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<h3>
Nilesh Patra pushed to branch master
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/b414d086386c00963314dc6aac91e5b7a7f50326">b414d086</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2020-11-01T12:53:13+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Finalize Autopkgtests
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<h4>6 changed files:</h4>
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<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<a href="#b0b27faaec19805ecb23943d9fc1baedadcc1d67">
debian/nim-hts-examples.install
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debian/tests/control
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debian/tests/run-unit-test
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debian/tests/test1.nim
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debian/tests/test2.nim
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<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/nim-hts/-/commit/b414d086386c00963314dc6aac91e5b7a7f50326#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,7 +19,7 @@ Rules-Requires-Root: no</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Package: nim-hts-dev</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Depends: ${misc:Depends}, nim</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext">Recommends: libhts3</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">Recommends: libhts3<span class="idiff left right">, libhts-dev</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Suggests: nim-hts-examples</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">Description: wrapper for hts C library</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> The hts library is well accepted for the handling of millions of</span>
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<li id="b0b27faaec19805ecb23943d9fc1baedadcc1d67">
<a href="https://salsa.debian.org/med-team/nim-hts/-/commit/b414d086386c00963314dc6aac91e5b7a7f50326#b0b27faaec19805ecb23943d9fc1baedadcc1d67"><strong>debian/nim-hts-examples.install</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">@@ -2,7 +2,7 @@ tests/*.nim usr/share/doc/hts-nim-examples</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="php"><span class="n" style="color: #333;">tests</span><span class="o" style="font-weight: 600;">/*.</span><span class="n" style="color: #333;">sam</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">share</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">doc</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">hts</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">nim</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">examples</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="php"><span class="n" style="color: #333;">tests</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">test_files</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">share</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">doc</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">hts</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">nim</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">examples</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="php"><span class="n" style="color: #333;">tests</span><span class="o" style="font-weight: 600;">/*.</span><span class="n" style="color: #333;">vcf</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">share</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">doc</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">hts</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">nim</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">examples</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="php"><span class="n" style="color: #333;">tests</span><span class="o" style="font-weight: 600;">/*.</span><span class="n" style="color: #333;">bcf</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">share</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">doc</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">hts</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">nim</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">examples</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="php"><span class="n" style="color: #333;">tests</span><span class="o" style="font-weight: 600;">/*.</span><span class="n" style="color: #333;">bcf</span><span class="o" style="font-weight: 600;"><span class="idiff left right">*</span></span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">share</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">doc</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">hts</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">nim</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">examples</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="php"><span class="n" style="color: #333;">tests</span><span class="o" style="font-weight: 600;">/*.</span><span class="n" style="color: #333;">bam</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">share</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">doc</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">hts</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">nim</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">examples</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="php"><span class="n" style="color: #333;">tests</span><span class="o" style="font-weight: 600;">/*.</span><span class="n" style="color: #333;">fa</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">share</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">doc</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">hts</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">nim</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">examples</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="php"><span class="n" style="color: #333;">debian</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">missing</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">sources</span><span class="o" style="font-weight: 600;">/*</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">share</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">doc</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">hts</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">nim</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">examples</span></span>
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<a href="https://salsa.debian.org/med-team/nim-hts/-/commit/b414d086386c00963314dc6aac91e5b7a7f50326#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @, libhts3, libhts-dev</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>
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<a href="https://salsa.debian.org/med-team/nim-hts/-/commit/b414d086386c00963314dc6aac91e5b7a7f50326#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"nim-hts-dev"</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="sb" style="color: #d14;">`</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/hts-nim-examples/<span class="k" style="font-weight: 600;">*</span> <span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: #000080;">-r</span> <span class="k" style="font-weight: 600;">*</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"TEST 1"</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">nim <span class="nt" style="color: #000080;">-p</span>:/usr/share/nimble/hts <span class="nt" style="color: #000080;">-p</span>:/usr/lib/x86_64-linux-gnu/ c test1.nim</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell">./test1</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> ./test1</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"======================================="</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"PASS"</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"TEST 2"</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell">nim <span class="nt" style="color: #000080;">-p</span>:/usr/share/nimble/hts/ c test2.nim</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell">./test2</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> ./test2</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"======================================="</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"PASS"</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"></span></pre>
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<a href="https://salsa.debian.org/med-team/nim-hts/-/commit/b414d086386c00963314dc6aac91e5b7a7f50326#26c002ccea16c715ff6a7903d1377d32012e5220"><strong>debian/tests/test1.nim</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="nim"><span class="k" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">hts</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="nim"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="nim"><span class="c" style="color: #998; font-style: italic;"># open a bam/cram and look for the index.</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="nim"><span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">b</span><span class="p">:</span><span class="n" style="color: #333;">Bam</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="nim"><span class="n" style="color: #333;">open</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="s" style="color: #d14;">"HG02002.bam"</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="kp" style="font-weight: 600;">true</span><span class="p">,</span> <span class="n" style="color: #333;">fai</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"aa.fa"</span><span class="p">)</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="nim"></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="nim"><span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">b</span><span class="p">:</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">mapping_quality</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">10u</span><span class="p">:</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="nim"> <span class="n" style="color: #333;">echo</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">stop</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="nim"></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="nim"><span class="c" style="color: #998; font-style: italic;"># regional queries:</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="nim"><span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">query</span><span class="p">(</span><span class="s" style="color: #d14;">"6"</span><span class="p">,</span> <span class="mi" style="color: #099;">30816675</span><span class="p">,</span> <span class="mi" style="color: #099;">32816675</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">flag</span><span class="p">.</span><span class="n" style="color: #333;">proper_pair</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">flag</span><span class="p">.</span><span class="n" style="color: #333;">reverse</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="nim"> <span class="c" style="color: #998; font-style: italic;"># cigar is an iterable of operations:</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="nim"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">op</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">cigar</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="nim"> <span class="c" style="color: #998; font-style: italic;"># $op gives the string repr of the operation, e.g. '151M'</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="nim"> <span class="n" style="color: #333;">echo</span> <span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">op</span><span class="p">,</span> <span class="s" style="color: #d14;">" "</span><span class="p">,</span> <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">consumes</span><span class="p">.</span><span class="n" style="color: #333;">reference</span><span class="p">,</span> <span class="s" style="color: #d14;">" "</span><span class="p">,</span> <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">consumes</span><span class="p">.</span><span class="n" style="color: #333;">query</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="nim"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="nim"> <span class="c" style="color: #998; font-style: italic;"># tags are pulled by type `ta`</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">mismatches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tag</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">]</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">,</span> <span class="s" style="color: #d14;">"NM"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">mismatches</span><span class="p">.</span><span class="n" style="color: #333;">isNone</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">mismatches</span><span class="p">.</span><span class="n" style="color: #333;">get</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">3</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">rg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tag</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="p">(</span><span class="n" style="color: #333;">record</span><span class="p">,</span> <span class="s" style="color: #d14;">"RG"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">rg</span><span class="p">.</span><span class="n" style="color: #333;">isNone</span><span class="p">:</span> <span class="n" style="color: #333;">echo</span> <span class="n" style="color: #333;">rg</span><span class="p">.</span><span class="n" style="color: #333;">get</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="nim"></span></pre>
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<a href="https://salsa.debian.org/med-team/nim-hts/-/commit/b414d086386c00963314dc6aac91e5b7a7f50326#d94882584e076df41a88fcb1e04fc719033d463b"><strong>debian/tests/test2.nim</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="nim"><span class="k" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">hts</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="nim"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="nim"><span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">tsamples</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">@[</span><span class="s" style="color: #d14;">"101976-101976"</span><span class="p">,</span> <span class="s" style="color: #d14;">"100920-100920"</span><span class="p">,</span> <span class="s" style="color: #d14;">"100231-100231"</span><span class="p">,</span> <span class="s" style="color: #d14;">"100232-100232"</span><span class="p">,</span> <span class="s" style="color: #d14;">"100919-100919"</span><span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="nim"><span class="c" style="color: #998; font-style: italic;"># VCF and BCF supported</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="nim"><span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">v</span><span class="p">:</span><span class="n" style="color: #333;">VCF</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="nim"><span class="n" style="color: #333;">doAssert</span><span class="p">(</span><span class="n" style="color: #333;">open</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">,</span> <span class="s" style="color: #d14;">"test.bcf"</span><span class="p">,</span> <span class="n" style="color: #333;">samples</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tsamples</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="nim"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="nim"><span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">afs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_seq</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">float32</span><span class="o" style="font-weight: 600;">]</span><span class="p">(</span><span class="mi" style="color: #099;">5</span><span class="p">)</span> <span class="c" style="color: #998; font-style: italic;"># size doesn't matter. this will be re-sized as needed</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="nim"><span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">acs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_seq</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">int32</span><span class="o" style="font-weight: 600;">]</span><span class="p">(</span><span class="mi" style="color: #099;">5</span><span class="p">)</span> <span class="c" style="color: #998; font-style: italic;"># size doesn't matter. this will be re-sized as needed</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="nim"><span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">csq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_string_of_cap</span><span class="p">(</span><span class="mi" style="color: #099;">20</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="nim"><span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">rec</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">v</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="nim"> <span class="n" style="color: #333;">echo</span> <span class="n" style="color: #333;">rec</span><span class="p">,</span> <span class="s" style="color: #d14;">" qual:"</span><span class="p">,</span> <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">QUAL</span><span class="p">,</span> <span class="s" style="color: #d14;">" filter:"</span><span class="p">,</span> <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">FILTER</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">info</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">info</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="nim"> <span class="c" style="color: #998; font-style: italic;"># accessing stuff from the INFO field is meant to be as fast as possible, allowing</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="nim"> <span class="c" style="color: #998; font-style: italic;"># the user to re-use memory as needed.</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="nim"> <span class="n" style="color: #333;">doAssert</span> <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"CSQ"</span><span class="p">,</span> <span class="n" style="color: #333;">csq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">Status</span><span class="p">.</span><span class="n" style="color: #333;">OK</span> <span class="c" style="color: #998; font-style: italic;"># string</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="nim"> <span class="n" style="color: #333;">doAssert</span> <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"AC"</span><span class="p">,</span> <span class="n" style="color: #333;">acs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">Status</span><span class="p">.</span><span class="n" style="color: #333;">OK</span> <span class="c" style="color: #998; font-style: italic;"># ints</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="nim"> <span class="n" style="color: #333;">doAssert</span> <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"AF"</span><span class="p">,</span> <span class="n" style="color: #333;">afs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">Status</span><span class="p">.</span><span class="n" style="color: #333;">OK</span> <span class="c" style="color: #998; font-style: italic;"># floats</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="nim"> <span class="n" style="color: #333;">echo</span> <span class="n" style="color: #333;">acs</span><span class="p">,</span> <span class="n" style="color: #333;">afs</span><span class="p">,</span> <span class="n" style="color: #333;">csq</span><span class="p">,</span> <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">has_flag</span><span class="p">(</span><span class="s" style="color: #d14;">"IN_EXAC"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="nim"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="nim"> <span class="c" style="color: #998; font-style: italic;"># accessing format fields is similar</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">dps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_seq</span><span class="o" style="font-weight: 600;">[</span><span class="kt" style="color: #458; font-weight: 600;">int32</span><span class="o" style="font-weight: 600;">]</span><span class="p">(</span><span class="n" style="color: #333;">len</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">samples</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="nim"> <span class="n" style="color: #333;">doAssert</span> <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">format</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"DP"</span><span class="p">,</span> <span class="n" style="color: #333;">dps</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">Status</span><span class="p">.</span><span class="n" style="color: #333;">OK</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="nim"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="nim"><span class="c" style="color: #998; font-style: italic;"># open a VCF for writing</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="nim"><span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">wtr</span><span class="p">:</span><span class="n" style="color: #333;">VCF</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="nim"><span class="n" style="color: #333;">doAssert</span><span class="p">(</span><span class="n" style="color: #333;">open</span><span class="p">(</span><span class="n" style="color: #333;">wtr</span><span class="p">,</span> <span class="s" style="color: #d14;">"outv.vcf"</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"w"</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="nim"><span class="n" style="color: #333;">wtr</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;">v</span><span class="p">.</span><span class="n" style="color: #333;">header</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="nim"><span class="n" style="color: #333;">doAssert</span><span class="p">(</span><span class="n" style="color: #333;">wtr</span><span class="p">.</span><span class="n" style="color: #333;">write_header</span><span class="p">())</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="nim"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="nim"><span class="c" style="color: #998; font-style: italic;"># regional queries look for index. works for VCF and BCF</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="nim"><span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">rec</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">query</span><span class="p">(</span><span class="s" style="color: #d14;">"1:15600-18250"</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="nim"> <span class="n" style="color: #333;">echo</span> <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">CHROM</span><span class="p">,</span> <span class="s" style="color: #d14;">":"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">POS</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="nim"> <span class="c" style="color: #998; font-style: italic;"># adjust some values in the INFO</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">22.3</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="nim"> <span class="n" style="color: #333;">doAssert</span> <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="kt" style="color: #458; font-weight: 600;">set</span><span class="p">(</span><span class="s" style="color: #d14;">"VQSLOD"</span><span class="p">,</span> <span class="n" style="color: #333;">val</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">Status</span><span class="p">.</span><span class="n" style="color: #333;">OK</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="nim"> <span class="n" style="color: #333;">doAssert</span> <span class="n" style="color: #333;">wtr</span><span class="p">.</span><span class="n" style="color: #333;">write_variant</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="nim"></span></pre>
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