="margin: 0;"> <span id="LC306" class="line" lang="cpp">        <span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC307" class="line" lang="cpp">  </span>

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<pre style="margin: 0;">-<span id="LC308" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">otherVariantIntervals</span><span class="p">.</span><span class="n" style="color: #333;">begin</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;">otherVariantIntervals</span><span class="p">.</span><span class="n" style="color: #333;">end</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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<pre style="margin: 0;">-<span id="LC309" class="line" lang="cpp">            <span class="n" style="color: #333;">variantIntervals</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;">first</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">IntervalTree</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*></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;">second</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC307" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">,</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">otherVariantIntervals</span><span class="p">.</span><span class="n" style="color: #333;">begin</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;">otherVariantIntervals</span><span class="p">.</span><span class="n" style="color: #333;">end</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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<pre style="margin: 0;">+<span id="LC308" class="line" lang="cpp">            <span class="n" style="color: #333;">variantIntervals</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;">first</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">IntervalTree</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">,</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*></span><span class="p">((</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">,</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">>&&</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;">second</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC309" class="line" lang="cpp">        <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC310" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC311" class="line" lang="cpp">    <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">@@ -323,10 +322,9 @@ int main(int argc, char** argv) {</td>

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<pre style="margin: 0;"> <span id="LC322" class="line" lang="cpp">            <span class="n" style="color: #333;">lastSequenceName</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">var</span><span class="p">.</span><span class="n" style="color: #333;">sequenceName</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC323" class="line" lang="cpp">        <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;">lastSequenceName</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">var</span><span class="p">.</span><span class="n" style="color: #333;">sequenceName</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC324" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">unioning</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC326" class="line" lang="cpp">                <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">previousRecords</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC325" class="line" lang="cpp">                <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lastSeqLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reference</span><span class="p">.</span><span class="n" style="color: #333;">sequenceLength</span><span class="p">(</span><span class="n" style="color: #333;">lastSequenceName</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC328" class="line" lang="cpp">                <span class="n" style="color: #333;">v<span class="idiff left">ariantIntervals</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">lastSequenceName</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">findContained</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">lastOutputPosition</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">lastSeqLength</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">previousRecords</span></span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC329" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">previousRecords</span><span class="p">.</span><span class="n" style="color: #333;">begin</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;">previousRecords</span><span class="p">.</span><span class="n" style="color: #333;">end</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="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC326" class="line" lang="cpp">                <span class="n" style="color: #333;">v<span class="idiff left">ector</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">Interval</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">size_t</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Variant</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*></span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">previousRecords</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">variantIntervals</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">lastSequenceName</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">findContained</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">lastOutputPosition</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">lastSeqLength</span></span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC327" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">size_t</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">previousRecords</span><span class="p">.</span><span class="n" style="color: #333;">begin</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;">previousRecords</span><span class="p">.</span><span class="n" style="color: #333;">end</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="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC328" class="line" lang="cpp">                    <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">v</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;">value</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC329" class="line" lang="cpp">                    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">outputVariants</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">outputVariants</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC330" class="line" lang="cpp">                        <span class="n" style="color: #333;">outputVariants</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -362,13 +360,12 @@ int main(int argc, char** argv) {</td>

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<pre style="margin: 0;"> <span id="LC360" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// hmm... for unioning, you might need to step through the original VCF records</span></span>

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<pre style="margin: 0;"> <span id="LC361" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// but the idea is to exclude the haplotype-based duplicates</span></span>

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<pre style="margin: 0;"> <span id="LC362" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC365" class="line" lang="cpp">            <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">results</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC366" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC367" class="line" lang="cpp">            <span class="n" style="color: #333;">variantIntervals</span><span class="p">[</span><span class="n" style="color: #333;">var</span><span class="p">.</span><span class="n" style="color: #333;">sequenceName</span><span class="p">].</span><span class="n" style="color: #333;">findContained</span><span class="p">(</span><span class="n" style="color: #333;">var</span><span class="p">.</span><span class="n" style="color: #333;">position</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">windowsize</span><span class="p">,</span> <span class="n" style="color: #333;">var</span><span class="p">.</span><span class="n" style="color: #333;">position</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">var</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="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">windowsize</span><span class="p">,</span> <span class="n" style="color: #333;">results</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC363" class="line" lang="cpp">            <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">,</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">results</span></span>

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<pre style="margin: 0;">+<span id="LC364" class="line" lang="cpp">                <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">variantIntervals</span><span class="p">[</span><span class="n" style="color: #333;">var</span><span class="p">.</span><span class="n" style="color: #333;">sequenceName</span><span class="p">].</span><span class="n" style="color: #333;">findContained</span><span class="p">(</span><span class="n" style="color: #333;">var</span><span class="p">.</span><span class="n" style="color: #333;">position</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">windowsize</span><span class="p">,</span> <span class="n" style="color: #333;">var</span><span class="p">.</span><span class="n" style="color: #333;">position</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">var</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="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">windowsize</span><span class="p">);</span></span>

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<td class="diff-line-num new_line" data-linenumber="365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC365" class="line" lang="cpp"></span>

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<td class="diff-line-num new_line" data-linenumber="366" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC366" class="line" lang="cpp">            <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*></span> <span class="n" style="color: #333;">overlapping</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC367" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC371" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">results</span><span class="p">.</span><span class="n" style="color: #333;">begin</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;">results</span><span class="p">.</span><span class="n" style="color: #333;">end</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="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC368" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">size_t</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">results</span><span class="p">.</span><span class="n" style="color: #333;">begin</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;">results</span><span class="p">.</span><span class="n" style="color: #333;">end</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="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC369" class="line" lang="cpp">                <span class="n" style="color: #333;">overlapping</span><span class="p">.</span><span class="n" style="color: #333;">push_back</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;">value</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC370" class="line" lang="cpp">            <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC371" class="line" lang="cpp"></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>

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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">@@ -381,13 +378,12 @@ int main(int argc, char** argv) {</td>

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<pre style="margin: 0;"> <span id="LC378" class="line" lang="cpp">                <span class="c1" style="color: #998; font-style: italic;">// between the last one printed out and the first</span></span>

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<pre style="margin: 0;"> <span id="LC379" class="line" lang="cpp">                <span class="c1" style="color: #998; font-style: italic;">// one we're about to print out</span></span>

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<pre style="margin: 0;"> <span id="LC380" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC384" class="line" lang="cpp">                <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">previousRecords</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC385" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC386" class="line" lang="cpp">                <span class="n" style="color: #333;">variantIntervals</span><span class="p">[</span><span class="n" style="color: #333;">var</span><span class="p">.</span><span class="n" style="color: #333;">sequenceName</span><span class="p">].</span><span class="n" style="color: #333;">findOverlapping</span><span class="p">(</span><span class="n" style="color: #333;">lastOutputPosition</span><span class="p">,</span> <span class="n" style="color: #333;">var</span><span class="p">.</span><span class="n" style="color: #333;">position</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">windowsize</span><span class="p">,</span> <span class="n" style="color: #333;">previousRecords</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC381" class="line" lang="cpp">                <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">,</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">previousRecords</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC382" class="line" lang="cpp">                    <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">variantIntervals</span><span class="p">[</span><span class="n" style="color: #333;">var</span><span class="p">.</span><span class="n" style="color: #333;">sequenceName</span><span class="p">].</span><span class="n" style="color: #333;">findOverlapping</span><span class="p">(</span><span class="n" style="color: #333;">lastOutputPosition</span><span class="p">,</span> <span class="n" style="color: #333;">var</span><span class="p">.</span><span class="n" style="color: #333;">position</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">windowsize</span><span class="p">);</span></span>

</pre>

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387

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<td class="diff-line-num new_line" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

383

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<pre style="margin: 0;"> <span id="LC383" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

388

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<td class="diff-line-num new_line" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC384" class="line" lang="cpp">                <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">variants</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

385

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<pre style="margin: 0;"> <span id="LC385" class="line" lang="cpp"></span>

</pre>

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390

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<td class="diff-line-num new_line old" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC390" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">previousRecords</span><span class="p">.</span><span class="n" style="color: #333;">begin</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;">previousRecords</span><span class="p">.</span><span class="n" style="color: #333;">end</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="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC386" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">size_t</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">previousRecords</span><span class="p">.</span><span class="n" style="color: #333;">begin</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;">previousRecords</span><span class="p">.</span><span class="n" style="color: #333;">end</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="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC387" class="line" lang="cpp">                    <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">v</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;">value</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC388" class="line" lang="cpp">                    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">outputVariants</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">outputVariants</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC389" class="line" lang="cpp">                        <span class="n" style="color: #333;">outputVariants</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">);</span></span>

</pre>

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<br>

</li>

<li id="b7af15dcd85a3603e7a069c58654922f58cb13f0">

<a href="https://salsa.debian.org/med-team/libvcflib/commit/18f9a56680d84676eadf8905cf2bd95b76fc9841#b7af15dcd85a3603e7a069c58654922f58cb13f0"><strong>src/vcfnormalizesvs.cpp</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="19" style="width: 35px; color: rgba(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="19" style="width: 35px; color: rgba(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">@@ -19,7 +19,7 @@ int main(int argc, char** argv) {</td>

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19

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<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

19

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="20" style="width: 35px; color: rgba(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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20

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp">    <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">ref_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

21

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp">    <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">insertion_files</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" 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">

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<td class="diff-line-num new_line 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">

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">m<span class="idiff left">ax_interval</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">m<span class="idiff left">in_size</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">replace_sequences</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</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>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="92" style="width: 35px; color: rgba(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="92" style="width: 35px; color: rgba(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">@@ -92,7 +92,7 @@ int main(int argc, char** argv) {</td>

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<pre style="margin: 0;"> <span id="LC92" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp">    <span class="n" style="color: #333;">Variant</span> <span class="n" style="color: #333;">var</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">variantFile</span><span class="p">.</span><span class="n" style="color: #333;">getNextVariant</span><span class="p">(</span><span class="n" style="color: #333;">var</span><span class="p">))</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC95" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">valid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">var</span><span class="p">.</span><span class="n" style="color: #333;">canonicalize<span class="idiff left">_sv</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ref</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">insertions</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">replace_sequences</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">max_interval</span></span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">valid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">var</span><span class="p">.</span><span class="n" style="color: #333;">canonicalize</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">ref</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">insertions</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">replace_sequences</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">min_size</span></span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC96" 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;">valid</span><span class="p">){</span></span>

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp">            <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Variant could not be normalized"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">var</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="cpp">        <span class="p">}</span></span>

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<br>

</li>

<li id="40f4482121a1441df05d09168d44fe98200323c7">

<a href="https://salsa.debian.org/med-team/libvcflib/commit/18f9a56680d84676eadf8905cf2bd95b76fc9841#40f4482121a1441df05d09168d44fe98200323c7"><strong>src/vcfroc.cpp</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -26,39 +26,38 @@ void printSummary(char** argv) {</td>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">buildVariantIntervalTree</span><span class="p">(</span><span class="n" style="color: #333;">VariantCallFile</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">variantFile</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="cpp">                              <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">IntervalTree</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">variantIntervals</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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">

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cpp">                              <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">IntervalTree</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">size_t</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">variantIntervals</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

30

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<td class="diff-line-num new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp">                              <span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">variants</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); 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="diff-line-num new_line old" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC32" class="line" lang="cpp">    <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">rawVariantIntervals</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cpp">    <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">size_t</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">rawVariantIntervals</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

33

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<td class="diff-line-num new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp">    <span class="n" style="color: #333;">Variant</span> <span class="n" style="color: #333;">var</span><span class="p">(</span><span class="n" style="color: #333;">variantFile</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">variantFile</span><span class="p">.</span><span class="n" style="color: #333;">getNextVariant</span><span class="p">(</span><span class="n" style="color: #333;">var</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">var</span><span class="p">.</span><span class="n" style="color: #333;">position</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">right</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">var</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="c1" style="color: #998; font-style: italic;">// this should be 1-past the end</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp">        <span class="n" style="color: #333;">variants</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">var</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp">        <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">variants</span><span class="p">.</span><span class="n" style="color: #333;">back</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); 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="diff-line-num new_line old" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC39" class="line" lang="cpp">        <span class="n" style="color: #333;">rawVariantIntervals</span><span class="p">[</span><span class="n" style="color: #333;">var</span><span class="p">.</span><span class="n" style="color: #333;">sequenceName</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*></span><span class="p">(</span><span class="n" style="color: #333;">left</span><span class="p">,</span> <span class="n" style="color: #333;">right</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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">

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp">        <span class="n" style="color: #333;">rawVariantIntervals</span><span class="p">[</span><span class="n" style="color: #333;">var</span><span class="p">.</span><span class="n" style="color: #333;">sequenceName</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">size_t</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*></span><span class="p">(</span><span class="n" style="color: #333;">left</span><span class="p">,</span> <span class="n" style="color: #333;">right</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp">   </span>

</pre>

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<pre style="margin: 0;">-<span id="LC42" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rawVariantIntervals</span><span class="p">.</span><span class="n" style="color: #333;">begin</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;">rawVariantIntervals</span><span class="p">.</span><span class="n" style="color: #333;">end</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="diff-line-num old old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="cpp">        <span class="n" style="color: #333;">variantIntervals</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;">first</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">IntervalTree</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;"><span class="idiff left">Variant</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*></span></span><span class="p"><span class="idiff right">(</span></span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">);</span></span>

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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">size_t</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rawVariantIntervals</span><span class="p">.</span><span class="n" style="color: #333;">begin</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;">rawVariantIntervals</span><span class="p">.</span><span class="n" style="color: #333;">end</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="diff-line-num new old_line" 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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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp">        <span class="n" style="color: #333;">variantIntervals</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;">first</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">IntervalTree</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">size_t</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Variant</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*></span></span><span class="p"><span class="idiff">((</span></span><span class="n" style="color: #333;"><span class="idiff">vector</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">Interval</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">size_t</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Variant</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*></span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">>&&</span></span><span class="p"><span class="idiff right">)</span></span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">);</span></span>

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<td class="diff-line-num old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cpp">    <span class="p">}</span></span>

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<td class="diff-line-num old_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cpp"><span class="p">}</span></span>

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<td class="diff-line-num old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_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">

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">intersectVariant</span><span class="p">(</span><span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">var</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC49" class="line" lang="cpp">                      <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">IntervalTree</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">variantIntervals</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp">                      <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">IntervalTree</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">size_t</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">variantIntervals</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp">                      <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">*>&</span> <span class="n" style="color: #333;">commonAlleles</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cpp">                      <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">*>&</span> <span class="n" style="color: #333;">uniqueAlleles</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cpp">                      <span class="n" style="color: #333;">FastaReference</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">reference</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cpp">                      <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">windowsize</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">50</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC55" class="line" lang="cpp">    <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">results</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC56" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC57" class="line" lang="cpp">    <span class="n" style="color: #333;">variantIntervals</span><span class="p">[</span><span class="n" style="color: #333;">var</span><span class="p">.</span><span class="n" style="color: #333;">sequenceName</span><span class="p">].</span><span class="n" style="color: #333;">findContained</span><span class="p">(</span><span class="n" style="color: #333;">var</span><span class="p">.</span><span class="n" style="color: #333;">position</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">windowsize</span><span class="p">,</span> <span class="n" style="color: #333;">var</span><span class="p">.</span><span class="n" style="color: #333;">position</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">var</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="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">windowsize</span><span class="p">,</span> <span class="n" style="color: #333;">results</span><span class="p">);</span></span>

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<td class="diff-line-num new old_line" 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">

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cpp">    <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">,</span> <span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">results</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cpp">        <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">variantIntervals</span><span class="p">[</span><span class="n" style="color: #333;">var</span><span class="p">.</span><span class="n" style="color: #333;">sequenceName</span><span class="p">].</span><span class="n" style="color: #333;">findContained</span><span class="p">(</span><span class="n" style="color: #333;">var</span><span class="p">.</span><span class="n" style="color: #333;">position</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">windowsize</span><span class="p">,</span> <span class="n" style="color: #333;">var</span><span class="p">.</span><span class="n" style="color: #333;">position</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">var</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="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">windowsize</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="cpp">    <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*></span> <span class="n" style="color: #333;">overlapping</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); 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="diff-line-num new_line old" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC61" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">results</span><span class="p">.</span><span class="n" style="color: #333;">begin</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;">results</span><span class="p">.</span><span class="n" style="color: #333;">end</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="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Interval</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">size_t</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">results</span><span class="p">.</span><span class="n" style="color: #333;">begin</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;">results</span><span class="p">.</span><span class="n" style="color: #333;">end</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="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="cpp">        <span class="n" style="color: #333;">overlapping</span><span class="p">.</span><span class="n" style="color: #333;">push_back</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;">value</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -223,11 +222,11 @@ int main(int argc, char** argv) {</td>

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<pre style="margin: 0;"> <span id="LC222" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// read the VCF file for union or intersection into an interval tree</span></span>

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<pre style="margin: 0;"> <span id="LC223" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// indexed using some proximity window</span></span>

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<pre style="margin: 0;"> <span id="LC224" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC226" class="line" lang="cpp">    <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">IntervalTree</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">truthVariantIntervals</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" 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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<pre style="margin: 0;">+<span id="LC225" class="line" lang="cpp">    <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">IntervalTree</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">size_t</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">truthVariantIntervals</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC226" class="line" lang="cpp">    <span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">truthVariants</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC227" class="line" lang="cpp">    <span class="n" style="color: #333;">buildVariantIntervalTree</span><span class="p">(</span><span class="n" style="color: #333;">truthVariantFile</span><span class="p">,</span> <span class="n" style="color: #333;">truthVariantIntervals</span><span class="p">,</span> <span class="n" style="color: #333;">truthVariants</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC228" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC230" class="line" lang="cpp">    <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">IntervalTree</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">testVariantIntervals</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<pre style="margin: 0;">+<span id="LC229" class="line" lang="cpp">    <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="n" style="color: #333;">IntervalTree</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">size_t</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">testVariantIntervals</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC230" class="line" lang="cpp">    <span class="n" style="color: #333;">list</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Variant</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">testVariants</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC231" class="line" lang="cpp">    <span class="n" style="color: #333;">buildVariantIntervalTree</span><span class="p">(</span><span class="n" style="color: #333;">variantFile</span><span class="p">,</span> <span class="n" style="color: #333;">testVariantIntervals</span><span class="p">,</span> <span class="n" style="color: #333;">testVariants</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC232" class="line" lang="cpp"></span>

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<br>

</li>

<li id="ece78a032e8effb46b4cccead2e1d42469704a62">

<a href="https://salsa.debian.org/med-team/libvcflib/commit/18f9a56680d84676eadf8905cf2bd95b76fc9841#ece78a032e8effb46b4cccead2e1d42469704a62"><strong>test/Makefile</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="20" style="width: 35px; color: rgba(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="20" style="width: 35px; color: rgba(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">@@ -20,4 +20,4 @@ tests/main: ../googletest/googletest/make/gtest_main.a</td>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="make"><span class="nl">run</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">tests/main</span></span>

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="make">  ./tests/main</span>

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="make"><span class="nl">clean</span><span class="o" style="font-weight: 600;">:</span></span>

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23

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="make">  <span class="nb" style="color: #0086b3;">rm </span>tests/main</span></pre>

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23

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="make">  <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> tests/main</span></pre>

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<li id="18cfe6cfeda7aa16dcc24f1650282d1367a79a65">

<a href="https://salsa.debian.org/med-team/libvcflib/commit/18f9a56680d84676eadf8905cf2bd95b76fc9841#18cfe6cfeda7aa16dcc24f1650282d1367a79a65"><strong>test/tests/main</strong>

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