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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/nim-hts">Debian Med / nim-hts</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/nim-hts/-/commit/05e0b475fe35f21817ad1fa3c0a8739c5c699389">05e0b475</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2020-11-26T11:52:20+00:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.3.13+ds</pre>
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<h4>6 changed files:</h4>
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<li class="file-stats">
<a href="#7facec255884dc55d3818e4dfbea89b1bdd7f49e">
CHANGES.md
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<a href="#6651ddff6eb82c840ced7c1dddee15c6e1913dd4">
Dockerfile
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−
Dockerfile.musl-hts-nim
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<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<a href="#ca825a47d973a01635e0751e33e26c3b765b2d2d">
src/hts/private/hts_concat.nim
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<li class="file-stats">
<a href="#af7f384ea46f18b33cf4aebdfce41183728786cf">
src/hts/vcf.nim
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<h4>Changes:</h4>
<li id="7facec255884dc55d3818e4dfbea89b1bdd7f49e">
<a href="https://salsa.debian.org/med-team/nim-hts/-/commit/05e0b475fe35f21817ad1fa3c0a8739c5c699389#7facec255884dc55d3818e4dfbea89b1bdd7f49e"><strong>CHANGES.md</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">v0.3.13</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">=======</span></span>
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<td class="diff-line-num new new_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="LC3" class="line" lang="markdown"><span class="p">+</span> changes for nim ORC/ARC GCs</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"></span>
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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">v0.3.11</span></span>
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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="markdown"><span class="gu" style="color: #800080; font-weight: 600;">=======</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"><span class="p">+</span> add bgzi.open which allows opening for reading and writing without quit() and replaces</span>
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<li id="6651ddff6eb82c840ced7c1dddee15c6e1913dd4">
<a href="https://salsa.debian.org/med-team/nim-hts/-/commit/05e0b475fe35f21817ad1fa3c0a8739c5c699389#6651ddff6eb82c840ced7c1dddee15c6e1913dd4"><strong>Dockerfile</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,7 +4,7 @@ FROM alpine:3.11.5</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="docker"><span class="k" style="font-weight: 600;">ENV</span><span class="s" style="color: #d14;"> CFLAGS="-fPIC -O3"</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="docker"></span>
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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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>apk add wget git xz bzip2-static musl m4 autoconf <span class="nb" style="color: #0086b3;">tar </span>xz-dev bzip2-dev build-base libpthread-stubs libzip-dev gfortran <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="docker"> openssl-libs-static openblas-static pcre-dev curl llvm-dev curl-static</span>
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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">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="docker"> openssl-libs-static openblas-static pcre-dev curl llvm-dev curl-static<span class="idiff left right"> bash</span></span>
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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">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="docker"></span>
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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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<pre style="margin: 0;"> <span id="LC9" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> /usr/local/include <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10" class="line" lang="docker"> git clone <span class="nt" style="color: #000080;">--depth</span> 1 https://github.com/ebiggers/libdeflate.git <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -38,7 +38,7 @@ ENV PATH=:/root/.nimble/bin:/nim/bin/:$PATH</td>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="docker"></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="docker"><span class="k" style="font-weight: 600;">RUN </span><span class="se" style="color: #d14;">\</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="docker"> git clone https://github.com/samtools/htslib <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num old old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="docker"> <span class="nb" style="color: #0086b3;">cd </span>htslib <span class="o" style="font-weight: 600;">&&</span> git checkout 1.1<span class="idiff left right">0.2</span> <span class="o" style="font-weight: 600;">&&</span> autoheader <span class="o" style="font-weight: 600;">&&</span> autoconf <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="docker"> <span class="nb" style="color: #0086b3;">cd </span>htslib <span class="o" style="font-weight: 600;">&&</span> git checkout 1.1<span class="idiff left right">1</span> <span class="o" style="font-weight: 600;">&&</span> autoheader <span class="o" style="font-weight: 600;">&&</span> autoconf <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="docker"> ./configure <span class="nt" style="color: #000080;">--disable-s3</span> <span class="nt" style="color: #000080;">--disable-libcurl</span> <span class="nt" style="color: #000080;">--with-libdeflate</span> <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="docker"> make <span class="nt" style="color: #000080;">-j4</span> <span class="nv" style="color: #008080;">CFLAGS</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"-fPIC -O3"</span> <span class="nb" style="color: #0086b3;">install</span> <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="docker"> <span class="nb" style="color: #0086b3;">cd</span> ../ <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</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">@@ -49,20 +49,20 @@ RUN \</td>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="docker"> <span class="nb" style="color: #0086b3;">cd</span> ../ <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> htslib bcftools</span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="docker"></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="docker"></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>sh <span class="nt" style="color: #000080;">-c</span> <span class="s1" style="color: #d14;">'curl --proto "=https" --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -q -y'</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;"># && apk add clang-libs</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="docker"></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>sh <span class="nt" style="color: #000080;">-c</span> <span class="s1" style="color: #d14;">'curl --proto "=https" --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -q -y'</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> apk add clang-libs</span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="docker"></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="docker"><span class="k" style="font-weight: 600;">ENV</span><span class="s" style="color: #d14;"> HTSLIB=dynamic</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="docker"><span class="k" style="font-weight: 600;">ENV</span><span class="s" style="color: #d14;"> HTSLIB=system</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="docker"><span class="k" style="font-weight: 600;">ENV</span><span class="s" style="color: #d14;"> PATH=$PATH:~/.cargo/bin/</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="docker"></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="docker"><span class="k" style="font-weight: 600;">COPY</span><span class="s" style="color: #d14;"> docker/d4.patch /tmp/</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>COPY docker/d4.patch /tmp/</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="docker"></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;">#&& git apply < /tmp/d4.patch \</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>~/.cargo/bin/rustup target add x86_64-unknown-linux-musl <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> git clone https://github.com/38/d4-format <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd </span>d4-format <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="docker"><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff right"> git apply < /tmp/d4.patch</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> ~/.cargo/bin/cargo build <span class="nt" style="color: #000080;">--target</span> x86_64-unknown-linux-musl <span class="nt" style="color: #000080;">--release</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="docker"><span class="idiff left"> </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">ln</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-s</span></span><span class="idiff right"> /usr/bin/gcc /usr/bin/musl-gcc</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> ~/.cargo/bin/cargo build <span class="nt" style="color: #000080;">--<span class="idiff left">all</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff right">--</span>target</span> x86_64-unknown-linux-musl <span class="nt" style="color: #000080;">--release</span></span>
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="docker"></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span><span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-m</span> 644 d4-format/target/x86_64-unknown-linux-musl/release/libd4binding.a /usr/lib <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="docker"> <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-m</span> 644 d4-format/d4binding/include/d4.h /usr/include</span>
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<a href="https://salsa.debian.org/med-team/nim-hts/-/commit/05e0b475fe35f21817ad1fa3c0a8739c5c699389#bc9f4eedc6018bfd9fc9677e6cf61e947987b248"><strong>Dockerfile.musl-hts-nim</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">## This dockerfile</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"># 1. builds htslib and all dependencies currently without libcurl</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"># 2. installs nim</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"># 3. sets up a nim binary (nsb) that is expected to be called from an external binary (static_builder)</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"># These facilitate building static binaries for projects using hts-nim.</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"># docker build -t brentp/musl-hts-nim:latest -f Dockerfile.musl-hts-nim .</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">FROM alpine:3.9</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">ENV LDFLAGS=-static PKG_CONFIG='pkg-config --static'</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">ENV curl_LDFLAGS=-all-static</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">RUN apk add curl musl build-base git autoconf zlib-dev bzip2-dev xz-dev curl-dev</span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">RUN cd / && \</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> git clone -b devel --depth 10 git://github.com/nim-lang/nim nim && \</span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> cd nim && sh ./build_all.sh</span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">RUN git clone --depth 1 https://github.com/ebiggers/libdeflate.git && \</span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> cd libdeflate && make -j 2 CFLAGS='-fPIC -O3' libdeflate.a && \</span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> cp libdeflate.a /usr/local/lib && cp libdeflate.h /usr/include && \</span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> cd .. && rm -rf libdeflate && \</span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> git clone https://github.com/samtools/htslib && \</span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> cd htslib && git checkout 1.9 && autoheader && autoconf && \</span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"> ./configure --enable-plugins --disable-libcurl --with-libdeflate && \</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"> make -j4 install && \</span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"> cd ../ && rm -rf htslib</span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">ADD . /src/</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext">ENV PATH=/root/.nimble/bin:/nim/bin/:$PATH</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext">RUN cat /src/docker/docker.nim.cfg >> /nim/config/nim.cfg && \</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext"> cd /src/ && nimble install -y && \</span>
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35
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext"> nimble install -y docopt && \</span>
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36
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext"> nimble install -y c2nim@#3ec45c24585ebaed && \</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext"> nim c -o:/usr/local/bin/nsb /src/docker/nsb.nim && \</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext"> rm -rf /src/</span></pre>
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<a href="https://salsa.debian.org/med-team/nim-hts/-/commit/05e0b475fe35f21817ad1fa3c0a8739c5c699389#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</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">@@ -17,7 +17,7 @@ too different to python.</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="markdown">If you use this library, please cite <span class="p">[</span><span class="nv" style="color: #008080;">the paper</span><span class="p">](</span><span class="sx" style="color: #d14;">https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/bty358/4990493</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="markdown">Projects using <span class="sb" style="color: #d14;">`hts-nim`</span> are accumulating <span class="p">[</span><span class="nv" style="color: #008080;">in the wiki</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/brentp/hts-nim/wiki/Example<span class="idiff left right">s</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown">Projects using <span class="sb" style="color: #d14;">`hts-nim`</span> are accumulating <span class="p">[</span><span class="nv" style="color: #008080;">in the wiki</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/brentp/hts-nim/wiki/Example<span class="idiff left right">-uses-of-hts-nim</span></span><span class="p">)</span></span>
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Installation</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="markdown"></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">@@ -29,7 +29,7 @@ Examples of `hts-nim` tools are available in the [hts-nim-tools repo](https://gi</td>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="markdown">below are examples of the syntax in this library see the <span class="p">[</span><span class="nv" style="color: #008080;">docs</span><span class="p">](</span><span class="sx" style="color: #d14;">https://brentp.github.io/hts-nim/</span><span class="p">)</span> for more info:</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="markdown">Also see examples and other repos using hts-nim in the <span class="p">[</span><span class="nv" style="color: #008080;">wiki</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/brentp/hts-nim/wiki/Example<span class="idiff left right">s</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="markdown">Also see examples and other repos using hts-nim in the <span class="p">[</span><span class="nv" style="color: #008080;">wiki</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/brentp/hts-nim/wiki/Example<span class="idiff left right">-uses-of-hts-nim</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## BAM / CRAM / SAM</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="markdown"></span>
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<li id="ca825a47d973a01635e0751e33e26c3b765b2d2d">
<a href="https://salsa.debian.org/med-team/nim-hts/-/commit/05e0b475fe35f21817ad1fa3c0a8739c5c699389#ca825a47d973a01635e0751e33e26c3b765b2d2d"><strong>src/hts/private/hts_concat.nim</strong></a>
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<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">@@ -8,9 +8,10 @@ elif defined(macosx):</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="nim"><span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="nim"> <span class="k" style="font-weight: 600;">const</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="nim"> <span class="n" style="color: #333;">libname</span><span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"libhts.so"</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="nim"><span class="k" style="font-weight: 600;">when</span> <span class="n" style="color: #333;">NimMajor</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="LC12" class="line" lang="nim"> <span class="k" style="font-weight: 600;">type</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="nim"> <span class="n" style="color: #333;">csize_t</span><span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">csize</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="nim"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="nim"><span class="k" style="font-weight: 600;">when</span> <span class="p">(</span><span class="n" style="color: #333;">NimMajor</span><span class="p">,</span> <span class="n" style="color: #333;">NimMinor</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">):</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="nim"> <span class="k" style="font-weight: 600;">type</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="nim"> <span class="n" style="color: #333;">csize_t</span><span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">csize</span></span>
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14
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="nim"><span class="sd" style="color: #d14;">##</span></span>
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15
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="nim"><span class="sd" style="color: #d14;">## enum hts_fmt_option {</span></span>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="nim"><span class="sd" style="color: #d14;">## // CRAM specific</span></span>
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<a href="https://salsa.debian.org/med-team/nim-hts/-/commit/05e0b475fe35f21817ad1fa3c0a8739c5c699389#af7f384ea46f18b33cf4aebdfce41183728786cf"><strong>src/hts/vcf.nim</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">@@ -73,6 +73,17 @@ var empty_samples: seq[string]</td>
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="nim"><span class="k" style="font-weight: 600;">converter</span> <span class="n" style="color: #333;">toInt</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">:</span><span class="n" style="color: #333;">BCF_HEADER_TYPE</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;">b</span><span class="p">.</span><span class="kt" style="color: #458; font-weight: 600;">int</span></span>
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74
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="nim"><span class="k" style="font-weight: 600;">converter</span> <span class="n" style="color: #333;">toCint</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">:</span><span class="n" style="color: #333;">BCF_HEADER_TYPE</span><span class="p">):</span> <span class="n" style="color: #333;">cint</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">cint</span></span>
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75
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="nim"></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">destroy_variant</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">:</span><span class="n" style="color: #333;">Variant</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span></span>
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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="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">nil</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">nil</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">own</span><span class="p">:</span></span>
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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="nim"> <span class="n" style="color: #333;">bcf_destroy</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">c</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="nim"> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">nil</span></span>
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<td class="diff-line-num new new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">nil</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="nim"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">p</span><span class="p">)</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="nim"></span>
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<td class="diff-line-num new new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">destroy_format</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">:</span><span class="n" style="color: #333;">Format</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span></span>
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<td class="diff-line-num new new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">nil</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">nil</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="nim"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">p</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="nim"></span>
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76
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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">n_samples</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">:</span><span class="n" style="color: #333;">VCF</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;">inline</span><span class="p">.}</span> <span class="o" style="font-weight: 600;">=</span></span>
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77
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88
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="nim"> <span class="n" style="color: #333;">bcf_hdr_nsamples</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">hdr</span><span class="p">).</span><span class="kt" style="color: #458; font-weight: 600;">int</span></span>
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78
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="nim"></span>
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<td class="diff-line-num unfold js-unfold old_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="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -175,15 +186,68 @@ proc remove_format*(h:Header, ID:string): Status =</td>
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175
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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">
186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="nim"> <span class="n" style="color: #333;">bcf_hdr_remove</span><span class="p">(</span><span class="n" style="color: #333;">h</span><span class="p">.</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="n" style="color: #333;">BCF_HEADER_TYPE</span><span class="p">.</span><span class="n" style="color: #333;">BCF_HL_FMT</span><span class="p">.</span><span class="n" style="color: #333;">cint</span><span class="p">,</span> <span class="n" style="color: #333;">ID</span><span class="p">.</span><span class="n" style="color: #333;">cstring</span><span class="p">)</span></span>
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<td class="diff-line-num old_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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<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">
187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="nim"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Status</span><span class="p">(</span><span class="n" style="color: #333;">bcf_hdr_sync</span><span class="p">(</span><span class="n" style="color: #333;">h</span><span class="p">.</span><span class="n" style="color: #333;">hdr</span><span class="p">))</span></span>
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177
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<td class="diff-line-num new_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="nim"></span>
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<td class="diff-line-num old old_line" 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">
178
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<td class="diff-line-num new_line old" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">info</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">:</span><span class="n" style="color: #333;">Variant</span><span class="p">):</span> <span class="n" style="color: #333;">INFO</span> <span class="p">{.</span><span class="n" style="color: #333;">inline</span><span class="p">,</span> <span class="n" style="color: #333;">noInit</span><span class="p">.}</span> <span class="o" style="font-weight: 600;">=</span></span>
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<td class="diff-line-num old old_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
179
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<td class="diff-line-num new_line old" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="nim"> <span class="k" style="font-weight: 600;">discard</span> <span class="n" style="color: #333;">bcf_unpack</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">BCF_UN_STR</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">BCF_UN_FLT</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">BCF_UN_INFO</span><span class="p">)</span></span>
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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="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">
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="nim"> <span class="n" style="color: #333;">result</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;">i</span><span class="p">:</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">v</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 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">
189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">destroy_vcf</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">:</span><span class="n" style="color: #333;">VCF</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span></span>
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<td class="diff-line-num new old_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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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">
190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="nim"> <span class="n" style="color: #333;">bcf_hdr_destroy</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">hdr</span><span class="p">)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">tidx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">nil</span><span class="p">:</span></span>
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<td class="diff-line-num new old_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="nim"> <span class="n" style="color: #333;">tbx_destroy</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">tidx</span><span class="p">)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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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">
193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">bidx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">nil</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="nim"> <span class="n" style="color: #333;">hts_idx_destroy</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">bidx</span><span class="p">)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">nil</span><span class="p">:</span></span>
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<td class="diff-line-num new old_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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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">
196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="nim"> <span class="n" style="color: #333;">bcf_destroy</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">c</span><span class="p">)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">fname</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"-"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">fname</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"/dev/stdin"</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">hts</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">nil</span><span class="p">:</span></span>
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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="nim"> <span class="k" style="font-weight: 600;">discard</span> <span class="n" style="color: #333;">hts_close</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">hts</span><span class="p">)</span></span>
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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">
200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="nim"> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">hts</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">nil</span></span>
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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="nim"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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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="nim"> <span class="n" style="color: #333;">flushFile</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">)</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="nim"></span>
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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">
204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="nim"><span class="k" style="font-weight: 600;">var</span></span>
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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="nim"> <span class="n" style="color: #333;">errno</span><span class="o" style="font-weight: 600;">*</span> <span class="p">{.</span><span class="n" style="color: #333;">importc</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">:</span> <span class="s" style="color: #d14;">"<errno.h>"</span><span class="p">.}:</span> <span class="n" style="color: #333;">cint</span></span>
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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="nim"></span>
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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">
207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">strerror</span><span class="p">(</span><span class="n" style="color: #333;">errnum</span><span class="p">:</span><span class="n" style="color: #333;">cint</span><span class="p">):</span> <span class="n" style="color: #333;">cstring</span> <span class="p">{.</span><span class="n" style="color: #333;">importc</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">:</span> <span class="s" style="color: #d14;">"<errno.h>"</span><span class="p">,</span> <span class="n" style="color: #333;">cdecl</span><span class="p">.}</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="nim"></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="nim"></span>
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<td class="diff-line-num new new_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">open</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">:</span><span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">VCF</span><span class="p">,</span> <span class="n" style="color: #333;">fname</span><span class="p">:</span><span class="kt" style="color: #458; font-weight: 600;">string</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="p">:</span><span class="kt" style="color: #458; font-weight: 600;">string</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"r"</span><span class="p">,</span> <span class="n" style="color: #333;">samples</span><span class="p">:</span><span class="kt" style="color: #458; font-weight: 600;">seq</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">string</span><span class="o" style="font-weight: 600;">]=</span><span class="n" style="color: #333;">empty_samples</span><span class="p">,</span> <span class="n" style="color: #333;">threads</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="mi" style="color: #099;">0</span><span class="p">):</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="o" style="font-weight: 600;">=</span></span>
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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">
211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="nim"> <span class="sd" style="color: #d14;">## open a VCF at the given path</span></span>
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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">
212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="nim"> <span class="n" style="color: #333;">new</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">,</span> <span class="n" style="color: #333;">destroy_vcf</span><span class="p">)</span></span>
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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">
213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">vmode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mode</span></span>
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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">
214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">vmode</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'w'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">vmode</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="p">:</span></span>
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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">
215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fname</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">".gz"</span><span class="p">):</span> <span class="n" style="color: #333;">vmode</span> <span class="o" style="font-weight: 600;">&=</span> <span class="s" style="color: #d14;">"z"</span></span>
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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">
216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="nim"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">fname</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">".bcf"</span><span class="p">):</span> <span class="n" style="color: #333;">vmode</span> <span class="o" style="font-weight: 600;">&=</span> <span class="s" style="color: #d14;">"b"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="nim"></span>
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<td class="diff-line-num new new_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">
218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="nim"> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">hts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hts_open</span><span class="p">(</span><span class="n" style="color: #333;">fname</span><span class="p">.</span><span class="n" style="color: #333;">cstring</span><span class="p">,</span> <span class="n" style="color: #333;">vmode</span><span class="p">.</span><span class="n" style="color: #333;">cstring</span><span class="p">)</span></span>
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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">
219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="nim"> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fname</span></span>
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<td class="diff-line-num new old_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<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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<pre style="margin: 0;">+<span id="LC220" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">hts</span> <span class="o" style="font-weight: 600;">==</span> <span class="k" style="font-weight: 600;">nil</span><span class="p">:</span></span>
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<td class="diff-line-num new old_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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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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<pre style="margin: 0;">+<span id="LC221" class="line" lang="nim"> <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">write_line</span> <span class="s" style="color: #d14;">"hts-nim/vcf: error opening file:"</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fname</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="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">strerror</span><span class="p">(</span><span class="n" style="color: #333;">errno</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="nim"> <span class="k" style="font-weight: 600;">return</span> <span class="kp" style="font-weight: 600;">false</span></span>
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<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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<pre style="margin: 0;">+<span id="LC223" class="line" lang="nim"></span>
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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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<pre style="margin: 0;">+<span id="LC224" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'w'</span><span class="p">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="kp" style="font-weight: 600;">true</span></span>
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<td class="diff-line-num new old_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_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">
225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="nim"></span>
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<td class="diff-line-num new old_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<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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<pre style="margin: 0;">+<span id="LC226" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'r'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">threads</span> <span class="ow" style="font-weight: 600;">and</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">hts_set_threads</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">hts</span><span class="p">,</span> <span class="n" style="color: #333;">cint</span><span class="p">(</span><span class="n" style="color: #333;">threads</span><span class="p">)):</span></span>
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<td class="diff-line-num new old_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<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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<pre style="margin: 0;">+<span id="LC227" class="line" lang="nim"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">newException</span><span class="p">(</span><span class="n" style="color: #333;">ValueError</span><span class="p">,</span> <span class="s" style="color: #d14;">"error setting number of threads"</span><span class="p">)</span></span>
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<td class="diff-line-num old_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">
181
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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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<pre style="margin: 0;"> <span id="LC228" class="line" lang="nim"></span>
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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="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="LC182" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">destroy_format</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">:</span><span class="n" style="color: #333;">Format</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span></span>
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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">
183
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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="LC183" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">nil</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">nil</span><span class="p">:</span></span>
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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="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="LC184" class="line" lang="nim"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">p</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
185
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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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<pre style="margin: 0;"> <span id="LC229" class="line" lang="nim"></span>
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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="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="LC186" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">:</span><span class="n" style="color: #333;">Variant</span><span class="p">):</span> <span class="n" style="color: #333;">FORMAT</span> <span class="p">{.</span><span class="n" style="color: #333;">inline</span><span class="p">,</span> <span class="n" style="color: #333;">noInit</span><span class="p">.}</span> <span class="o" style="font-weight: 600;">=</span></span>
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<td class="diff-line-num new old_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_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">
230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="nim"> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Header</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">:</span><span class="n" style="color: #333;">bcf_hdr_read</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">hts</span><span class="p">))</span></span>
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<td class="diff-line-num new old_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<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="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">hdr</span> <span class="o" style="font-weight: 600;">==</span> <span class="k" style="font-weight: 600;">nil</span><span class="p">:</span></span>
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<td class="diff-line-num new old_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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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">
232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="nim"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">newException</span><span class="p">(</span><span class="n" style="color: #333;">OSError</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="s" style="color: #d14;">"[hts-nim/vcf] error reading VCF header from '{fname}'"</span><span class="p">)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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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">
233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">samples</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;">0</span><span class="p">:</span></span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="nim"> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">set_samples</span><span class="p">(</span><span class="n" style="color: #333;">samples</span><span class="p">)</span></span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="nim"></span>
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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">
236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="nim"> <span class="n" style="color: #333;">v</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;">bcf_init</span><span class="p">()</span></span>
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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">
237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="nim"></span>
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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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<pre style="margin: 0;">+<span id="LC238" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="k" style="font-weight: 600;">nil</span><span class="p">:</span></span>
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<td class="diff-line-num new old_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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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">
239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="nim"> <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">write_line</span> <span class="s" style="color: #d14;">"hts-nim/vcf: error opening file:"</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fname</span></span>
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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">
240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="nim"> <span class="k" style="font-weight: 600;">return</span> <span class="kp" style="font-weight: 600;">false</span></span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="nim"></span>
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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">
242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="nim"> <span class="k" style="font-weight: 600;">return</span> <span class="kp" style="font-weight: 600;">true</span></span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="nim"></span>
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<td class="diff-line-num new new_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">
244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">newVariant</span><span class="o" style="font-weight: 600;">*</span><span class="p">():</span> <span class="n" style="color: #333;">Variant</span> <span class="p">{.</span><span class="n" style="color: #333;">noInit</span><span class="p">.}</span> <span class="o" style="font-weight: 600;">=</span></span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="nim"> <span class="sd" style="color: #d14;">## make an empty variant.</span></span>
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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">
246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="nim"> <span class="n" style="color: #333;">new</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">,</span> <span class="n" style="color: #333;">destroy_variant</span><span class="p">)</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">
247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="nim"> <span class="n" style="color: #333;">result</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;">bcf_init</span><span class="p">()</span></span>
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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">
248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="nim"> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">own</span> <span class="o" style="font-weight: 600;">=</span> <span class="kp" style="font-weight: 600;">true</span></span>
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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">
249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="nim"></span>
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<td class="diff-line-num new old_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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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">
250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">format</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">:</span><span class="n" style="color: #333;">Variant</span><span class="p">):</span> <span class="n" style="color: #333;">FORMAT</span> <span class="p">{.</span><span class="n" style="color: #333;">inline</span><span class="p">.}</span> <span class="o" style="font-weight: 600;">=</span></span>
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<td class="diff-line-num old_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">
187
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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC251" class="line" lang="nim"> <span class="k" style="font-weight: 600;">discard</span> <span class="n" style="color: #333;">bcf_unpack</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">BCF_UN_ALL</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
188
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<td class="diff-line-num new_line" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
252
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="nim"> <span class="n" style="color: #333;">new</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">,</span> <span class="n" style="color: #333;">destroy_format</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
189
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253
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="nim"> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">v</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="396" style="width: 35px; color: rgba(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="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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -396,44 +460,6 @@ proc set*(i:INFO, key:string, values:var seq[int32]): Status {.inline.} =</td>
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396
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460
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<pre style="margin: 0;"> <span id="LC460" class="line" lang="nim"> <span class="n" style="color: #333;">values</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]</span><span class="p">.</span><span class="k" style="font-weight: 600;">addr</span><span class="p">.</span><span class="n" style="color: #333;">pointer</span><span class="p">,</span> <span class="n" style="color: #333;">len</span><span class="p">(</span><span class="n" style="color: #333;">values</span><span class="p">).</span><span class="n" style="color: #333;">cint</span><span class="p">,</span> <span class="n" style="color: #333;">BCF_HT_INT</span><span class="p">.</span><span class="n" style="color: #333;">cint</span><span class="p">)</span></span>
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397
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<td class="diff-line-num new_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
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<pre style="margin: 0;"> <span id="LC461" class="line" lang="nim"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Status</span><span class="p">(</span><span class="n" style="color: #333;">ret</span><span class="p">.</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span></span>
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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
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<td class="diff-line-num new_line" data-linenumber="462" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
462
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<pre style="margin: 0;"> <span id="LC462" class="line" lang="nim"></span>
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399
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<td class="diff-line-num new_line old" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC399" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">destroy_variant</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">:</span><span class="n" style="color: #333;">Variant</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span></span>
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<td class="diff-line-num old old_line" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
400
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<td class="diff-line-num new_line old" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC400" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">nil</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">nil</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">own</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
401
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<td class="diff-line-num new_line old" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC401" class="line" lang="nim"> <span class="n" style="color: #333;">bcf_destroy</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">c</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
402
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<td class="diff-line-num new_line old" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC402" class="line" lang="nim"> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">nil</span></span>
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<td class="diff-line-num old old_line" data-linenumber="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
403
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<td class="diff-line-num new_line old" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC403" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">nil</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
404
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<td class="diff-line-num new_line old" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC404" class="line" lang="nim"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">p</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
405
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<td class="diff-line-num new_line old" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC405" class="line" lang="nim"></span>
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<td class="diff-line-num old old_line" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
406
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<td class="diff-line-num new_line old" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC406" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">from_string</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">:</span> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">Variant</span><span class="p">,</span> <span class="n" style="color: #333;">h</span><span class="p">:</span> <span class="n" style="color: #333;">Header</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">:</span><span class="k" style="font-weight: 600;">var</span> <span class="kt" style="color: #458; font-weight: 600;">string</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span></span>
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<td class="diff-line-num old old_line" data-linenumber="407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
407
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<td class="diff-line-num new_line old" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC407" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kstring_t</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">:</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">cstring</span><span class="p">,</span> <span class="n" style="color: #333;">l</span><span class="p">:</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">.</span><span class="n" style="color: #333;">csize_t</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">:</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">.</span><span class="n" style="color: #333;">csize_t</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" 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">
408
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<td class="diff-line-num new_line old" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC408" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;">==</span> <span class="k" style="font-weight: 600;">nil</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
409
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<td class="diff-line-num new_line old" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC409" class="line" lang="nim"> <span class="n" style="color: #333;">new</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">,</span> <span class="n" style="color: #333;">destroy_variant</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
410
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<td class="diff-line-num new_line old" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC410" class="line" lang="nim"> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">own</span> <span class="o" style="font-weight: 600;">=</span> <span class="kp" style="font-weight: 600;">true</span></span>
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<td class="diff-line-num old old_line" data-linenumber="411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
411
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<td class="diff-line-num new_line old" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC411" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="k" style="font-weight: 600;">nil</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
412
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<td class="diff-line-num new_line old" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC412" class="line" lang="nim"> <span class="n" style="color: #333;">v</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;">bcf_init</span><span class="p">()</span></span>
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<td class="diff-line-num old old_line" data-linenumber="413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
413
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<td class="diff-line-num new_line old" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC413" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">vcf_parse</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="p">.</span><span class="k" style="font-weight: 600;">addr</span><span class="p">,</span> <span class="n" style="color: #333;">h</span><span class="p">.</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">c</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" 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">
414
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<td class="diff-line-num new_line old" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC414" class="line" lang="nim"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">newException</span><span class="p">(</span><span class="n" style="color: #333;">ValueError</span><span class="p">,</span> <span class="s" style="color: #d14;">"hts-nim/Variant/from_string: error parsing variant:"</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">s</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
415
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<pre style="margin: 0;">-<span id="LC415" class="line" lang="nim"></span>
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416
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<pre style="margin: 0;">-<span id="LC416" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">newVariant</span><span class="o" style="font-weight: 600;">*</span><span class="p">():</span> <span class="n" style="color: #333;">Variant</span> <span class="p">{.</span><span class="n" style="color: #333;">noInit</span><span class="p">.}</span> <span class="o" style="font-weight: 600;">=</span></span>
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417
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<pre style="margin: 0;">-<span id="LC417" class="line" lang="nim"> <span class="sd" style="color: #d14;">## make an empty variant.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
418
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<pre style="margin: 0;">-<span id="LC418" class="line" lang="nim"> <span class="n" style="color: #333;">new</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">,</span> <span class="n" style="color: #333;">destroy_variant</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
419
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<td class="diff-line-num new_line old" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC419" class="line" lang="nim"> <span class="n" style="color: #333;">result</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;">bcf_init</span><span class="p">()</span></span>
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<td class="diff-line-num old old_line" data-linenumber="420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
420
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<pre style="margin: 0;">-<span id="LC420" class="line" lang="nim"> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">own</span> <span class="o" style="font-weight: 600;">=</span> <span class="kp" style="font-weight: 600;">true</span></span>
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<td class="diff-line-num old old_line" 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">
421
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<pre style="margin: 0;">-<span id="LC421" class="line" lang="nim"></span>
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<td class="diff-line-num old old_line" data-linenumber="422" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
422
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<td class="diff-line-num new_line old" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC422" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">destroy_vcf</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">:</span><span class="n" style="color: #333;">VCF</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span></span>
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<td class="diff-line-num old old_line" data-linenumber="423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
423
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<pre style="margin: 0;">-<span id="LC423" class="line" lang="nim"> <span class="n" style="color: #333;">bcf_hdr_destroy</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">hdr</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
424
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<td class="diff-line-num new_line old" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC424" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">tidx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">nil</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
425
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<pre style="margin: 0;">-<span id="LC425" class="line" lang="nim"> <span class="n" style="color: #333;">tbx_destroy</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">tidx</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
426
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<pre style="margin: 0;">-<span id="LC426" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">bidx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">nil</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
427
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<pre style="margin: 0;">-<span id="LC427" class="line" lang="nim"> <span class="n" style="color: #333;">hts_idx_destroy</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">bidx</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
428
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<td class="diff-line-num new_line old" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC428" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">nil</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
429
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<td class="diff-line-num new_line old" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC429" class="line" lang="nim"> <span class="n" style="color: #333;">bcf_destroy</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">c</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
430
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<td class="diff-line-num new_line old" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC430" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">fname</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"-"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">fname</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"/dev/stdin"</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
431
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<td class="diff-line-num new_line old" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); 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="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">hts</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">nil</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
432
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<td class="diff-line-num new_line old" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC432" class="line" lang="nim"> <span class="k" style="font-weight: 600;">discard</span> <span class="n" style="color: #333;">hts_close</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">hts</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
433
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<td class="diff-line-num new_line old" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC433" class="line" lang="nim"> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">hts</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">nil</span></span>
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<td class="diff-line-num old old_line" data-linenumber="434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
434
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<td class="diff-line-num new_line old" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC434" class="line" lang="nim"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
435
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<td class="diff-line-num new_line old" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC435" class="line" lang="nim"> <span class="n" style="color: #333;">flushFile</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="436" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
436
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<td class="diff-line-num new_line old" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC436" class="line" lang="nim"></span>
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<pre style="margin: 0;"> <span id="LC463" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">close</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">:</span><span class="n" style="color: #333;">VCF</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;"> <span id="LC464" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">fname</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"-"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">fname</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"/dev/stdin"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">hts</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">nil</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC465" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">hts_close</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">hts</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<td class="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="495" style="width: 35px; color: rgba(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">@@ -469,44 +495,9 @@ proc write_variant*(v:VCF, variant:Variant): bool =</td>
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469
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<pre style="margin: 0;"> <span id="LC495" class="line" lang="nim"> <span class="n" style="color: #333;">doAssert</span> <span class="n" style="color: #333;">bcf_hdr_sync</span><span class="p">(</span><span class="n" style="color: #333;">variant</span><span class="p">.</span><span class="n" style="color: #333;">vcf</span><span class="p">.</span><span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">hdr</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span></span>
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470
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496
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<pre style="margin: 0;"> <span id="LC496" class="line" lang="nim"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">bcf_write</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">hts</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="n" style="color: #333;">variant</span><span class="p">.</span><span class="n" style="color: #333;">c</span><span class="p">)</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="LC497" class="line" lang="nim"></span>
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<pre style="margin: 0;">-<span id="LC472" class="line" lang="nim"><span class="k" style="font-weight: 600;">var</span></span>
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<pre style="margin: 0;">-<span id="LC473" class="line" lang="nim"> <span class="n" style="color: #333;">errno</span><span class="o" style="font-weight: 600;">*</span> <span class="p">{.</span><span class="n" style="color: #333;">importc</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">:</span> <span class="s" style="color: #d14;">"<errno.h>"</span><span class="p">.}:</span> <span class="n" style="color: #333;">cint</span></span>
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<pre style="margin: 0;">-<span id="LC474" class="line" lang="nim"></span>
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<pre style="margin: 0;">-<span id="LC475" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">strerror</span><span class="p">(</span><span class="n" style="color: #333;">errnum</span><span class="p">:</span><span class="n" style="color: #333;">cint</span><span class="p">):</span> <span class="n" style="color: #333;">cstring</span> <span class="p">{.</span><span class="n" style="color: #333;">importc</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">:</span> <span class="s" style="color: #d14;">"<errno.h>"</span><span class="p">,</span> <span class="n" style="color: #333;">cdecl</span><span class="p">.}</span></span>
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<pre style="margin: 0;">-<span id="LC476" class="line" lang="nim"></span>
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<pre style="margin: 0;">-<span id="LC477" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">open</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">:</span><span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">VCF</span><span class="p">,</span> <span class="n" style="color: #333;">fname</span><span class="p">:</span><span class="kt" style="color: #458; font-weight: 600;">string</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="p">:</span><span class="kt" style="color: #458; font-weight: 600;">string</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"r"</span><span class="p">,</span> <span class="n" style="color: #333;">samples</span><span class="p">:</span><span class="kt" style="color: #458; font-weight: 600;">seq</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">string</span><span class="o" style="font-weight: 600;">]=</span><span class="n" style="color: #333;">empty_samples</span><span class="p">,</span> <span class="n" style="color: #333;">threads</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="mi" style="color: #099;">0</span><span class="p">):</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;">-<span id="LC478" class="line" lang="nim"> <span class="sd" style="color: #d14;">## open a VCF at the given path</span></span>
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<pre style="margin: 0;">-<span id="LC479" class="line" lang="nim"> <span class="n" style="color: #333;">new</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">,</span> <span class="n" style="color: #333;">destroy_vcf</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC480" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">vmode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mode</span></span>
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<pre style="margin: 0;">-<span id="LC481" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">vmode</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'w'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">vmode</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="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC482" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fname</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">".gz"</span><span class="p">):</span> <span class="n" style="color: #333;">vmode</span> <span class="o" style="font-weight: 600;">&=</span> <span class="s" style="color: #d14;">"z"</span></span>
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<pre style="margin: 0;">-<span id="LC483" class="line" lang="nim"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">fname</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">".bcf"</span><span class="p">):</span> <span class="n" style="color: #333;">vmode</span> <span class="o" style="font-weight: 600;">&=</span> <span class="s" style="color: #d14;">"b"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
484
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<td class="diff-line-num new_line old" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC484" class="line" lang="nim"></span>
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<td class="diff-line-num old old_line" data-linenumber="485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
485
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<td class="diff-line-num new_line old" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC485" class="line" lang="nim"> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">hts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hts_open</span><span class="p">(</span><span class="n" style="color: #333;">fname</span><span class="p">.</span><span class="n" style="color: #333;">cstring</span><span class="p">,</span> <span class="n" style="color: #333;">vmode</span><span class="p">.</span><span class="n" style="color: #333;">cstring</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="486" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
486
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<td class="diff-line-num new_line old" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC486" class="line" lang="nim"> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fname</span></span>
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<td class="diff-line-num old old_line" data-linenumber="487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
487
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<td class="diff-line-num new_line old" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC487" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">hts</span> <span class="o" style="font-weight: 600;">==</span> <span class="k" style="font-weight: 600;">nil</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
488
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<td class="diff-line-num new_line old" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC488" class="line" lang="nim"> <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">write_line</span> <span class="s" style="color: #d14;">"hts-nim/vcf: error opening file:"</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fname</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="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">strerror</span><span class="p">(</span><span class="n" style="color: #333;">errno</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
489
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<td class="diff-line-num new_line old" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC489" class="line" lang="nim"> <span class="k" style="font-weight: 600;">return</span> <span class="kp" style="font-weight: 600;">false</span></span>
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490
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<td class="diff-line-num new_line old" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC490" class="line" lang="nim"></span>
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<td class="diff-line-num old old_line" data-linenumber="491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
491
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<td class="diff-line-num new_line old" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC491" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'w'</span><span class="p">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="kp" style="font-weight: 600;">true</span></span>
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<td class="diff-line-num old old_line" data-linenumber="492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
492
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<td class="diff-line-num new_line old" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC492" class="line" lang="nim"></span>
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<td class="diff-line-num old old_line" data-linenumber="493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
493
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<td class="diff-line-num new_line old" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC493" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'r'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">threads</span> <span class="ow" style="font-weight: 600;">and</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">hts_set_threads</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">hts</span><span class="p">,</span> <span class="n" style="color: #333;">cint</span><span class="p">(</span><span class="n" style="color: #333;">threads</span><span class="p">)):</span></span>
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<td class="diff-line-num old old_line" data-linenumber="494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
494
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<td class="diff-line-num new_line old" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC494" class="line" lang="nim"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">newException</span><span class="p">(</span><span class="n" style="color: #333;">ValueError</span><span class="p">,</span> <span class="s" style="color: #d14;">"error setting number of threads"</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
495
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<td class="diff-line-num new_line old" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC495" class="line" lang="nim"></span>
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<td class="diff-line-num old old_line" data-linenumber="496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
496
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<td class="diff-line-num new_line old" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC496" class="line" lang="nim"></span>
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<td class="diff-line-num old old_line" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
497
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<td class="diff-line-num new_line old" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC497" class="line" lang="nim"> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Header</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">:</span><span class="n" style="color: #333;">bcf_hdr_read</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">hts</span><span class="p">))</span></span>
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<td class="diff-line-num old old_line" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
498
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<td class="diff-line-num new_line old" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC498" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">hdr</span> <span class="o" style="font-weight: 600;">==</span> <span class="k" style="font-weight: 600;">nil</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
499
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<td class="diff-line-num new_line old" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC499" class="line" lang="nim"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">newException</span><span class="p">(</span><span class="n" style="color: #333;">OSError</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="s" style="color: #d14;">"[hts-nim/vcf] error reading VCF header from '{fname}'"</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
500
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<td class="diff-line-num new_line old" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC500" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">samples</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;">0</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
501
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<td class="diff-line-num new_line old" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC501" class="line" lang="nim"> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">set_samples</span><span class="p">(</span><span class="n" style="color: #333;">samples</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="502" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
502
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<td class="diff-line-num new_line old" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC502" class="line" lang="nim"></span>
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<td class="diff-line-num old old_line" data-linenumber="503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
503
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<pre style="margin: 0;">-<span id="LC503" class="line" lang="nim"> <span class="n" style="color: #333;">v</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;">bcf_init</span><span class="p">()</span></span>
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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="498" style="width: 35px; color: rgba(0,0,0,0.3); 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="nim"></span>
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<td class="diff-line-num old old_line" data-linenumber="505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
505
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<td class="diff-line-num new_line old" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC505" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="k" style="font-weight: 600;">nil</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
506
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<td class="diff-line-num new_line old" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC506" class="line" lang="nim"> <span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">write_line</span> <span class="s" style="color: #d14;">"hts-nim/vcf: error opening file:"</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fname</span></span>
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<td class="diff-line-num old old_line" data-linenumber="507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
507
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<td class="diff-line-num new_line old" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC507" class="line" lang="nim"> <span class="k" style="font-weight: 600;">return</span> <span class="kp" style="font-weight: 600;">false</span></span>
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<td class="diff-line-num old old_line" data-linenumber="508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
508
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<td class="diff-line-num new_line old" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC508" class="line" lang="nim"></span>
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<td class="diff-line-num old old_line" data-linenumber="509" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
509
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<td class="diff-line-num new_line old" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC509" class="line" lang="nim"> <span class="k" style="font-weight: 600;">return</span> <span class="kp" style="font-weight: 600;">true</span></span>
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<td class="diff-line-num new old_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">
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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="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">info</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">:</span><span class="n" style="color: #333;">Variant</span><span class="p">):</span> <span class="n" style="color: #333;">INFO</span> <span class="p">{.</span><span class="n" style="color: #333;">inline</span><span class="p">,</span> <span class="n" style="color: #333;">noInit</span><span class="p">.}</span> <span class="o" style="font-weight: 600;">=</span></span>
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<td class="diff-line-num new old_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">
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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="nim"> <span class="k" style="font-weight: 600;">discard</span> <span class="n" style="color: #333;">bcf_unpack</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">BCF_UN_STR</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">BCF_UN_FLT</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">BCF_UN_INFO</span><span class="p">)</span></span>
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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="nim"> <span class="n" style="color: #333;">result</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;">i</span><span class="p">:</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="p">:</span><span class="n" style="color: #333;">v</span><span class="p">)</span></span>
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510
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501
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<pre style="margin: 0;"> <span id="LC501" class="line" lang="nim"></span>
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511
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502
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<pre style="margin: 0;"> <span id="LC502" class="line" lang="nim"><span class="k" style="font-weight: 600;">proc </span><span class="nf" style="color: #900; font-weight: 600;">bcf_hdr_int2id</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">:</span> <span class="k" style="font-weight: 600;">ptr</span> <span class="n" style="color: #333;">bcf_hdr_t</span><span class="p">,</span> <span class="n" style="color: #333;">typ</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;">rid</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;">cstring</span> <span class="p">{.</span><span class="n" style="color: #333;">inline</span><span class="p">.}</span> <span class="o" style="font-weight: 600;">=</span></span>
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<td class="diff-line-num old_line" data-linenumber="512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
512
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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC503" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">cast</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">CPtr</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">bcf_idpair_t</span><span class="o" style="font-weight: 600;">]]</span><span class="p">(</span><span class="n" style="color: #333;">hdr</span><span class="p">.</span><span class="n" style="color: #333;">id</span><span class="o" style="font-weight: 600;">[</span><span class="n" style="color: #333;">typ</span><span class="o" style="font-weight: 600;">]</span><span class="p">)</span></span>
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