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<h3>
Michael R. Crusoe pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/bcftools">Debian Med / bcftools</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bcftools/commit/e439282c1235fa123a822dbcd7dae553cf4cb693">e439282c</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-12-25T16:58:15Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.10.2</pre>
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<h4>24 changed files:</h4>
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<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
Makefile
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<li class="file-stats">
<a href="#9f621eb5fd3bcb2fa5c7bd228c9b1ad42edc46c8">
NEWS
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<li class="file-stats">
<a href="#155bba183d1c525bb29e6a8f0a6f4d5203059fad">
doc/bcftools.1
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<li class="file-stats">
<a href="#10c81da16b14b79039d2fb8ea89464665683576e">
doc/bcftools.html
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<li class="file-stats">
<a href="#9a2b5aa2613ebd6ba3159cd62c01d98d9d354e6a">
doc/bcftools.txt
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<li class="file-stats">
<a href="#4d72baccd6137d90f7fe3c30aee27c7d1ce4319f">
plugins/trio-dnm.c
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<a href="#78bcfa40e5186627dc23148a193ec136329a9225">
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test/norm.split.3.out
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<a href="#960c309f8321419550169434fc1c66000c135cd5">
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test/norm.split.3.vcf
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<a href="#1dafee15289de195cc70f0739a91d5b95f8e8889">
test/test.pl
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test/trio-dnm.2.out
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test/trio-dnm.2.vcf
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test/view64bit.1.out
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test/view64bit.1.vcf
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test/view64bit.2.out
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test/view64bit.2.vcf
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test/view64bit.3.out
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test/view64bit.3.vcf
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test/view64bit.4.out
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test/view64bit.4.vcf
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test/view64bit.5.out
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test/view64bit.5.vcf
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<a href="#87f8f8e172c330f38bf1e2a45d891e6150990187">
vcfisec.c
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<a href="#5bb5b301a5d8cf43cad4dd1061b35189fca4b2a3">
vcfnorm.c
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<li class="file-stats">
<a href="#79af080a263b467ea1886b300bde6b2d35c43aa8">
version.sh
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<h4>Changes:</h4>
<li id="836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
<a href="https://salsa.debian.org/med-team/bcftools/commit/e439282c1235fa123a822dbcd7dae553cf4cb693#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c"><strong>Makefile</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="103" style="width: 35px; color: rgba(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="103" style="width: 35px; color: rgba(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">@@ -103,7 +103,7 @@ endif</td>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="make"></span>
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<td class="diff-line-num old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="104" style="width: 35px; color: rgba(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="LC104" class="line" lang="make"><span class="k" style="font-weight: 600;">include</span><span class="sx" style="color: #d14;"> config.mk</span></span>
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<td class="diff-line-num old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="105" style="width: 35px; color: rgba(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="LC105" class="line" lang="make"></span>
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<td class="diff-line-num old old_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="make"><span class="nv" style="color: #008080;">PACKAGE_VERSION</span> <span class="o" style="font-weight: 600;">=</span> 1.10</span>
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<td class="diff-line-num new old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="make"><span class="nv" style="color: #008080;">PACKAGE_VERSION</span> <span class="o" style="font-weight: 600;">=</span> 1.10<span class="idiff left right">.2</span></span>
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<td class="diff-line-num old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="make"></span>
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<td class="diff-line-num old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># If building from a Git repository, replace $(PACKAGE_VERSION) with the Git</span></span>
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<td class="diff-line-num old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># description of the working tree: either a release tag with the same value</span></span>
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<li id="9f621eb5fd3bcb2fa5c7bd228c9b1ad42edc46c8">
<a href="https://salsa.debian.org/med-team/bcftools/commit/e439282c1235fa123a822dbcd7dae553cf4cb693#9f621eb5fd3bcb2fa5c7bd228c9b1ad42edc46c8"><strong>NEWS</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">## Release 1.10.2 (19th December 2019)</span>
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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></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="plaintext">This is a release fix that corrects minor inconsistencies discovered in</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">previous deliverables.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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1
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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">## Release 1.10 (6th December 2019)</span>
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2
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></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">@@ -2,12 +2,12 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">.\" Title: bcftools</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">.\" Author: [see the "AUTHORS" section]</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">.\" Date: 2019-12-<span class="idiff left right">06</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.\" Date: 2019-12-<span class="idiff left right">19</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">.\" Manual: \ \&</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">.\" Source: \ \&</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">.\" Language: English</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">.\"</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">.TH "BCFTOOLS" "1" "2019\-12\-<span class="idiff left right">06</span>" "\ \&" "\ \&"</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.TH "BCFTOOLS" "1" "2019\-12\-<span class="idiff left right">19</span>" "\ \&" "\ \&"</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">.\" -----------------------------------------------------------------</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">.\" * Define some portability stuff</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">.\" -----------------------------------------------------------------</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">@@ -41,7 +41,7 @@ Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatica</td>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext">BCFtools is designed to work on a stream\&. It regards an input file "\-" as the standard input (stdin) and outputs to the standard output (stdout)\&. Several commands can thus be combined with Unix pipes\&.</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext">.SS "VERSION"</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext">.sp</span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext">This manual page was last updated \fB2019\-12\-<span class="idiff left right">06\fR and refers to bcftools git version \fB1\&.10</span>\fR\&.</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">This manual page was last updated \fB2019\-12\-<span class="idiff left right">19\fR and refers to bcftools git version \fB1\&.10\&.2</span>\fR\&.</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext">.SS "BCF1"</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext">.sp</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext">The BCF1 format output by versions of samtools <= 0\&.1\&.19 is \fBnot\fR compatible with this version of bcftools\&. To read BCF1 files one can use the view command from old versions of bcftools packaged with samtools versions <= 0\&.1\&.19 to convert to VCF, which can then be read by this version of bcftools\&.</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">@@ -3130,6 +3130,13 @@ reference sequence\&. Supplying this option will turn on left\-alignment and nor</td>
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3130
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<pre style="margin: 0;"> <span id="LC3130" class="line" lang="plaintext">option below\&.</span>
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3131
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<td class="diff-line-num new_line" data-linenumber="3131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3131
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<pre style="margin: 0;"> <span id="LC3131" class="line" lang="plaintext">.RE</span>
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3132
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<td class="diff-line-num new_line" data-linenumber="3132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3132
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<pre style="margin: 0;"> <span id="LC3132" class="line" lang="plaintext">.PP</span>
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3133
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<pre style="margin: 0;">+<span id="LC3133" class="line" lang="plaintext">\fB\-\-force\fR</span>
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3134
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<pre style="margin: 0;">+<span id="LC3134" class="line" lang="plaintext">.RS 4</span>
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3135
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<pre style="margin: 0;">+<span id="LC3135" class="line" lang="plaintext">try to proceed with</span>
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3136
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<pre style="margin: 0;">+<span id="LC3136" class="line" lang="plaintext">\fB\-m\-\fR</span>
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3137
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<pre style="margin: 0;">+<span id="LC3137" class="line" lang="plaintext">even if malformed tags with incorrect number of fields are encountered, discarding such tags\&. (Experimental, use at your own risk\&.)</span>
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3138
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<pre style="margin: 0;">+<span id="LC3138" class="line" lang="plaintext">.RE</span>
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3139
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<pre style="margin: 0;">+<span id="LC3139" class="line" lang="plaintext">.PP</span>
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3133
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3140
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<pre style="margin: 0;"> <span id="LC3140" class="line" lang="plaintext">\fB\-m, \-\-multiallelics\fR \fB\-\fR|\fB+\fR[\fIsnps\fR|\fIindels\fR|\fIboth\fR|\fIany\fR]</span>
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3134
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3141
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<pre style="margin: 0;"> <span id="LC3141" class="line" lang="plaintext">.RS 4</span>
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3135
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3142
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<pre style="margin: 0;"> <span id="LC3142" class="line" lang="plaintext">split multiallelic sites into biallelic records (\fB\-\fR) or join biallelic sites into multiallelic records (\fB+\fR)\&. An optional type string can follow which controls variant types which should be split or merged together: If only SNP records should be split or merged, specify</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="html"><span class="nt" style="color: #000080;"><html</span> <span class="na" style="color: #008080;">xmlns=</span><span class="s" style="color: #d14;">"http://www.w3.org/1999/xhtml"</span><span class="nt" style="color: #000080;">><head><meta</span> <span class="na" style="color: #008080;">http-equiv=</span><span class="s" style="color: #d14;">"Content-Type"</span> <span class="na" style="color: #008080;">content=</span><span class="s" style="color: #d14;">"text/html; charset=UTF-8"</span> <span class="nt" style="color: #000080;">/><title></span>bcftools<span class="nt" style="color: #000080;"></title><link</span> <span class="na" style="color: #008080;">rel=</span><span class="s" style="color: #d14;">"stylesheet"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"text/css"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"docbook-xsl.css"</span> <span class="nt" style="color: #000080;">/><meta</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"generator"</span> <span class="na" style="color: #008080;">content=</span><span class="s" style="color: #d14;">"DocBook XSL Stylesheets V1.76.1"</span> <span class="nt" style="color: #000080;">/></head><body><div</span> <span class="na" style="color: #008080;">xml:lang=</span><span class="s" style="color: #d14;">"en"</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"refentry"</span> <span class="na" style="color: #008080;">title=</span><span class="s" style="color: #d14;">"bcftools"</span> <span class="na" style="color: #008080;">lang=</span><span class="s" style="color: #d14;">"en"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"idp2<span class="idiff left right">12896</span>"</span><span class="nt" style="color: #000080;">></a><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"titlepage"</span><span class="nt" style="color: #000080;">></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"refnamediv"</span><span class="nt" style="color: #000080;">><h2></span>Name<span class="nt" style="color: #000080;"></h2><p></span>bcftools — utilities for variant calling and manipulating VCFs and BCFs.<span class="nt" style="color: #000080;"></p></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"refsynopsisdiv"</span> <span class="na" style="color: #008080;">title=</span><span class="s" style="color: #d14;">"Synopsis"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"_synopsis"</span><span class="nt" style="color: #000080;">></a><h2></span>Synopsis<span class="nt" style="color: #000080;"></h2><p><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"strong"</span><span class="nt" style="color: #000080;">><strong></span>bcftools<span class="nt" style="color: #000080;"></strong></span></span> [--version|--version-only] [--help] [<span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"emphasis"</span><span class="nt" style="color: #000080;">><em></span>COMMAND<span class="nt" style="color: #000080;"></em></span></span>] [<span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"emphasis"</span><span class="nt" style="color: #000080;">><em></span>OPTIONS<span class="nt" style="color: #000080;"></em></span></span>]<span class="nt" style="color: #000080;"></p></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"refsect1"</span> <span class="na" style="color: #008080;">title=</span><span class="s" style="color: #d14;">"DESCRIPTION"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"_description"</span><span class="nt" style="color: #000080;">></a><h2></span>DESCRIPTION<span class="nt" style="color: #000080;"></h2><p></span>BCFtools is a set of utilities that manipulate variant calls in the Variant</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="html"><span class="nt" style="color: #000080;"><html</span> <span class="na" style="color: #008080;">xmlns=</span><span class="s" style="color: #d14;">"http://www.w3.org/1999/xhtml"</span><span class="nt" style="color: #000080;">><head><meta</span> <span class="na" style="color: #008080;">http-equiv=</span><span class="s" style="color: #d14;">"Content-Type"</span> <span class="na" style="color: #008080;">content=</span><span class="s" style="color: #d14;">"text/html; charset=UTF-8"</span> <span class="nt" style="color: #000080;">/><title></span>bcftools<span class="nt" style="color: #000080;"></title><link</span> <span class="na" style="color: #008080;">rel=</span><span class="s" style="color: #d14;">"stylesheet"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"text/css"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"docbook-xsl.css"</span> <span class="nt" style="color: #000080;">/><meta</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"generator"</span> <span class="na" style="color: #008080;">content=</span><span class="s" style="color: #d14;">"DocBook XSL Stylesheets V1.76.1"</span> <span class="nt" style="color: #000080;">/></head><body><div</span> <span class="na" style="color: #008080;">xml:lang=</span><span class="s" style="color: #d14;">"en"</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"refentry"</span> <span class="na" style="color: #008080;">title=</span><span class="s" style="color: #d14;">"bcftools"</span> <span class="na" style="color: #008080;">lang=</span><span class="s" style="color: #d14;">"en"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"idp2<span class="idiff left right">5229120</span>"</span><span class="nt" style="color: #000080;">></a><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"titlepage"</span><span class="nt" style="color: #000080;">></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"refnamediv"</span><span class="nt" style="color: #000080;">><h2></span>Name<span class="nt" style="color: #000080;"></h2><p></span>bcftools — utilities for variant calling and manipulating VCFs and BCFs.<span class="nt" style="color: #000080;"></p></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"refsynopsisdiv"</span> <span class="na" style="color: #008080;">title=</span><span class="s" style="color: #d14;">"Synopsis"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"_synopsis"</span><span class="nt" style="color: #000080;">></a><h2></span>Synopsis<span class="nt" style="color: #000080;"></h2><p><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"strong"</span><span class="nt" style="color: #000080;">><strong></span>bcftools<span class="nt" style="color: #000080;"></strong></span></span> [--version|--version-only] [--help] [<span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"emphasis"</span><span class="nt" style="color: #000080;">><em></span>COMMAND<span class="nt" style="color: #000080;"></em></span></span>] [<span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"emphasis"</span><span class="nt" style="color: #000080;">><em></span>OPTIONS<span class="nt" style="color: #000080;"></em></span></span>]<span class="nt" style="color: #000080;"></p></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"refsect1"</span> <span class="na" style="color: #008080;">title=</span><span class="s" style="color: #d14;">"DESCRIPTION"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"_description"</span><span class="nt" style="color: #000080;">></a><h2></span>DESCRIPTION<span class="nt" style="color: #000080;"></h2><p></span>BCFtools is a set of utilities that manipulate variant calls in the Variant</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="html">Call Format (VCF) and its binary counterpart BCF. All commands work</span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="html">transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.<span class="nt" style="color: #000080;"></p><p></span>Most commands accept VCF, bgzipped VCF and BCF with filetype detected</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="html">automatically even when streaming from a pipe. Indexed VCF and BCF</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,7 +10,7 @@ read simultaneously, they must be indexed and therefore also compressed.</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="html">(Note that files with non-standard index names can be accessed as e.g.</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="html">"<span class="nt" style="color: #000080;"><code</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"literal"</span><span class="nt" style="color: #000080;">></span>bcftools view -r X:2928329 file.vcf.gz##idx##non-standard-index-name<span class="nt" style="color: #000080;"></code></span>".)<span class="nt" style="color: #000080;"></p><p></span>BCFtools is designed to work on a stream. It regards an input file "-" as the</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="html">standard input (stdin) and outputs to the standard output (stdout). Several</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="html">commands can thus be combined with Unix pipes.<span class="nt" style="color: #000080;"></p><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"refsect2"</span> <span class="na" style="color: #008080;">title=</span><span class="s" style="color: #d14;">"VERSION"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"_version"</span><span class="nt" style="color: #000080;">></a><h3></span>VERSION<span class="nt" style="color: #000080;"></h3><p></span>This manual page was last updated <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"strong"</span><span class="nt" style="color: #000080;">><strong></span>2019-12-<span class="idiff left">06</span><span class="nt" style="color: #000080;"><span class="idiff"></strong></span></span></span><span class="idiff"> and refers to bcftools git version </span><span class="nt" style="color: #000080;"><span class="idiff"><span</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"strong"</span></span><span class="nt" style="color: #000080;"><span class="idiff">><strong></span></span><span class="idiff right">1.10</span><span class="nt" style="color: #000080;"></strong></span></span>.<span class="nt" style="color: #000080;"></p></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"refsect2"</span> <span class="na" style="color: #008080;">title=</span><span class="s" style="color: #d14;">"BCF1"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"_bcf1"</span><span class="nt" style="color: #000080;">></a><h3></span>BCF1<span class="nt" style="color: #000080;"></h3><p></span>The BCF1 format output by versions of samtools <span class="ni" style="color: #800080;"><</span>= 0.1.19 is <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"strong"</span><span class="nt" style="color: #000080;">><strong></span>not<span class="nt" style="color: #000080;"></strong></span></span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="html">commands can thus be combined with Unix pipes.<span class="nt" style="color: #000080;"></p><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"refsect2"</span> <span class="na" style="color: #008080;">title=</span><span class="s" style="color: #d14;">"VERSION"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"_version"</span><span class="nt" style="color: #000080;">></a><h3></span>VERSION<span class="nt" style="color: #000080;"></h3><p></span>This manual page was last updated <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"strong"</span><span class="nt" style="color: #000080;">><strong></span>2019-12-<span class="idiff left">19</span><span class="nt" style="color: #000080;"><span class="idiff"></strong></span></span></span><span class="idiff"> and refers to bcftools git version </span><span class="nt" style="color: #000080;"><span class="idiff"><span</span></span><span class="idiff"> </span><span class="na" style="color: #008080;"><span class="idiff">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"strong"</span></span><span class="nt" style="color: #000080;"><span class="idiff">><strong></span></span><span class="idiff right">1.10.2</span><span class="nt" style="color: #000080;"></strong></span></span>.<span class="nt" style="color: #000080;"></p></div><div</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"refsect2"</span> <span class="na" style="color: #008080;">title=</span><span class="s" style="color: #d14;">"BCF1"</span><span class="nt" style="color: #000080;">><a</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"_bcf1"</span><span class="nt" style="color: #000080;">></a><h3></span>BCF1<span class="nt" style="color: #000080;"></h3><p></span>The BCF1 format output by versions of samtools <span class="ni" style="color: #800080;"><</span>= 0.1.19 is <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"strong"</span><span class="nt" style="color: #000080;">><strong></span>not<span class="nt" style="color: #000080;"></strong></span></span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="html">compatible with this version of bcftools. To read BCF1 files one can use</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="html">the view command from old versions of bcftools packaged with samtools</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="html">versions <span class="ni" style="color: #800080;"><</span>= 0.1.19 to convert to VCF, which can then be read by</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1895" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1895,6 +1895,11 @@ the <span class="strong"><strong><a class="link" href="#fasta_ref">--fasta-ref</</td>
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<pre style="margin: 0;"> <span id="LC1895" class="line" lang="html"> and normalization, however, see also the <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"strong"</span><span class="nt" style="color: #000080;">><strong><a</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"link"</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"#do_not_normalize"</span><span class="nt" style="color: #000080;">></span>--do-not-normalize<span class="nt" style="color: #000080;"></a></strong></span></span></span>
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<pre style="margin: 0;"> <span id="LC1896" class="line" lang="html"> option below.</span>
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1897
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<pre style="margin: 0;"> <span id="LC1897" class="line" lang="html"><span class="nt" style="color: #000080;"></dd><dt><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"term"</span><span class="nt" style="color: #000080;">></span></span>
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1898
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<pre style="margin: 0;">+<span id="LC1898" class="line" lang="html"><span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"strong"</span><span class="nt" style="color: #000080;">><strong></span>--force<span class="nt" style="color: #000080;"></strong></span></span></span>
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1899
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<pre style="margin: 0;">+<span id="LC1899" class="line" lang="html"><span class="nt" style="color: #000080;"></span></dt><dd></span></span>
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1900
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<pre style="margin: 0;">+<span id="LC1900" class="line" lang="html"> try to proceed with <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"strong"</span><span class="nt" style="color: #000080;">><strong></span>-m-<span class="nt" style="color: #000080;"></strong></span></span> even if malformed tags with incorrect number of fields</span>
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1901
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<pre style="margin: 0;">+<span id="LC1901" class="line" lang="html"> are encountered, discarding such tags. (Experimental, use at your own risk.)</span>
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1902
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<pre style="margin: 0;">+<span id="LC1902" class="line" lang="html"><span class="nt" style="color: #000080;"></dd><dt><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"term"</span><span class="nt" style="color: #000080;">></span></span>
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1898
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1903
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<pre style="margin: 0;"> <span id="LC1903" class="line" lang="html"><span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"strong"</span><span class="nt" style="color: #000080;">><strong></span>-m, --multiallelics<span class="nt" style="color: #000080;"></strong></span></span> <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"strong"</span><span class="nt" style="color: #000080;">><strong></span>-<span class="nt" style="color: #000080;"></strong></span></span>|<span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"strong"</span><span class="nt" style="color: #000080;">><strong></span>+<span class="nt" style="color: #000080;"></strong></span></span>[<span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"emphasis"</span><span class="nt" style="color: #000080;">><em></span>snps<span class="nt" style="color: #000080;"></em></span></span>|<span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"emphasis"</span><span class="nt" style="color: #000080;">><em></span>indels<span class="nt" style="color: #000080;"></em></span></span>|<span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"emphasis"</span><span class="nt" style="color: #000080;">><em></span>both<span class="nt" style="color: #000080;"></em></span></span>|<span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"emphasis"</span><span class="nt" style="color: #000080;">><em></span>any<span class="nt" style="color: #000080;"></em></span></span>]</span>
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1904
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<pre style="margin: 0;"> <span id="LC1904" class="line" lang="html"><span class="nt" style="color: #000080;"></span></dt><dd></span></span>
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1900
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1905
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<pre style="margin: 0;"> <span id="LC1905" class="line" lang="html"> split multiallelic sites into biallelic records (<span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"strong"</span><span class="nt" style="color: #000080;">><strong></span>-<span class="nt" style="color: #000080;"></strong></span></span>) or join</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">@@ -1924,6 +1924,10 @@ the *<<fasta_ref,--fasta-ref>>* option is supplied.</td>
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<pre style="margin: 0;"> <span id="LC1924" class="line" lang="plaintext"> and normalization, however, see also the *<<do_not_normalize,--do-not-normalize>>*</span>
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1925
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<pre style="margin: 0;"> <span id="LC1925" class="line" lang="plaintext"> option below.</span>
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1926
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1926
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<pre style="margin: 0;"> <span id="LC1926" class="line" lang="plaintext"></span>
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1927
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<pre style="margin: 0;">+<span id="LC1927" class="line" lang="plaintext">*--force*::</span>
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1928
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<pre style="margin: 0;">+<span id="LC1928" class="line" lang="plaintext"> try to proceed with *-m-* even if malformed tags with incorrect number of fields</span>
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1929
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<pre style="margin: 0;">+<span id="LC1929" class="line" lang="plaintext"> are encountered, discarding such tags. (Experimental, use at your own risk.)</span>
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1930
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<pre style="margin: 0;">+<span id="LC1930" class="line" lang="plaintext"></span>
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1927
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1931
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<pre style="margin: 0;"> <span id="LC1931" class="line" lang="plaintext">*-m, --multiallelics* *-*|*+*['snps'|'indels'|'both'|'any']::</span>
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1928
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1932
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<pre style="margin: 0;"> <span id="LC1932" class="line" lang="plaintext"> split multiallelic sites into biallelic records (*-*) or join</span>
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1929
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1933
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<pre style="margin: 0;"> <span id="LC1933" class="line" lang="plaintext"> biallelic sites into multiallelic records (*+*). An optional type string</span>
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<a href="https://salsa.debian.org/med-team/bcftools/commit/e439282c1235fa123a822dbcd7dae553cf4cb693#4d72baccd6137d90f7fe3c30aee27c7d1ce4319f"><strong>plugins/trio-dnm.c</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* The MIT License</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Copyright (c) 2018 Genome Research Ltd.</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Copyright (c) 2018<span class="idiff left right">-2019</span> Genome Research Ltd.</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Author: Petr Danecek <pd3@sanger.ac.uk></span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> </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">@@ -72,7 +72,7 @@ typedef struct</td>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">min_score</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">aprob</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// proband's allele probabilities</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pl3</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// normalized PLs converted to probs for proband,father,mother</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maprob</span><span class="p">,</span> <span class="n" style="color: #333;">mpl3</span><span class="p">,</span> <span class="n" style="color: #333;">midx</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">idx</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maprob</span><span class="p">,</span> <span class="n" style="color: #333;">mpl3</span><span class="p">,</span> <span class="n" style="color: #333;">midx</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">idx</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">force_ad</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="c"><span class="n" style="color: #333;">args_t</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="c"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -91,6 +91,7 @@ static const char *usage_text(void)</td>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="c"> <span class="s" style="color: #d14;">"Usage: bcftools +trio-dnm [Plugin Options]</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="c"> <span class="s" style="color: #d14;">"Plugin options:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="c"> <span class="s" style="color: #d14;">" -e, --exclude EXPR exclude sites and samples for which the expression is true</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="c"> <span class="s" style="color: #d14;">" --force-AD calculate VAF even if the number of FMT/AD fields is incorrect. Use at your own risk!</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="c"> <span class="s" style="color: #d14;">" -i, --include EXPR include sites and samples for which the expression is true</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="c"> <span class="s" style="color: #d14;">" -m, --min-score NUM do not add FMT/DNM annotation if the score is smaller than NUM</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="c"> <span class="s" style="color: #d14;">" -o, --output FILE output file name [stdout]</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -293,13 +294,25 @@ static void process_record(args_t *args, bcf1_t *rec)</td>
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293
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">bcf_write</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">out_fh</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="n" style="color: #333;">rec</span><span class="p">)</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">0</span> <span class="p">)</span> <span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"[%s] Error: cannot write to %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">__func__</span><span class="p">,</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">output_fname</span><span class="p">);</span></span>
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294
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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296
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="c"> <span class="p">}</span></span>
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296
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<pre style="margin: 0;">-<span id="LC296" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nret</span><span class="p">,</span> <span class="n" style="color: #333;">nsmpl</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bcf_hdr_nsamples</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">hdr</span><span class="p">),</span> <span class="n" style="color: #333;">has_fmt_ad</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">has_fmt_ad</span><span class="p">;</span></span>
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297
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">has_fmt_ad</span> <span class="p">)</span></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n_ad_warned</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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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nret</span><span class="p">,</span> <span class="n" style="color: #333;">nsmpl</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bcf_hdr_nsamples</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">hdr</span><span class="p">),</span> <span class="n" style="color: #333;">n_ad</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">has_fmt_ad</span><span class="p">;</span></span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">n_ad</span> <span class="p">)</span></span>
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298
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="c"> <span class="p">{</span></span>
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299
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301
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="c"> <span class="n" style="color: #333;">nret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bcf_get_format_int32</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">hdr</span><span class="p">,</span><span class="n" style="color: #333;">rec</span><span class="p">,</span><span class="s" style="color: #d14;">"AD"</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ad</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mad</span><span class="p">);</span></span>
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300
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">nret</span><span class="o" style="font-weight: 600;"><=</span><span class="mi" style="color: #099;">0</span> <span class="p">)</span> <span class="n" style="color: #333;">has_fmt_ad</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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301
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">nret</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">nsmpl</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_allele</span> <span class="p">)</span></span>
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302
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<td class="diff-line-num new_line old" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC302" class="line" lang="c"> <span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"Incorrect number of fields for FORMAT/AD at %s:%"</span><span class="n" style="color: #333;">PRId64</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">bcf_seqname</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">hdr</span><span class="p">,</span><span class="n" style="color: #333;">rec</span><span class="p">),(</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="p">)</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">nret</span><span class="o" style="font-weight: 600;"><=</span><span class="mi" style="color: #099;">0</span> <span class="p">)</span> <span class="n" style="color: #333;">n_ad</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="c"> <span class="n" style="color: #333;">n_ad</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nret</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">nsmpl</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">nret</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">nsmpl</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_allele</span> <span class="p">)</span></span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="c"> <span class="p">{</span></span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">n_ad_warned</span> <span class="p">)</span></span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="c"> <span class="n" style="color: #333;">hts_log_warning</span><span class="p">(</span><span class="s" style="color: #d14;">"Incorrect number of fields for FORMAT/AD at %s:%"</span><span class="n" style="color: #333;">PRId64</span><span class="s" style="color: #d14;">". This warning is printed only once"</span><span class="p">,</span> <span class="n" style="color: #333;">bcf_seqname</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">hdr</span><span class="p">,</span><span class="n" style="color: #333;">rec</span><span class="p">),(</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="p">)</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="c"> <span class="n" style="color: #333;">n_ad_warned</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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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="c"> <span class="p">}</span></span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">force_ad</span> <span class="p">)</span> <span class="n" style="color: #333;">n_ad</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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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="c"> <span class="p">}</span></span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="c"> <span class="p">}</span></span>
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303
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316
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="c"> <span class="p">}</span></span>
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304
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<td class="diff-line-num new_line" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
317
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="c"> <span class="n" style="color: #333;">nret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bcf_get_format_int32</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">hdr</span><span class="p">,</span><span class="n" style="color: #333;">rec</span><span class="p">,</span><span class="s" style="color: #d14;">"PL"</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pl</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mpl</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
305
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<td class="diff-line-num new_line" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
318
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">nret</span><span class="o" style="font-weight: 600;"><=</span><span class="mi" style="color: #099;">0</span> <span class="p">)</span> <span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"The FORMAT/PL tag not present at %s:%"</span><span class="n" style="color: #333;">PRId64</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">bcf_seqname</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">hdr</span><span class="p">,</span><span class="n" style="color: #333;">rec</span><span class="p">),(</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="p">)</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="307" style="width: 35px; color: rgba(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="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -307,7 +320,7 @@ static void process_record(args_t *args, bcf1_t *rec)</td>
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307
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320
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">npl1</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_allele</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_allele</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">2</span> <span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
308
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<td class="diff-line-num new_line" data-linenumber="321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
321
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="c"> <span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"fixme: not a diploid site at %s:%"</span><span class="n" style="color: #333;">PRId64</span><span class="s" style="color: #d14;">": %d alleles, %d PLs</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">bcf_seqname</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">hdr</span><span class="p">,</span><span class="n" style="color: #333;">rec</span><span class="p">),(</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="p">)</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_allele</span><span class="p">,</span><span class="n" style="color: #333;">npl1</span><span class="p">);</span></span>
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309
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<td class="diff-line-num new_line" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
322
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="c"> <span class="n" style="color: #333;">hts_expand</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">,</span><span class="mi" style="color: #099;">3</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">npl1</span><span class="p">,</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mpl3</span><span class="p">,</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pl3</span><span class="p">);</span></span>
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310
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">al0</span><span class="p">,</span> <span class="n" style="color: #333;">al1</span><span class="p">,</span> <span class="n" style="color: #333;">write_dnm</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">al0</span><span class="p">,</span> <span class="n" style="color: #333;">al1</span><span class="p">,</span> <span class="n" style="color: #333;">write_dnm</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ad_set</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">;</span></span>
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311
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324
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">nsmpl</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">dnm_qual</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bcf_int32_missing</span><span class="p">;</span></span>
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312
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ntrio</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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326
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="c"> <span class="p">{</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -327,23 +340,32 @@ static void process_record(args_t *args, bcf1_t *rec)</td>
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="c"> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">dnm_qual</span><span class="p">[</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">trio</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">idx</span><span class="p">[</span><span class="n" style="color: #333;">iCHILD</span><span class="p">]</span> <span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;"><span class="idiff left right">has_fmt</span>_ad</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;"><span class="idiff left right">n</span>_ad</span> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="c"> <span class="k" style="font-weight: 600;"><span class="idiff left">for</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">j</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">j</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="mi" style="color: #099;"><span class="idiff">3</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">j</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">++</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="c"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">al0</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">n_ad</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">al1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">n_ad</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">src</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ad</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_allele</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">trio</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">idx</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="c"> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">vaf</span><span class="p">[</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">trio</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">idx</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">src</span><span class="p">[</span><span class="n" style="color: #333;">al0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">src</span><span class="p">[</span><span class="n" style="color: #333;">al1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">round</span><span class="p">(</span><span class="n" style="color: #333;">src</span><span class="p">[</span><span class="n" style="color: #333;">al1</span><span class="p">]</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">100</span><span class="p">.</span><span class="o" style="font-weight: 600;">/</span><span class="p">(</span><span class="n" style="color: #333;">src</span><span class="p">[</span><span class="n" style="color: #333;">al0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">src</span><span class="p">[</span><span class="n" style="color: #333;">al1</span><span class="p">]))</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="c"> <span class="n" style="color: #333;">ad_set</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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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">3</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">src</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ad</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">n_ad</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">trio</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">idx</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="c"> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">vaf</span><span class="p">[</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">trio</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">idx</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">src</span><span class="p">[</span><span class="n" style="color: #333;">al0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">src</span><span class="p">[</span><span class="n" style="color: #333;">al1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">round</span><span class="p">(</span><span class="n" style="color: #333;">src</span><span class="p">[</span><span class="n" style="color: #333;">al1</span><span class="p">]</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">100</span><span class="p">.</span><span class="o" style="font-weight: 600;">/</span><span class="p">(</span><span class="n" style="color: #333;">src</span><span class="p">[</span><span class="n" style="color: #333;">al0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">src</span><span class="p">[</span><span class="n" style="color: #333;">al1</span><span class="p">]))</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="c"> <span class="p">}</span></span>
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353
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="c"> <span class="p">}</span></span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="diff-line-num new new_line" data-linenumber="355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">3</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">vaf</span><span class="p">[</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">trio</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">idx</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bcf_int32_missing</span><span class="p">;</span></span>
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337
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356
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="c"> <span class="p">}</span></span>
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357
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<pre style="margin: 0;"> <span id="LC357" class="line" lang="c"> <span class="p">}</span></span>
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339
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358
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<pre style="margin: 0;"> <span id="LC358" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">write_dnm</span> <span class="p">)</span></span>
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340
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359
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<pre style="margin: 0;"> <span id="LC359" class="line" lang="c"> <span class="p">{</span></span>
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341
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360
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">bcf_update_format_int32</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span><span class="n" style="color: #333;">rec</span><span class="p">,</span><span class="s" style="color: #d14;">"DNM"</span><span class="p">,</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">dnm_qual</span><span class="p">,</span><span class="n" style="color: #333;">nsmpl</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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342
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361
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<pre style="margin: 0;"> <span id="LC361" class="line" lang="c"> <span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"Failed to write FORMAT/DNM at %s:%"</span><span class="n" style="color: #333;">PRId64</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">bcf_seqname</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">hdr</span><span class="p">,</span><span class="n" style="color: #333;">rec</span><span class="p">),(</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="p">)</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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343
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<pre style="margin: 0;">-<span id="LC343" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">has_fmt_ad</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">bcf_update_format_int32</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span><span class="n" style="color: #333;">rec</span><span class="p">,</span><span class="s" style="color: #d14;">"VAF"</span><span class="p">,</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">vaf</span><span class="p">,</span><span class="n" style="color: #333;">nsmpl</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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344
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<pre style="margin: 0;">-<span id="LC344" class="line" lang="c"> <span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"Failed to write FORMAT/VAF at %s:%"</span><span class="n" style="color: #333;">PRId64</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">bcf_seqname</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">hdr</span><span class="p">,</span><span class="n" style="color: #333;">rec</span><span class="p">),(</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="p">)</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">ad_set</span> <span class="p">)</span></span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="c"> <span class="p">{</span></span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">bcf_update_format_int32</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span><span class="n" style="color: #333;">rec</span><span class="p">,</span><span class="s" style="color: #d14;">"VAF"</span><span class="p">,</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">vaf</span><span class="p">,</span><span class="n" style="color: #333;">nsmpl</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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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="c"> <span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"Failed to write FORMAT/VAF at %s:%"</span><span class="n" style="color: #333;">PRId64</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">bcf_seqname</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">hdr</span><span class="p">,</span><span class="n" style="color: #333;">rec</span><span class="p">),(</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="p">)</span> <span class="n" style="color: #333;">rec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="c"> <span class="p">}</span></span>
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345
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<td class="diff-line-num new_line" data-linenumber="367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
367
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<pre style="margin: 0;"> <span id="LC367" class="line" lang="c"> <span class="p">}</span></span>
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346
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">bcf_write</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">out_fh</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="n" style="color: #333;">rec</span><span class="p">)</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">0</span> <span class="p">)</span> <span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"[%s] Error: cannot write to %s</span><span class="se" style="color: #d14;"><span class="idiff left">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">__func__</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff right">output_fname</span></span><span class="p">);</span></span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">bcf_write</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">out_fh</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">hdr_out</span><span class="p">,</span> <span class="n" style="color: #333;">rec</span><span class="p">)</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">0</span> <span class="p">)</span> <span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"[%s] Error: cannot write to %s<span class="idiff left"> at %s:%"</span></span><span class="n" style="color: #333;"><span class="idiff">PRId64</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">__func__</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">output_fname</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">bcf_seqname</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">hdr</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">rec</span></span><span class="p"><span class="idiff">),(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int64_t</span></span><span class="p"><span class="idiff">)</span></span><span class="n" style="color: #333;"><span class="idiff">rec</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">pos</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">);</span></span>
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347
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369
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="c"><span class="p">}</span></span>
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348
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370
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="c"></span>
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349
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371
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<pre style="margin: 0;"> <span id="LC371" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">run</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">argv</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="353" style="width: 35px; color: rgba(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="375" style="width: 35px; color: rgba(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">@@ -353,6 +375,7 @@ int run(int argc, char **argv)</td>
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353
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375
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="c"> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">output_fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"-"</span><span class="p">;</span></span>
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354
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376
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">option</span> <span class="n" style="color: #333;">loptions</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span></span>
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355
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377
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<pre style="margin: 0;"> <span id="LC377" class="line" lang="c"> <span class="p">{</span></span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="c"> <span class="p">{</span><span class="s" style="color: #d14;">"force-AD"</span><span class="p">,</span><span class="n" style="color: #333;">no_argument</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">},</span></span>
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356
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379
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="c"> <span class="p">{</span><span class="s" style="color: #d14;">"min-score"</span><span class="p">,</span><span class="n" style="color: #333;">required_argument</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="sc" style="color: #d14;">'m'</span><span class="p">},</span></span>
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357
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380
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="c"> <span class="p">{</span><span class="s" style="color: #d14;">"include"</span><span class="p">,</span><span class="n" style="color: #333;">required_argument</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="sc" style="color: #d14;">'i'</span><span class="p">},</span></span>
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<td class="diff-line-num old_line" data-linenumber="358" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
358
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<td class="diff-line-num new_line" data-linenumber="381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
381
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="c"> <span class="p">{</span><span class="s" style="color: #d14;">"exclude"</span><span class="p">,</span><span class="n" style="color: #333;">required_argument</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="sc" style="color: #d14;">'e'</span><span class="p">},</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -372,6 +395,7 @@ int run(int argc, char **argv)</td>
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372
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395
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="c"> <span class="p">{</span></span>
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373
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<td class="diff-line-num new_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">
396
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="c"> <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">)</span> </span>
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374
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397
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">1</span> <span class="p">:</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">force_ad</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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375
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<td class="diff-line-num new_line" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
399
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'e'</span><span class="p">:</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">filter_str</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optarg</span><span class="p">;</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">filter_logic</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">FLT_EXCLUDE</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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376
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<td class="diff-line-num new_line" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
400
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'i'</span><span class="p">:</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">filter_str</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optarg</span><span class="p">;</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">filter_logic</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">FLT_INCLUDE</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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377
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401
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'t'</span><span class="p">:</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">targets</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optarg</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<li id="78bcfa40e5186627dc23148a193ec136329a9225">
<a href="https://salsa.debian.org/med-team/bcftools/commit/e439282c1235fa123a822dbcd7dae553cf4cb693#78bcfa40e5186627dc23148a193ec136329a9225"><strong>test/norm.split.3.out</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">##fileformat=VCFv4.2</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">##FILTER=<ID=PASS,Description="All filters passed"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled likelihood"></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Depth"></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">##contig=<ID=1,length=2147483647></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">##contig=<ID=2,length=2147483647></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">##contig=<ID=20,length=2147483647></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">##contig=<ID=21,length=2147483647></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">##INFO=<ID=XRF,Number=R,Type=Float,Description="Test Number=AGR in INFO"></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">##INFO=<ID=XAF,Number=A,Type=Float,Description="Test Number=AGR in INFO"></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">##INFO=<ID=XGF,Number=G,Type=Float,Description="Test Number=AGR in INFO"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">##INFO=<ID=XRI,Number=R,Type=Integer,Description="Test Number=AGR in INFO"></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">##INFO=<ID=XAI,Number=A,Type=Integer,Description="Test Number=AGR in INFO"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">##INFO=<ID=XGI,Number=G,Type=Integer,Description="Test Number=AGR in INFO"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">##INFO=<ID=XRS,Number=R,Type=String,Description="Test Number=AGR in INFO"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">##INFO=<ID=XAS,Number=A,Type=String,Description="Test Number=AGR in INFO"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">##INFO=<ID=XGS,Number=G,Type=String,Description="Test Number=AGR in INFO"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">##FORMAT=<ID=FRF,Number=R,Type=Float,Description="Test Number=AGR in FORMAT"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">##FORMAT=<ID=FAF,Number=A,Type=Float,Description="Test Number=AGR in FORMAT"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">##FORMAT=<ID=FGF,Number=G,Type=Float,Description="Test Number=AGR in FORMAT"></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">##FORMAT=<ID=FRI,Number=R,Type=Integer,Description="Test Number=AGR in FORMAT"></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">##FORMAT=<ID=FAI,Number=A,Type=Integer,Description="Test Number=AGR in FORMAT"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">##FORMAT=<ID=FGI,Number=G,Type=Integer,Description="Test Number=AGR in FORMAT"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">##FORMAT=<ID=FRS,Number=R,Type=String,Description="Test Number=AGR in FORMAT"></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">##FORMAT=<ID=FAS,Number=A,Type=String,Description="Test Number=AGR in FORMAT"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">##FORMAT=<ID=FGS,Number=G,Type=String,Description="Test Number=AGR in FORMAT"></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">##FORMAT=<ID=FSTR,Number=1,Type=String,Description="Test String in FORMAT"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">##INFO=<ID=ISTR,Number=1,Type=String,Description="Test String in INFO"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT XY00001 XY00002</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">1 105 . TAAACCCTAAA TAA 999 PASS INDEL;AN=4;DP=19;ISTR=SomeString;XRS=AAA,BBB;XAS=AAA;XGS=A,B,C GT:DP:FRS:FAS:FGF 1/0:1:AAAA,BBB:A:1e+06,2e+06,3e+06 1/0:1:AAAA,BBB:A:1e+06,2e+06,3e+06</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">1 105 . TAAACCCTAAA TAACCCTAAA 999 PASS INDEL;AN=4;DP=19;ISTR=SomeString;XRS=AAA,DDD;XAS=DDD;XGS=A,E,F GT:DP:FRS:FAS:FGF 0/1:1:AAAA,CC:BB:1e+06,500000,9e+09 0/1:1:AAAA,CC:BB:1e+06,500000,9e+09</span></pre>
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<a href="https://salsa.debian.org/med-team/bcftools/commit/e439282c1235fa123a822dbcd7dae553cf4cb693#960c309f8321419550169434fc1c66000c135cd5"><strong>test/norm.split.3.vcf</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">##fileformat=VCFv4.2</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">##FILTER=<ID=PASS,Description="All filters passed"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled likelihood"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Depth"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">##contig=<ID=1,length=2147483647></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">##contig=<ID=2,length=2147483647></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">##contig=<ID=20,length=2147483647></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">##contig=<ID=21,length=2147483647></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">##INFO=<ID=XRF,Number=R,Type=Float,Description="Test Number=AGR in INFO"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">##INFO=<ID=XAF,Number=A,Type=Float,Description="Test Number=AGR in INFO"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">##INFO=<ID=XGF,Number=G,Type=Float,Description="Test Number=AGR in INFO"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">##INFO=<ID=XRI,Number=R,Type=Integer,Description="Test Number=AGR in INFO"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">##INFO=<ID=XAI,Number=A,Type=Integer,Description="Test Number=AGR in INFO"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">##INFO=<ID=XGI,Number=G,Type=Integer,Description="Test Number=AGR in INFO"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">##INFO=<ID=XRS,Number=R,Type=String,Description="Test Number=AGR in INFO"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">##INFO=<ID=XAS,Number=A,Type=String,Description="Test Number=AGR in INFO"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">##INFO=<ID=XGS,Number=G,Type=String,Description="Test Number=AGR in INFO"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">##FORMAT=<ID=FRF,Number=R,Type=Float,Description="Test Number=AGR in FORMAT"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">##FORMAT=<ID=FAF,Number=A,Type=Float,Description="Test Number=AGR in FORMAT"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">##FORMAT=<ID=FGF,Number=G,Type=Float,Description="Test Number=AGR in FORMAT"></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">##FORMAT=<ID=FRI,Number=R,Type=Integer,Description="Test Number=AGR in FORMAT"></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">##FORMAT=<ID=FAI,Number=A,Type=Integer,Description="Test Number=AGR in FORMAT"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">##FORMAT=<ID=FGI,Number=G,Type=Integer,Description="Test Number=AGR in FORMAT"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">##FORMAT=<ID=FRS,Number=R,Type=String,Description="Test Number=AGR in FORMAT"></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">##FORMAT=<ID=FAS,Number=A,Type=String,Description="Test Number=AGR in FORMAT"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">##FORMAT=<ID=FGS,Number=G,Type=String,Description="Test Number=AGR in FORMAT"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">##INFO=<ID=ISTR,Number=1,Type=String,Description="Test String in INFO"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT XY00001 XY00002</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">1 105 . TAAACCCTAAA TAA,TAACCCTAAA 999 PASS INDEL;AN=4;AC=2,2,7;DP=19;ISTR=SomeString;XRF=1e+06,2e+06,500000,7;XRI=1111,2222,5555,7;XRS=AAA,BBB,DDD,xx;XAF=1e+06,500000,7;XAI=1111,5555,7;XAS=AAA,DDD,xx;XGF=1e+06,2e+06,3e+06,500000,.,9e+09,7;XGI=1111,2222,3333,5555,.,9999,7;XGS=A,B,C,E,.,F,x GT:PL:DP:FRF:FRI:FRS:FAF:FAI:FAS:FGF:FGI:FGS 1/2:1,2,3,4,5,6:1:1e+06,2e+06,500000:1111,2222,5555:AAAA,BBB,CC:1e+06,500000:1111,5555:A,BB:1e+06,2e+06,3e+06,500000,.,9e+09:1111,2222,3333,5555,.,9999:A,BB,CCC,EEEE,.,FFFFF 1/2:1,2,3,4,5,6,7:1:1e+06,2e+06,500000,7:1111,2222,5555,7:AAAA,BBB,CC:1e+06,500000,7:1111,5555,7:A,BB:1e+06,2e+06,3e+06,500000,.,9e+09:1111,2222,3333,5555,.,9999,7:A,BB,CCC,EEEE,.,FFFFF,XX</span></pre>
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<a href="https://salsa.debian.org/med-team/bcftools/commit/e439282c1235fa123a822dbcd7dae553cf4cb693#1dafee15289de195cc70f0739a91d5b95f8e8889"><strong>test/test.pl</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">@@ -175,6 +175,7 @@ test_vcf_query($opts,in=>'query.filter.10',out=>'query.74.out',args=>q[-f'%POS</td>
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="perl"><span class="nv" style="color: #008080;">test_vcf_norm</span><span class="p">(</span><span class="nv" style="color: #008080;">$opts</span><span class="p">,</span><span class="nv" style="color: #008080;">in</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">norm</span><span class="p">',</span><span class="nv" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">norm.out</span><span class="p">',</span><span class="nv" style="color: #008080;">fai</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">norm</span><span class="p">',</span><span class="nv" style="color: #008080;">args</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">-cx</span><span class="p">');</span></span>
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="perl"><span class="nv" style="color: #008080;">test_vcf_norm</span><span class="p">(</span><span class="nv" style="color: #008080;">$opts</span><span class="p">,</span><span class="nv" style="color: #008080;">in</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">norm.split</span><span class="p">',</span><span class="nv" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">norm.split.out</span><span class="p">',</span><span class="nv" style="color: #008080;">args</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">-m-</span><span class="p">');</span></span>
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="perl"><span class="nv" style="color: #008080;">test_vcf_norm</span><span class="p">(</span><span class="nv" style="color: #008080;">$opts</span><span class="p">,</span><span class="nv" style="color: #008080;">in</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">norm.split.2</span><span class="p">',</span><span class="nv" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">norm.split.2.out</span><span class="p">',</span><span class="nv" style="color: #008080;">args</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">-m-</span><span class="p">');</span></span>
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="perl"><span class="nv" style="color: #008080;">test_vcf_norm</span><span class="p">(</span><span class="nv" style="color: #008080;">$opts</span><span class="p">,</span><span class="nv" style="color: #008080;">in</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">norm.split.3</span><span class="p">',</span><span class="nv" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">norm.split.3.out</span><span class="p">',</span><span class="nv" style="color: #008080;">args</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">-m- --force</span><span class="p">');</span></span>
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178
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="perl"><span class="nv" style="color: #008080;">test_vcf_norm</span><span class="p">(</span><span class="nv" style="color: #008080;">$opts</span><span class="p">,</span><span class="nv" style="color: #008080;">in</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">norm.split</span><span class="p">',</span><span class="nv" style="color: #008080;">fai</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">norm</span><span class="p">',</span><span class="nv" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">norm.split.and.norm.out</span><span class="p">',</span><span class="nv" style="color: #008080;">args</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">-m-</span><span class="p">');</span></span>
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="perl"><span class="nv" style="color: #008080;">test_vcf_norm</span><span class="p">(</span><span class="nv" style="color: #008080;">$opts</span><span class="p">,</span><span class="nv" style="color: #008080;">in</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">norm.merge</span><span class="p">',</span><span class="nv" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">norm.merge.out</span><span class="p">',</span><span class="nv" style="color: #008080;">args</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">-m+</span><span class="p">');</span></span>
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<td class="diff-line-num old_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
180
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="perl"><span class="nv" style="color: #008080;">test_vcf_norm</span><span class="p">(</span><span class="nv" style="color: #008080;">$opts</span><span class="p">,</span><span class="nv" style="color: #008080;">in</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">norm.merge.2</span><span class="p">',</span><span class="nv" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">norm.merge.2.out</span><span class="p">',</span><span class="nv" style="color: #008080;">args</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">-m+</span><span class="p">');</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -225,6 +226,11 @@ test_vcf_view($opts,in=>'idx.2',out=>'idx.2.out',args=>q[-H -r 1:1172777-1172804</td>
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225
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226
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="perl"><span class="nv" style="color: #008080;">test_vcf_view</span><span class="p">(</span><span class="nv" style="color: #008080;">$opts</span><span class="p">,</span><span class="nv" style="color: #008080;">in</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">idx.2</span><span class="p">',</span><span class="nv" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">idx.2.out</span><span class="p">',</span><span class="nv" style="color: #008080;">args</span><span class="o" style="font-weight: 600;">=></span><span class="sx" style="color: #d14;">q[-H -R {PATH}/idx.2.bed]</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
226
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<td class="diff-line-num new_line" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
227
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="perl"><span class="nv" style="color: #008080;">test_vcf_view</span><span class="p">(</span><span class="nv" style="color: #008080;">$opts</span><span class="p">,</span><span class="nv" style="color: #008080;">in</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">idx.3</span><span class="p">',</span><span class="nv" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">idx.3.out</span><span class="p">',</span><span class="nv" style="color: #008080;">args</span><span class="o" style="font-weight: 600;">=></span><span class="sx" style="color: #d14;">q[-H -R {PATH}/idx.3.bed]</span><span class="p">);</span></span>
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227
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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="perl"><span class="nv" style="color: #008080;">test_vcf_view</span><span class="p">(</span><span class="nv" style="color: #008080;">$opts</span><span class="p">,</span><span class="nv" style="color: #008080;">in</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">idx.4</span><span class="p">',</span><span class="nv" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">idx.4.out</span><span class="p">',</span><span class="nv" style="color: #008080;">args</span><span class="o" style="font-weight: 600;">=></span><span class="sx" style="color: #d14;">q[-H -R {PATH}/idx.4.bed]</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="perl"><span class="nv" style="color: #008080;">test_vcf_64bit</span><span class="p">(</span><span class="nv" style="color: #008080;">$opts</span><span class="p">,</span><span class="nv" style="color: #008080;">in</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">view64bit.1</span><span class="p">',</span><span class="nv" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">view64bit.1.out</span><span class="p">',</span><span class="nv" style="color: #008080;">do_bcf</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="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="perl"><span class="nv" style="color: #008080;">test_vcf_64bit</span><span class="p">(</span><span class="nv" style="color: #008080;">$opts</span><span class="p">,</span><span class="nv" style="color: #008080;">in</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">view64bit.2</span><span class="p">',</span><span class="nv" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">view64bit.2.out</span><span class="p">',</span><span class="nv" style="color: #008080;">do_bcf</span><span class="o" style="font-weight: 600;">=></span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="perl"><span class="nv" style="color: #008080;">test_vcf_64bit</span><span class="p">(</span><span class="nv" style="color: #008080;">$opts</span><span class="p">,</span><span class="nv" style="color: #008080;">in</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">view64bit.3</span><span class="p">',</span><span class="nv" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">view64bit.3.out</span><span class="p">');</span> <span class="c1" style="color: #998; font-style: italic;"># large coordinates don't work with BCF</span></span>
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<td class="diff-line-num new old_line" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-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="perl"><span class="nv" style="color: #008080;">test_vcf_64bit</span><span class="p">(</span><span class="nv" style="color: #008080;">$opts</span><span class="p">,</span><span class="nv" style="color: #008080;">in</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">view64bit.4</span><span class="p">',</span><span class="nv" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">view64bit.4.out</span><span class="p">',</span><span class="nv" style="color: #008080;">do_bcf</span><span class="o" style="font-weight: 600;">=></span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="perl"><span class="nv" style="color: #008080;">test_vcf_64bit</span><span class="p">(</span><span class="nv" style="color: #008080;">$opts</span><span class="p">,</span><span class="nv" style="color: #008080;">in</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">view64bit.5</span><span class="p">',</span><span class="nv" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">view64bit.5.out</span><span class="p">',</span><span class="nv" style="color: #008080;">do_bcf</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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228
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<td class="diff-line-num new_line" data-linenumber="234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
234
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="perl"><span class="nv" style="color: #008080;">test_vcf_filter</span><span class="p">(</span><span class="nv" style="color: #008080;">$opts</span><span class="p">,</span><span class="nv" style="color: #008080;">in</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">view.filter</span><span class="p">',</span><span class="nv" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">view.filter.6.out</span><span class="p">',</span><span class="nv" style="color: #008080;">args</span><span class="o" style="font-weight: 600;">=></span><span class="sx" style="color: #d14;">q[-S. -e'TXT0="text"']</span><span class="p">,</span><span class="nv" style="color: #008080;">reg</span><span class="o" style="font-weight: 600;">=></span><span class="p">'');</span></span>
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229
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<td class="diff-line-num new_line" data-linenumber="235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
235
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="perl"><span class="nv" style="color: #008080;">test_vcf_filter</span><span class="p">(</span><span class="nv" style="color: #008080;">$opts</span><span class="p">,</span><span class="nv" style="color: #008080;">in</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">view.filter</span><span class="p">',</span><span class="nv" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">view.filter.7.out</span><span class="p">',</span><span class="nv" style="color: #008080;">args</span><span class="o" style="font-weight: 600;">=></span><span class="sx" style="color: #d14;">q[-S. -e'FMT/FRS[*:1]="BB"']</span><span class="p">,</span><span class="nv" style="color: #008080;">reg</span><span class="o" style="font-weight: 600;">=></span><span class="p">'');</span></span>
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230
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<td class="diff-line-num new_line" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
236
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="perl"><span class="nv" style="color: #008080;">test_vcf_filter</span><span class="p">(</span><span class="nv" style="color: #008080;">$opts</span><span class="p">,</span><span class="nv" style="color: #008080;">in</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">view.filter</span><span class="p">',</span><span class="nv" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">view.filter.8.out</span><span class="p">',</span><span class="nv" style="color: #008080;">args</span><span class="o" style="font-weight: 600;">=></span><span class="sx" style="color: #d14;">q[-S. -e'FMT/FGS[*:0]="AAAAAA"']</span><span class="p">,</span><span class="nv" style="color: #008080;">reg</span><span class="o" style="font-weight: 600;">=></span><span class="p">'');</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -402,6 +408,8 @@ test_vcf_plugin($opts,in=>'mendelian',out=>'mendelian.3.out',cmd=>'+mendelian',a</td>
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402
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<td class="diff-line-num new_line" data-linenumber="408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
408
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<pre style="margin: 0;"> <span id="LC408" class="line" lang="perl"><span class="nv" style="color: #008080;">test_vcf_plugin</span><span class="p">(</span><span class="nv" style="color: #008080;">$opts</span><span class="p">,</span><span class="nv" style="color: #008080;">in</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">contrast</span><span class="p">',</span><span class="nv" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">contrast.out</span><span class="p">',</span><span class="nv" style="color: #008080;">cmd</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">+contrast</span><span class="p">',</span><span class="nv" style="color: #008080;">args</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">-0 a,b -1 c</span><span class="p">');</span></span>
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<td class="diff-line-num old_line" data-linenumber="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
403
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<td class="diff-line-num new_line" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
409
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<pre style="margin: 0;"> <span id="LC409" class="line" lang="perl"><span class="nv" style="color: #008080;">test_vcf_plugin</span><span class="p">(</span><span class="nv" style="color: #008080;">$opts</span><span class="p">,</span><span class="nv" style="color: #008080;">in</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">contrast</span><span class="p">',</span><span class="nv" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">contrast.out</span><span class="p">',</span><span class="nv" style="color: #008080;">cmd</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">+contrast</span><span class="p">',</span><span class="nv" style="color: #008080;">args</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">-0 {PATH}/contrast0.txt -1 {PATH}/contrast1.txt</span><span class="p">');</span></span>
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<td class="diff-line-num old_line" data-linenumber="404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
404
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<td class="diff-line-num new_line" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
410
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<pre style="margin: 0;"> <span id="LC410" class="line" lang="perl"><span class="nv" style="color: #008080;">test_vcf_plugin</span><span class="p">(</span><span class="nv" style="color: #008080;">$opts</span><span class="p">,</span><span class="nv" style="color: #008080;">in</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">trio-dnm.1</span><span class="p">',</span><span class="nv" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">trio-dnm.1.out</span><span class="p">',</span><span class="nv" style="color: #008080;">cmd</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">+trio-dnm</span><span class="p">',</span><span class="nv" style="color: #008080;">args</span><span class="o" style="font-weight: 600;">=></span><span class="p">"</span><span class="s2" style="color: #d14;">-p proband,father,mother | $</span><span class="si" style="color: #d14;">$opts</span><span class="s2" style="color: #d14;">{bin}/bcftools query -f'%CHROM[</span><span class="se" style="color: #d14;">\\</span><span class="s2" style="color: #d14;">t%DNM]</span><span class="se" style="color: #d14;">\\</span><span class="s2" style="color: #d14;">t[</span><span class="se" style="color: #d14;">\\</span><span class="s2" style="color: #d14;">t%VAF]</span><span class="se" style="color: #d14;">\\</span><span class="s2" style="color: #d14;">n'</span><span class="p">");</span></span>
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<td class="diff-line-num new old_line" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="perl"><span class="nv" style="color: #008080;">test_vcf_plugin</span><span class="p">(</span><span class="nv" style="color: #008080;">$opts</span><span class="p">,</span><span class="nv" style="color: #008080;">in</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">trio-dnm.2</span><span class="p">',</span><span class="nv" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">trio-dnm.1.out</span><span class="p">',</span><span class="nv" style="color: #008080;">cmd</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">+trio-dnm</span><span class="p">',</span><span class="nv" style="color: #008080;">args</span><span class="o" style="font-weight: 600;">=></span><span class="p">"</span><span class="s2" style="color: #d14;">-p proband,father,mother --force-AD | $</span><span class="si" style="color: #d14;">$opts</span><span class="s2" style="color: #d14;">{bin}/bcftools query -f'%CHROM[</span><span class="se" style="color: #d14;">\\</span><span class="s2" style="color: #d14;">t%DNM]</span><span class="se" style="color: #d14;">\\</span><span class="s2" style="color: #d14;">t[</span><span class="se" style="color: #d14;">\\</span><span class="s2" style="color: #d14;">t%VAF]</span><span class="se" style="color: #d14;">\\</span><span class="s2" style="color: #d14;">n'</span><span class="p">");</span></span>
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<td class="diff-line-num new old_line" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="perl"><span class="nv" style="color: #008080;">test_vcf_plugin</span><span class="p">(</span><span class="nv" style="color: #008080;">$opts</span><span class="p">,</span><span class="nv" style="color: #008080;">in</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">trio-dnm.2</span><span class="p">',</span><span class="nv" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">trio-dnm.2.out</span><span class="p">',</span><span class="nv" style="color: #008080;">cmd</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">+trio-dnm</span><span class="p">',</span><span class="nv" style="color: #008080;">args</span><span class="o" style="font-weight: 600;">=></span><span class="p">"</span><span class="s2" style="color: #d14;">-p proband,father,mother | $</span><span class="si" style="color: #d14;">$opts</span><span class="s2" style="color: #d14;">{bin}/bcftools query -f'%CHROM[</span><span class="se" style="color: #d14;">\\</span><span class="s2" style="color: #d14;">t%DNM]</span><span class="se" style="color: #d14;">\\</span><span class="s2" style="color: #d14;">t[</span><span class="se" style="color: #d14;">\\</span><span class="s2" style="color: #d14;">t%VAF]</span><span class="se" style="color: #d14;">\\</span><span class="s2" style="color: #d14;">n'</span><span class="p">");</span></span>
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<td class="diff-line-num old_line" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
405
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<td class="diff-line-num new_line" data-linenumber="413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
413
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<pre style="margin: 0;"> <span id="LC413" class="line" lang="perl"><span class="nv" style="color: #008080;">test_vcf_plugin</span><span class="p">(</span><span class="nv" style="color: #008080;">$opts</span><span class="p">,</span><span class="nv" style="color: #008080;">in</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">gvcfz</span><span class="p">',</span><span class="nv" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">gvcfz.1.out</span><span class="p">',</span><span class="nv" style="color: #008080;">cmd</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">+gvcfz</span><span class="p">',</span><span class="nv" style="color: #008080;">args</span><span class="o" style="font-weight: 600;">=></span><span class="sx" style="color: #d14;">qq[-g 'PASS:GT!="alt"' -a | $$opts{bin}/bcftools query -f'%POS\\t%REF\\t%ALT\\t%END[\\t%GT][\\t%DP][\\t%GQ][\\t%RGQ]\\n']</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
406
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<td class="diff-line-num new_line" data-linenumber="414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
414
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<pre style="margin: 0;"> <span id="LC414" class="line" lang="perl"><span class="nv" style="color: #008080;">test_vcf_plugin</span><span class="p">(</span><span class="nv" style="color: #008080;">$opts</span><span class="p">,</span><span class="nv" style="color: #008080;">in</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">gvcfz</span><span class="p">',</span><span class="nv" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">gvcfz.2.out</span><span class="p">',</span><span class="nv" style="color: #008080;">cmd</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">+gvcfz</span><span class="p">',</span><span class="nv" style="color: #008080;">args</span><span class="o" style="font-weight: 600;">=></span><span class="sx" style="color: #d14;">qq[-g 'PASS:GQ>10; FLT:-' -a | $$opts{bin}/bcftools query -f'%POS\\t%REF\\t%ALT\\t%FILTER\\t%END[\\t%GT][\\t%DP][\\t%GQ][\\t%RGQ]\\n']</span><span class="p">);</span></span>
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407
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<td class="diff-line-num new_line" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
415
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<pre style="margin: 0;"> <span id="LC415" class="line" lang="perl"><span class="nv" style="color: #008080;">test_vcf_plugin</span><span class="p">(</span><span class="nv" style="color: #008080;">$opts</span><span class="p">,</span><span class="nv" style="color: #008080;">in</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">gvcfz.2</span><span class="p">',</span><span class="nv" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">gvcfz.2.1.out</span><span class="p">',</span><span class="nv" style="color: #008080;">cmd</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">+gvcfz</span><span class="p">',</span><span class="nv" style="color: #008080;">args</span><span class="o" style="font-weight: 600;">=></span><span class="sx" style="color: #d14;">qq[-g 'PASS:GT!="alt"' -a | $$opts{bin}/bcftools query -f'%POS\\t%REF\\t%ALT\\t%FILTER\\t%END[\\t%GT][\\t%DP]\\n']</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="956" style="width: 35px; color: rgba(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="964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -956,6 +964,16 @@ sub test_vcf_view</td>
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<td class="diff-line-num old_line" data-linenumber="956" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
956
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<td class="diff-line-num new_line" data-linenumber="964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
964
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<pre style="margin: 0;"> <span id="LC964" class="line" lang="perl"> <span class="nv" style="color: #008080;">test_cmd</span><span class="p">(</span><span class="nv" style="color: #008080;">$opts</span><span class="p">,</span><span class="o" style="font-weight: 600;">%</span><span class="nv" style="color: #008080;">args</span><span class="p">,</span><span class="nv" style="color: #008080;">cmd</span><span class="o" style="font-weight: 600;">=></span><span class="p">"</span><span class="s2" style="color: #d14;">$</span><span class="si" style="color: #d14;">$opts</span><span class="s2" style="color: #d14;">{bin}/bcftools view -Ob </span><span class="si" style="color: #d14;">$args</span><span class="s2" style="color: #d14;">{args} $</span><span class="si" style="color: #d14;">$opts</span><span class="s2" style="color: #d14;">{tmp}/</span><span class="si" style="color: #d14;">$args</span><span class="s2" style="color: #d14;">{in}.vcf.gz </span><span class="si" style="color: #d14;">$args</span><span class="s2" style="color: #d14;">{reg} | $</span><span class="si" style="color: #d14;">$opts</span><span class="s2" style="color: #d14;">{bin}/bcftools view | grep -v ^##bcftools_</span><span class="p">",</span> <span class="nv" style="color: #008080;">exp_fix</span><span class="o" style="font-weight: 600;">=></span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
957
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<td class="diff-line-num new_line" data-linenumber="965" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
965
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<pre style="margin: 0;"> <span id="LC965" class="line" lang="perl"> <span class="p">}</span></span>
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958
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966
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<pre style="margin: 0;"> <span id="LC966" class="line" lang="perl"><span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="967" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
967
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<pre style="margin: 0;">+<span id="LC967" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">test_vcf_64bit</span></span>
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968
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<pre style="margin: 0;">+<span id="LC968" class="line" lang="perl"><span class="p">{</span></span>
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969
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<pre style="margin: 0;">+<span id="LC969" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: #008080;">$opts</span><span class="p">,</span><span class="o" style="font-weight: 600;">%</span><span class="nv" style="color: #008080;">args</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">@_</span><span class="p">;</span></span>
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970
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<pre style="margin: 0;">+<span id="LC970" class="line" lang="perl"> <span class="nv" style="color: #008080;">test_cmd</span><span class="p">(</span><span class="nv" style="color: #008080;">$opts</span><span class="p">,</span><span class="o" style="font-weight: 600;">%</span><span class="nv" style="color: #008080;">args</span><span class="p">,</span><span class="nv" style="color: #008080;">cmd</span><span class="o" style="font-weight: 600;">=></span><span class="p">"</span><span class="s2" style="color: #d14;">$</span><span class="si" style="color: #d14;">$opts</span><span class="s2" style="color: #d14;">{bin}/bcftools view $</span><span class="si" style="color: #d14;">$opts</span><span class="s2" style="color: #d14;">{path}/</span><span class="si" style="color: #d14;">$args</span><span class="s2" style="color: #d14;">{in}.vcf -H</span><span class="p">",</span> <span class="nv" style="color: #008080;">exp_fix</span><span class="o" style="font-weight: 600;">=></span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="971" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
971
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<pre style="margin: 0;">+<span id="LC971" class="line" lang="perl"> <span class="nv" style="color: #008080;">test_cmd</span><span class="p">(</span><span class="nv" style="color: #008080;">$opts</span><span class="p">,</span><span class="o" style="font-weight: 600;">%</span><span class="nv" style="color: #008080;">args</span><span class="p">,</span><span class="nv" style="color: #008080;">cmd</span><span class="o" style="font-weight: 600;">=></span><span class="p">"</span><span class="s2" style="color: #d14;">$</span><span class="si" style="color: #d14;">$opts</span><span class="s2" style="color: #d14;">{bin}/bcftools view $</span><span class="si" style="color: #d14;">$opts</span><span class="s2" style="color: #d14;">{path}/</span><span class="si" style="color: #d14;">$args</span><span class="s2" style="color: #d14;">{in}.vcf | $</span><span class="si" style="color: #d14;">$opts</span><span class="s2" style="color: #d14;">{bin}/bcftools view -H</span><span class="p">",</span> <span class="nv" style="color: #008080;">exp_fix</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="972" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
972
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<pre style="margin: 0;">+<span id="LC972" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: #008080;">$args</span><span class="p">{</span><span class="nv" style="color: #008080;">do_bcf</span><span class="p">}</span> <span class="p">)</span></span>
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973
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<pre style="margin: 0;">+<span id="LC973" class="line" lang="perl"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="974" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
974
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<pre style="margin: 0;">+<span id="LC974" class="line" lang="perl"> <span class="nv" style="color: #008080;">test_cmd</span><span class="p">(</span><span class="nv" style="color: #008080;">$opts</span><span class="p">,</span><span class="o" style="font-weight: 600;">%</span><span class="nv" style="color: #008080;">args</span><span class="p">,</span><span class="nv" style="color: #008080;">cmd</span><span class="o" style="font-weight: 600;">=></span><span class="p">"</span><span class="s2" style="color: #d14;">$</span><span class="si" style="color: #d14;">$opts</span><span class="s2" style="color: #d14;">{bin}/bcftools view $</span><span class="si" style="color: #d14;">$opts</span><span class="s2" style="color: #d14;">{path}/</span><span class="si" style="color: #d14;">$args</span><span class="s2" style="color: #d14;">{in}.vcf -Ou | $</span><span class="si" style="color: #d14;">$opts</span><span class="s2" style="color: #d14;">{bin}/bcftools view -H</span><span class="p">",</span> <span class="nv" style="color: #008080;">exp_fix</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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975
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<pre style="margin: 0;">+<span id="LC975" class="line" lang="perl"> <span class="p">}</span></span>
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976
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<pre style="margin: 0;">+<span id="LC976" class="line" lang="perl"><span class="p">}</span></span>
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959
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977
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<pre style="margin: 0;"> <span id="LC977" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">test_vcf_call</span></span>
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960
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978
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<pre style="margin: 0;"> <span id="LC978" class="line" lang="perl"><span class="p">{</span></span>
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961
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979
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<pre style="margin: 0;"> <span id="LC979" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: #008080;">$opts</span><span class="p">,</span><span class="o" style="font-weight: 600;">%</span><span class="nv" style="color: #008080;">args</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">@_</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/bcftools/commit/e439282c1235fa123a822dbcd7dae553cf4cb693#7ae1c7764315501f2021a90cae77edd0ebe9a1bd"><strong>test/trio-dnm.2.out</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">1 100 . . . . .</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">1 98 . . . . .</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">1 99 . . . . .</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">1 98 . . . . .</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">1 92 . . . . .</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">1 98 . . . . .</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">2 5 . . . . .</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">2 6 . . . . .</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">2 5 . . . . .</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">3 3 . . . . .</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">3 3 . . . . .</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">3 3 . . . . .</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">3 0 . . . . .</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">3 3 . . . . .</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">3 3 . . . . .</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">3 3 . . . . .</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">3 3 . . . . .</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">3 3 . . . . .</span></pre>
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<li id="8c01ce7e82715db734b9f58d908a5efee7b2d6f0">
<a href="https://salsa.debian.org/med-team/bcftools/commit/e439282c1235fa123a822dbcd7dae553cf4cb693#8c01ce7e82715db734b9f58d908a5efee7b2d6f0"><strong>test/trio-dnm.2.vcf</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">##fileformat=VCFv4.2</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">##FILTER=<ID=LowQual,Description="Low quality"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">##INFO=<ID=TP,Number=0,Type=Flag,Description="true positive"></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">##INFO=<ID=FP,Number=0,Type=Flag,Description="false positive"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">##INFO=<ID=UN,Number=0,Type=Flag,Description="uncertain"></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">##contig=<ID=1,length=249250621></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">##contig=<ID=2,length=249250621></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">##contig=<ID=3,length=249250621></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">##reference=file:///lustre/scratch113/resources/ref/Homo_sapiens/1000Genomes_hs37d5/hs37d5.fa</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT proband father mother</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">1 1 . G A,T . . TP GT:AD:PL 0/2:62,0,27,0:733,919,3060,0,2141,2060 0/0:35,0,0:0,99,1485,99,1485,1485 0/0:38,0,0:0,102,1530,102,1530,1530</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">1 2 . G T,A . . TP GT:AD:PL 0/1:67,14,0,0:257,0,2105,458,2146,2605 0/0:36,0,0:0,99,1485,99,1485,1485 0/0:36,0,0:0,99,1485,99,1485,1485</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">1 3 . G A . . TP GT:AD:PL 0/1:71,14,0:241,0,2314 0/0:45,0:0,101,1530 0/0:43,0:0,99,1485</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">1 4 . C T . . TP GT:AD:PL 0/1:111,24,0:504,0,3776 0/0:35,0:0,99,1485 0/0:36,0:0,99,1485</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">1 5 . C A . . TP GT:AD:PL 0/1:30,6,0:124,0,981 0/0:37,0:0,99,1485 0/0:32,0:0,90,1350</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">1 8 . A G . . TP GT:AD:PL 0/1:434,52,0:859,0,18086 0/0:38,0:0,99,1485 0/0:38,0:0,99,1485</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">2 1 . A G . . UN GT:AD:PL 0/1:2,5,0:179,0,55 0/0:7,0:0,0,180 0/0:4,0:0,12,148</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">2 2 . A G . . UN GT:AD:PL 0/1:4,5,0:159,0,126 0/0:1,0:0,3,39 0/0:4,0:0,9,135</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">2 3 . A G . . UN GT:AD:PL 0/1:4,4,0:137,0,107 0/0:6,0:0,18,213 0/0:8,0:0,0,232</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">3 1 . A G . . FP GT:AD:PL 0/1:7,9,0,0:357,0,408 0/0:15,0:0,39,585 0/1:4,3:114,0,550</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">3 2 . C A . . FP GT:AD:PL 0/1:13,15,0:453,0,442 0/1:29,30:913,0,1011 0/0:39,0:0,99,1485</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">3 3 . A G . . FP GT:AD:PL 0/1:11,12,0:361,0,358 0/0:21,0:0,51,765 0/1:10,15:538,0,292</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">3 4 . A G,C . . FP GT:PL:AD 0/0:0,255,255,255,255,255:306,11,0,0 0/0:0,255,255,255,255,255:328,1,1 0/0:0,255,255,255,255,255:318,0,0</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">3 5 . A G . . FP GT:AD:PL 0/1:33,32,0:890,0,963 0/1:56,45:1328,0,1809 0/0:36,0:0,99,1485</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">3 6 . A G . . FP GT:AD:PL 0/1:19,24,0:737,0,649 0/0:48,0:0,108,1620 0/1:25,22:644,0,836</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">3 7 . A G . . FP GT:AD:PL 0/1:73,90,0:2864,0,2197 0/0:42,0:0,99,1485 0/1:69,74:2395,0,2064</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">3 8 . A G . . FP GT:AD:PL 0/1:115,128,0:4130,0,3542 0/0:34,0:0,99,1360 0/1:137,89:2571,0,4411</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">3 9 . A G . . FP GT:AD:PL 0/1:18,11,0:311,0,627 0/1:3,3:51,0,105 0/0:19,0:0,57,764</span></pre>
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<a href="https://salsa.debian.org/med-team/bcftools/commit/e439282c1235fa123a822dbcd7dae553cf4cb693#c826d79f3bdcef449634ef18e099537368988faa"><strong>test/view64bit.1.out</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">chr1 1 . G C . . MPOS=.;XPOS=.,.,.;NALOD=-0.8279;NLOD=15.45;POPAF=6</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">chr1 2 . G C . . MPOS=.;XPOS=.,.,.;NALOD=-0.8279;NLOD=15.45;POPAF=6</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">##fileformat=VCFv4.2</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">##INFO=<ID=MPOS,Number=A,Type=Integer,Description="dummy"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">##INFO=<ID=XPOS,Number=.,Type=Integer,Description="dummy"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">##INFO=<ID=NALOD,Number=A,Type=Float,Description="dummy"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">##INFO=<ID=NLOD,Number=A,Type=Float,Description="dummy"></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">##INFO=<ID=POPAF,Number=A,Type=Float,Description="dummy"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">##contig=<ID=chr1,length=248956422></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">#CHROM POS ID REF ALT QUAL FILTER INFO</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">chr1 1 . G C . . MPOS=-2147483641;XPOS=-2147483641,-2147483641,-2147483641;NALOD=-8.279e-01;NLOD=15.45;POPAF=6.00</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">chr1 2 . G C . . MPOS=-2147483648;XPOS=-2147483648,-2147483648,-2147483648;NALOD=-8.279e-01;NLOD=15.45;POPAF=6.00</span></pre>
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<a href="https://salsa.debian.org/med-team/bcftools/commit/e439282c1235fa123a822dbcd7dae553cf4cb693#a8c36a363319954b629ec23859ab7b9f64ae12fa"><strong>test/view64bit.2.out</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">chr1 1 . G C . . MPOS=.;XPOS=.,.,. MPOS:XPOS .:.,.,.</span></pre>
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<a href="https://salsa.debian.org/med-team/bcftools/commit/e439282c1235fa123a822dbcd7dae553cf4cb693#712d5c20caba0103b546e7abf34e3dcc5203bbad"><strong>test/view64bit.2.vcf</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">##fileformat=VCFv4.2</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">##INFO=<ID=MPOS,Number=A,Type=Integer,Description="dummy"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">##INFO=<ID=XPOS,Number=.,Type=Integer,Description="dummy"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">##FORMAT=<ID=MPOS,Number=.,Type=Integer,Description="dummy"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">##FORMAT=<ID=XPOS,Number=.,Type=Integer,Description="dummy"></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">##contig=<ID=chr1,length=248956422></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">chr1 1 . G C . . MPOS=42949672950;XPOS=42949672950,42949672950,42949672950 MPOS:XPOS 42949672950:42949672950,42949672950,42949672950</span></pre>
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<a href="https://salsa.debian.org/med-team/bcftools/commit/e439282c1235fa123a822dbcd7dae553cf4cb693#84da6b1f45bb71ebd9c02b90437caf5c3dcbb7f1"><strong>test/view64bit.3.out</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">chr1 42949672950 . G C . . MPOS=.;XPOS=.,.,. MPOS:XPOS .:.,.,.</span></pre>
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<a href="https://salsa.debian.org/med-team/bcftools/commit/e439282c1235fa123a822dbcd7dae553cf4cb693#577aaa2559e1e22c1ef8843732358a6c5718a53c"><strong>test/view64bit.3.vcf</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">##fileformat=VCFv4.2</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">##INFO=<ID=MPOS,Number=A,Type=Integer,Description="dummy"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">##INFO=<ID=XPOS,Number=.,Type=Integer,Description="dummy"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">##FORMAT=<ID=MPOS,Number=.,Type=Integer,Description="dummy"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">##FORMAT=<ID=XPOS,Number=.,Type=Integer,Description="dummy"></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">##contig=<ID=chr1,length=248956422></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">chr1 42949672950 . G C . . MPOS=42949672950;XPOS=42949672950,42949672950,42949672950 MPOS:XPOS 42949672950:42949672950,42949672950,42949672950</span></pre>
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<a href="https://salsa.debian.org/med-team/bcftools/commit/e439282c1235fa123a822dbcd7dae553cf4cb693#3600a0fd1dc0ec0296d33982bdcaddcb99d93486"><strong>test/view64bit.4.out</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">chr1 1 . G C . . MPOS=.;XPOS=.,.,. MPOS:XPOS .:.,.,.</span></pre>
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<a href="https://salsa.debian.org/med-team/bcftools/commit/e439282c1235fa123a822dbcd7dae553cf4cb693#c40536ba41427bdbae640af88c2f808bb1ebdc88"><strong>test/view64bit.4.vcf</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">##fileformat=VCFv4.2</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">##INFO=<ID=MPOS,Number=A,Type=Integer,Description="dummy"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">##INFO=<ID=XPOS,Number=.,Type=Integer,Description="dummy"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">##FORMAT=<ID=MPOS,Number=.,Type=Integer,Description="dummy"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">##FORMAT=<ID=XPOS,Number=.,Type=Integer,Description="dummy"></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">##contig=<ID=chr1,length=248956422></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">chr1 1 . G C . . MPOS=.;XPOS=.,.,. MPOS:XPOS .:.,.,.</span></pre>
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<a href="https://salsa.debian.org/med-team/bcftools/commit/e439282c1235fa123a822dbcd7dae553cf4cb693#d1aed07c190908a2445a7adfad3027f13db3223c"><strong>test/view64bit.5.out</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">chr1 1 . G C . . END=42949672,1,.;MPOS=100000000 XX 1,-2147483640,.,.,.,2147483647,.</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">chr1 1 . G C . . END=-2147483640 XX -2147483640</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">chr1 1 . G C . . END=. XX .</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">chr1 1 . G C . . END=. XX .</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">chr1 1 . G C . . END=. XX .</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">chr1 1 . G C . . END=. XX .</span></pre>
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<a href="https://salsa.debian.org/med-team/bcftools/commit/e439282c1235fa123a822dbcd7dae553cf4cb693#8ebc00332e408804bab37c027c66bb19d0833efb"><strong>test/view64bit.5.vcf</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">##fileformat=VCFv4.2</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">##INFO=<ID=END,Number=A,Type=Integer,Description="dummy"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">##INFO=<ID=MPOS,Number=A,Type=Integer,Description="dummy"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">##FORMAT=<ID=XX,Number=A,Type=Integer,Description="dummy"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">##contig=<ID=chr1,length=248956422></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S1</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">chr1 1 . G C . . END=42949672,1,5000000000;MPOS=100000000 XX 1,-2147483640,-2147483641,-2147483647,-2147483648,2147483647,2147483648</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">chr1 1 . G C . . END=-2147483640 XX -2147483640</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">chr1 1 . G C . . END=-2147483641 XX -2147483641</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">chr1 1 . G C . . END=-2147483647 XX -2147483647</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">chr1 1 . G C . . END=-2147483648 XX -2147483648</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">chr1 1 . G C . . END=-2147483649 XX -2147483649</span></pre>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* vcfisec.c -- Create intersections, unions and complements of VCF files.</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Copyright (C) 2012-201<span class="idiff left right">4</span> Genome Research Ltd.</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Copyright (C) 2012-201<span class="idiff left right">9</span> Genome Research Ltd.</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Author: Petr Danecek <pd3@sanger.ac.uk></span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="c"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -486,6 +486,9 @@ static void usage(void)</td>
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<pre style="margin: 0;"> <span id="LC486" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" # Extract and write records from A shared by both A and B using exact allele match</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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487
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<pre style="margin: 0;"> <span id="LC487" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" bcftools isec A.vcf.gz B.vcf.gz -p dir -n =2 -w 1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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488
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488
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<pre style="margin: 0;"> <span id="LC488" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" # Extract and write records from C found in A and C but not in B</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" bcftools isec A.vcf.gz B.vcf.gz C.vcf.gz -p dir -n~101 -w 3</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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492
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<pre style="margin: 0;"> <span id="LC492" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" # Extract records private to A or B comparing by position only</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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493
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<pre style="margin: 0;"> <span id="LC493" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" bcftools isec A.vcf.gz B.vcf.gz -p dir -n -1 -c all</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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494
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<pre style="margin: 0;"> <span id="LC494" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/bcftools/commit/e439282c1235fa123a822dbcd7dae553cf4cb693#5bb5b301a5d8cf43cad4dd1061b35189fca4b2a3"><strong>vcfnorm.c</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -97,7 +97,7 @@ typedef struct</td>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">output_fname</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ref_fname</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">vcf_fname</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">region</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">targets</span><span class="p">;</span></span>
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98
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">rmdup</span><span class="p">,</span> <span class="n" style="color: #333;">output_type</span><span class="p">,</span> <span class="n" style="color: #333;">n_threads</span><span class="p">,</span> <span class="n" style="color: #333;">check_ref</span><span class="p">,</span> <span class="n" style="color: #333;">strict_filter</span><span class="p">,</span> <span class="n" style="color: #333;">do_indels</span><span class="p">;</span></span>
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99
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nchanged</span><span class="p">,</span> <span class="n" style="color: #333;">nskipped</span><span class="p">,</span> <span class="n" style="color: #333;">nsplit</span><span class="p">,</span> <span class="n" style="color: #333;">ntotal</span><span class="p">,</span> <span class="n" style="color: #333;">mrows_op</span><span class="p">,</span> <span class="n" style="color: #333;">mrows_collapse</span><span class="p">,</span> <span class="n" style="color: #333;">parsimonious</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">record_cmd_line</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">record_cmd_line</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">force</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">force_warned</span></span><span class="p">;</span></span>
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="c"><span class="p">}</span></span>
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="c"><span class="n" style="color: #333;">args_t</span><span class="p">;</span></span>
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="c"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -466,23 +466,68 @@ static void split_info_numeric(args_t *args, bcf1_t *src, bcf_info_t *info, int</td>
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466
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<pre style="margin: 0;"> <span id="LC466" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if ( len==BCF_VL_A ) \</span></span>
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467
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<pre style="margin: 0;"> <span id="LC467" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> { \</span></span>
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<pre style="margin: 0;"> <span id="LC468" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if ( ret!=src->n_allele-1 ) \</span></span>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> { \</span></span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if ( args->force && !args->force_warned ) \</span></span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> { \</span></span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> fprintf(stderr, \</span></span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> "Warning: wrong number of fields in INFO/%s at %s:%"PRId64", expected %d, found %d\n" \</span></span>
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> " (This warning is printed only once.)\n", \</span></span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,src->n_allele-1,ret); \</span></span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> args->force_warned = 1; \</span></span>
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477
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> } \</span></span>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if ( args->force ) \</span></span>
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479
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> { \</span></span>
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480
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> bcf_update_info_##type(args->hdr,dst,tag,NULL,0); \</span></span>
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481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> return; \</span></span>
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482
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> } \</span></span>
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469
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483
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<pre style="margin: 0;"> <span id="LC483" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> error("Error: wrong number of fields in INFO/%s at %s:%"PRId64", expected %d, found %d\n", \</span></span>
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470
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484
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<pre style="margin: 0;"> <span id="LC484" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,src->n_allele-1,ret); \</span></span>
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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> } \</span></span>
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471
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486
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<pre style="margin: 0;"> <span id="LC486" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> bcf_update_info_##type(args->hdr,dst,tag,vals+ialt,1); \</span></span>
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472
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487
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<pre style="margin: 0;"> <span id="LC487" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> } \</span></span>
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473
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488
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<pre style="margin: 0;"> <span id="LC488" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> else if ( len==BCF_VL_R ) \</span></span>
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474
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489
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<pre style="margin: 0;"> <span id="LC489" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> { \</span></span>
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475
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490
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<pre style="margin: 0;"> <span id="LC490" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if ( ret!=src->n_allele ) \</span></span>
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> { \</span></span>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if ( args->force && !args->force_warned ) \</span></span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> { \</span></span>
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494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> fprintf(stderr, \</span></span>
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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> "Warning: wrong number of fields in INFO/%s at %s:%"PRId64", expected %d, found %d\n" \</span></span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> " (This warning is printed only once.)\n", \</span></span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,src->n_allele,ret); \</span></span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> args->force_warned = 1; \</span></span>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> } \</span></span>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if ( args->force ) \</span></span>
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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> { \</span></span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> bcf_update_info_##type(args->hdr,dst,tag,NULL,0); \</span></span>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> return; \</span></span>
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504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> } \</span></span>
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476
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505
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<pre style="margin: 0;"> <span id="LC505" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> error("Error: wrong number of fields in INFO/%s at %s:%"PRId64", expected %d, found %d\n", \</span></span>
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477
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506
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<pre style="margin: 0;"> <span id="LC506" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,src->n_allele,ret); \</span></span>
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507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> } \</span></span>
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478
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508
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<pre style="margin: 0;"> <span id="LC508" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if ( ialt!=0 ) vals[1] = vals[ialt+1]; \</span></span>
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479
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509
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<pre style="margin: 0;"> <span id="LC509" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> bcf_update_info_##type(args->hdr,dst,tag,vals,2); \</span></span>
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480
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510
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<pre style="margin: 0;"> <span id="LC510" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> } \</span></span>
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481
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511
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<pre style="margin: 0;"> <span id="LC511" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> else if ( len==BCF_VL_G ) \</span></span>
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482
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512
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<pre style="margin: 0;"> <span id="LC512" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> { \</span></span>
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483
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513
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<pre style="margin: 0;"> <span id="LC513" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if ( ret!=src->n_allele*(src->n_allele+1)/2 ) \</span></span>
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514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> { \</span></span>
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515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if ( args->force && !args->force_warned ) \</span></span>
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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> { \</span></span>
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517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> fprintf(stderr, \</span></span>
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518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> "Warning: wrong number of fields in INFO/%s at %s:%"PRId64", expected %d, found %d\n" \</span></span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> " (This warning is printed only once.)\n", \</span></span>
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520
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,src->n_allele*(src->n_allele+1)/2,ret); \</span></span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> args->force_warned = 1; \</span></span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> } \</span></span>
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523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if ( args->force ) \</span></span>
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524
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> { \</span></span>
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525
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> bcf_update_info_##type(args->hdr,dst,tag,NULL,0); \</span></span>
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526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> return; \</span></span>
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527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> } \</span></span>
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484
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528
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<pre style="margin: 0;"> <span id="LC528" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> error("Error: wrong number of fields in INFO/%s at %s:%"PRId64", expected %d, found %d\n", \</span></span>
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485
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529
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<pre style="margin: 0;"> <span id="LC529" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,src->n_allele*(src->n_allele+1)/2,ret); \</span></span>
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530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> } \</span></span>
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486
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531
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<pre style="margin: 0;"> <span id="LC531" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if ( ialt!=0 ) \</span></span>
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487
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532
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<pre style="margin: 0;"> <span id="LC532" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> { \</span></span>
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488
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533
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<pre style="margin: 0;"> <span id="LC533" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> vals[1] = vals[bcf_alleles2gt(0,ialt+1)]; \</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -627,8 +672,23 @@ static void split_format_numeric(args_t *args, bcf1_t *src, bcf_fmt_t *fmt, int</td>
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627
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672
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<pre style="margin: 0;"> <span id="LC672" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if ( len==BCF_VL_A ) \</span></span>
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628
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673
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<pre style="margin: 0;"> <span id="LC673" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> { \</span></span>
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629
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674
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<pre style="margin: 0;"> <span id="LC674" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if ( nvals!=(src->n_allele-1)*nsmpl ) \</span></span>
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675
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> { \</span></span>
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676
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if ( args->force && !args->force_warned ) \</span></span>
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677
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> { \</span></span>
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678
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> fprintf(stderr, \</span></span>
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679
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> "Warning: wrong number of fields in FMT/%s at %s:%"PRId64", expected %d, found %d. Removing the field.\n" \</span></span>
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680
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> " (This warning is printed only once.)\n", \</span></span>
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681
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,(src->n_allele-1)*nsmpl,nvals); \</span></span>
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682
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> args->force_warned = 1; \</span></span>
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683
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> } \</span></span>
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684
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if ( args->force ) \</span></span>
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> { \</span></span>
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686
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> bcf_update_format_##type(args->hdr,dst,tag,NULL,0); \</span></span>
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687
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> return; \</span></span>
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688
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> } \</span></span>
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630
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689
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<pre style="margin: 0;"> <span id="LC689" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> error("Error: wrong number of fields in FMT/%s at %s:%"PRId64", expected %d, found %d\n", \</span></span>
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631
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690
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<pre style="margin: 0;"> <span id="LC690" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,(src->n_allele-1)*nsmpl,nvals); \</span></span>
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691
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> } \</span></span>
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632
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692
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<pre style="margin: 0;"> <span id="LC692" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> nvals /= nsmpl; \</span></span>
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633
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693
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<pre style="margin: 0;"> <span id="LC693" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> type_t *src_vals = vals, *dst_vals = vals; \</span></span>
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634
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694
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<pre style="margin: 0;"> <span id="LC694" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> for (i=0; i<nsmpl; i++) \</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -642,8 +702,23 @@ static void split_format_numeric(args_t *args, bcf1_t *src, bcf_fmt_t *fmt, int</td>
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642
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702
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<pre style="margin: 0;"> <span id="LC702" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> else if ( len==BCF_VL_R ) \</span></span>
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643
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703
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<pre style="margin: 0;"> <span id="LC703" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> { \</span></span>
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644
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704
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<pre style="margin: 0;"> <span id="LC704" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if ( nvals!=src->n_allele*nsmpl ) \</span></span>
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705
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> { \</span></span>
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706
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if ( args->force && !args->force_warned ) \</span></span>
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707
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> { \</span></span>
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708
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> fprintf(stderr, \</span></span>
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709
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> "Warning: wrong number of fields in FMT/%s at %s:%"PRId64", expected %d, found %d. Removing the field.\n" \</span></span>
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710
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> " (This warning is printed only once.)\n", \</span></span>
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711
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<pre style="margin: 0;">+<span id="LC711" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,(src->n_allele-1)*nsmpl,nvals); \</span></span>
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712
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> args->force_warned = 1; \</span></span>
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713
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> } \</span></span>
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714
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if ( args->force ) \</span></span>
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715
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> { \</span></span>
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716
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> bcf_update_format_##type(args->hdr,dst,tag,NULL,0); \</span></span>
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717
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> return; \</span></span>
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718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> } \</span></span>
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645
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719
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<pre style="margin: 0;"> <span id="LC719" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> error("Error: wrong number of fields in FMT/%s at %s:%"PRId64", expected %d, found %d\n", \</span></span>
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646
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720
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<pre style="margin: 0;"> <span id="LC720" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,src->n_allele*nsmpl,nvals); \</span></span>
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721
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> } \</span></span>
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647
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722
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<pre style="margin: 0;"> <span id="LC722" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> nvals /= nsmpl; \</span></span>
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648
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723
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<pre style="margin: 0;"> <span id="LC723" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> type_t *src_vals = vals, *dst_vals = vals; \</span></span>
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649
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724
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<pre style="margin: 0;"> <span id="LC724" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> for (i=0; i<nsmpl; i++) \</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="658" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -658,7 +733,22 @@ static void split_format_numeric(args_t *args, bcf1_t *src, bcf_fmt_t *fmt, int</td>
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658
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733
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<pre style="margin: 0;"> <span id="LC733" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> else if ( len==BCF_VL_G ) \</span></span>
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659
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734
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<pre style="margin: 0;"> <span id="LC734" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> { \</span></span>
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660
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735
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<pre style="margin: 0;"> <span id="LC735" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if ( nvals!=src->n_allele*(src->n_allele+1)/2*nsmpl && nvals!=src->n_allele*nsmpl ) \</span></span>
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736
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> { \</span></span>
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737
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if ( args->force && !args->force_warned ) \</span></span>
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738
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> { \</span></span>
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739
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> fprintf(stderr, \</span></span>
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740
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<pre style="margin: 0;">+<span id="LC740" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> "Warning: wrong number of fields in FMT/%s at %s:%"PRId64", expected %d, found %d. Removing the field.\n" \</span></span>
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741
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> " (This warning is printed only once.)\n", \</span></span>
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742
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> tag,bcf_seqname(args->hdr,src),(int64_t) src->pos+1,(src->n_allele-1)*nsmpl,nvals); \</span></span>
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743
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> args->force_warned = 1; \</span></span>
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744
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> } \</span></span>
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745
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> if ( args->force ) \</span></span>
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746
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<pre style="margin: 0;">+<span id="LC746" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> { \</span></span>
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> bcf_update_format_##type(args->hdr,dst,tag,NULL,0); \</span></span>
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<pre style="margin: 0;">+<span id="LC748" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> return; \</span></span>
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749
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<pre style="margin: 0;">+<span id="LC749" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> } \</span></span>
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661
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750
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<pre style="margin: 0;"> <span id="LC750" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> error("Error at %s:%"PRId64", the tag %s has wrong number of fields\n", bcf_seqname(args->hdr,src),(int64_t) src->pos+1,bcf_hdr_int2id(args->hdr,BCF_DT_ID,fmt->id)); \</span></span>
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751
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<pre style="margin: 0;">+<span id="LC751" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> } \</span></span>
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752
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<pre style="margin: 0;"> <span id="LC752" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> nvals /= nsmpl; \</span></span>
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753
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<pre style="margin: 0;"> <span id="LC753" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> int all_haploid = nvals==src->n_allele ? 1 : 0; \</span></span>
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754
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<pre style="margin: 0;"> <span id="LC754" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> type_t *src_vals = vals, *dst_vals = vals; \</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">@@ -770,8 +860,23 @@ static void split_format_string(args_t *args, bcf1_t *src, bcf_fmt_t *fmt, int i</td>
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860
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<pre style="margin: 0;"> <span id="LC860" class="line" lang="c"> <span class="p">}</span></span>
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771
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861
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<pre style="margin: 0;"> <span id="LC861" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">nfields</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">se</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">ptr</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ptr</span><span class="o" style="font-weight: 600;">==</span><span class="sc" style="color: #d14;">'.'</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// missing value</span></span>
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772
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862
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<pre style="margin: 0;"> <span id="LC862" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">nfields</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">src</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_allele</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">src</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_allele</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">nfields</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">src</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_allele</span> <span class="p">)</span></span>
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863
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<pre style="margin: 0;">+<span id="LC863" class="line" lang="c"> <span class="p">{</span></span>
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864
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<pre style="margin: 0;">+<span id="LC864" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">force</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">force_warned</span> <span class="p">)</span></span>
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865
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<pre style="margin: 0;">+<span id="LC865" class="line" lang="c"> <span class="p">{</span></span>
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866
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<pre style="margin: 0;">+<span id="LC866" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span></span>
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867
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<pre style="margin: 0;">+<span id="LC867" class="line" lang="c"> <span class="s" style="color: #d14;">"Warning: wrong number of fields in FMT/%s at %s:%"</span><span class="n" style="color: #333;">PRId64</span><span class="s" style="color: #d14;">", expected %d or %d, found %d. Removing the field.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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868
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<pre style="margin: 0;">+<span id="LC868" class="line" lang="c"> <span class="s" style="color: #d14;">" (This warning is printed only once.)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="869" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
869
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<pre style="margin: 0;">+<span id="LC869" class="line" lang="c"> <span class="n" style="color: #333;">tag</span><span class="p">,</span><span class="n" style="color: #333;">bcf_seqname</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">hdr</span><span class="p">,</span><span class="n" style="color: #333;">src</span><span class="p">),(</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="p">)</span><span class="n" style="color: #333;">src</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">src</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_allele</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">src</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_allele</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">2</span><span class="p">,</span><span class="n" style="color: #333;">src</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_allele</span><span class="p">,</span><span class="n" style="color: #333;">nfields</span><span class="p">);</span></span>
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870
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<pre style="margin: 0;">+<span id="LC870" class="line" lang="c"> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">force_warned</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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871
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<pre style="margin: 0;">+<span id="LC871" class="line" lang="c"> <span class="p">}</span></span>
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872
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<pre style="margin: 0;">+<span id="LC872" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">force</span> <span class="p">)</span></span>
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873
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<pre style="margin: 0;">+<span id="LC873" class="line" lang="c"> <span class="p">{</span></span>
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874
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<pre style="margin: 0;">+<span id="LC874" class="line" lang="c"> <span class="n" style="color: #333;">bcf_update_format_char</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">hdr</span><span class="p">,</span><span class="n" style="color: #333;">dst</span><span class="p">,</span><span class="n" style="color: #333;">tag</span><span class="p">,</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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875
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<pre style="margin: 0;">+<span id="LC875" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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876
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<pre style="margin: 0;">+<span id="LC876" class="line" lang="c"> <span class="p">}</span></span>
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773
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<td class="diff-line-num new_line" data-linenumber="877" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
877
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<pre style="margin: 0;"> <span id="LC877" class="line" lang="c"> <span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: wrong number of fields in FMT/%s at %s:%"</span><span class="n" style="color: #333;">PRId64</span><span class="s" style="color: #d14;">", expected %d or %d, found %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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774
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<td class="diff-line-num new_line" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
878
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<pre style="margin: 0;"> <span id="LC878" class="line" lang="c"> <span class="n" style="color: #333;">tag</span><span class="p">,</span><span class="n" style="color: #333;">bcf_seqname</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">hdr</span><span class="p">,</span><span class="n" style="color: #333;">src</span><span class="p">),(</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="p">)</span> <span class="n" style="color: #333;">src</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">src</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_allele</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">src</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_allele</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">2</span><span class="p">,</span><span class="n" style="color: #333;">src</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_allele</span><span class="p">,</span><span class="n" style="color: #333;">nfields</span><span class="p">);</span></span>
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879
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<pre style="margin: 0;">+<span id="LC879" class="line" lang="c"> <span class="p">}</span></span>
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775
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880
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<pre style="margin: 0;"> <span id="LC880" class="line" lang="c"></span>
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776
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881
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<pre style="margin: 0;"> <span id="LC881" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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777
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882
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<pre style="margin: 0;"> <span id="LC882" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">nfields</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">src</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_allele</span> <span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">// haploid</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1849" style="width: 35px; color: rgba(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="1954" style="width: 35px; color: rgba(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">@@ -1849,7 +1954,8 @@ static void usage(void)</td>
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1849
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<td class="diff-line-num new_line" data-linenumber="1954" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1954
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<pre style="margin: 0;"> <span id="LC1954" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" -c, --check-ref <e|w|x|s> check REF alleles and exit (e), warn (w), exclude (x), or set (s) bad sites [e]</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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1850
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1955
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<pre style="margin: 0;"> <span id="LC1955" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" -D, --remove-duplicates remove duplicate lines of the same type.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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1851
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<td class="diff-line-num new_line" data-linenumber="1956" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1956
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<pre style="margin: 0;"> <span id="LC1956" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" -d, --rm-dup <type> remove duplicate snps|indels|both|all|exact</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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1852
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<td class="diff-line-num new_line old" data-linenumber="1957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1852" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" -f, --fasta-ref <file> reference sequence (MANDATORY)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1957
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<pre style="margin: 0;">+<span id="LC1957" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" -f, --fasta-ref <file> reference sequence</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1958
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<pre style="margin: 0;">+<span id="LC1958" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" --force try to proceed even if malformed tags are encountered. Experimental, use at your own risk</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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1853
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1959
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<pre style="margin: 0;"> <span id="LC1959" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" -m, --multiallelics <-|+>[type] split multiallelics (-) or join biallelics (+), type: snps|indels|both|any [both]</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1854
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<td class="diff-line-num new_line" data-linenumber="1960" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1960
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<pre style="margin: 0;"> <span id="LC1960" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" --no-version do not append version and command line to the header</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1855
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<td class="diff-line-num new_line" data-linenumber="1961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1961
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<pre style="margin: 0;"> <span id="LC1961" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" -N, --do-not-normalize do not normalize indels (with -m or -c s)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1863" style="width: 35px; color: rgba(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="1969" style="width: 35px; color: rgba(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">@@ -1863,6 +1969,13 @@ static void usage(void)</td>
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1863
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<td class="diff-line-num new_line" data-linenumber="1969" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1969
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<pre style="margin: 0;"> <span id="LC1969" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" --threads <int> use multithreading with <int> worker threads [0]</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1864
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<td class="diff-line-num new_line" data-linenumber="1970" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1970
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<pre style="margin: 0;"> <span id="LC1970" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" -w, --site-win <int> buffer for sorting lines which changed position during realignment [1000]</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1865
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<td class="diff-line-num new_line" data-linenumber="1971" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1971
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<pre style="margin: 0;"> <span id="LC1971" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1866" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1972" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1972
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<pre style="margin: 0;">+<span id="LC1972" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Examples:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1866" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1973" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1973
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<pre style="margin: 0;">+<span id="LC1973" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" # normalize and left-align indels</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1866" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1974" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1974
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<pre style="margin: 0;">+<span id="LC1974" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" bcftools norm -f ref.fa in.vcf</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1866" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1975" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1975
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<pre style="margin: 0;">+<span id="LC1975" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1866" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1976" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1976
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<pre style="margin: 0;">+<span id="LC1976" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" # split multi-allelic sites</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1866" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1977" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1977
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<pre style="margin: 0;">+<span id="LC1977" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" bcftools norm -m- in.vcf</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1866" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1978" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1978
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<pre style="margin: 0;">+<span id="LC1978" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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1866
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<td class="diff-line-num new_line" data-linenumber="1979" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1979
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<pre style="margin: 0;"> <span id="LC1979" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1867" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1867
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<td class="diff-line-num new_line" data-linenumber="1980" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1980
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<pre style="margin: 0;"> <span id="LC1980" class="line" lang="c"><span class="p">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1868" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1868
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<td class="diff-line-num new_line" data-linenumber="1981" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1981
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<pre style="margin: 0;"> <span id="LC1981" class="line" lang="c"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1886" style="width: 35px; color: rgba(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="1999" style="width: 35px; color: rgba(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">@@ -1886,6 +1999,7 @@ int main_vcfnorm(int argc, char *argv[])</td>
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1886
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<td class="diff-line-num new_line" data-linenumber="1999" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1999
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<pre style="margin: 0;"> <span id="LC1999" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">option</span> <span class="n" style="color: #333;">loptions</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1887
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<td class="diff-line-num new_line" data-linenumber="2000" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2000
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2000" class="line" lang="c"> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1888
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<td class="diff-line-num new_line" data-linenumber="2001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2001
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2001" class="line" lang="c"> <span class="p">{</span><span class="s" style="color: #d14;">"help"</span><span class="p">,</span><span class="n" style="color: #333;">no_argument</span><span class="p">,</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="sc" style="color: #d14;">'h'</span><span class="p">},</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1889" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2002
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<pre style="margin: 0;">+<span id="LC2002" class="line" lang="c"> <span class="p">{</span><span class="s" style="color: #d14;">"force"</span><span class="p">,</span><span class="n" style="color: #333;">no_argument</span><span class="p">,</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="mi" style="color: #099;">7</span><span class="p">},</span></span>
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<td class="diff-line-num old_line" data-linenumber="1889" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1889
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<td class="diff-line-num new_line" data-linenumber="2003" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2003
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<pre style="margin: 0;"> <span id="LC2003" class="line" lang="c"> <span class="p">{</span><span class="s" style="color: #d14;">"fasta-ref"</span><span class="p">,</span><span class="n" style="color: #333;">required_argument</span><span class="p">,</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="sc" style="color: #d14;">'f'</span><span class="p">},</span></span>
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<td class="diff-line-num old_line" data-linenumber="1890" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1890
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<td class="diff-line-num new_line" data-linenumber="2004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2004
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<pre style="margin: 0;"> <span id="LC2004" class="line" lang="c"> <span class="p">{</span><span class="s" style="color: #d14;">"do-not-normalize"</span><span class="p">,</span><span class="n" style="color: #333;">no_argument</span><span class="p">,</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="sc" style="color: #d14;">'N'</span><span class="p">},</span></span>
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<td class="diff-line-num old_line" data-linenumber="1891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1891
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<td class="diff-line-num new_line" data-linenumber="2005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2005
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<pre style="margin: 0;"> <span id="LC2005" class="line" lang="c"> <span class="p">{</span><span class="s" style="color: #d14;">"multiallelics"</span><span class="p">,</span><span class="n" style="color: #333;">required_argument</span><span class="p">,</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="sc" style="color: #d14;">'m'</span><span class="p">},</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1963" style="width: 35px; color: rgba(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="2077" style="width: 35px; color: rgba(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">@@ -1963,6 +2077,7 @@ int main_vcfnorm(int argc, char *argv[])</td>
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<td class="diff-line-num old_line" data-linenumber="1963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1963
</td>
<td class="diff-line-num new_line" data-linenumber="2077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2077
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<pre style="margin: 0;"> <span id="LC2077" class="line" lang="c"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1964
</td>
<td class="diff-line-num new_line" data-linenumber="2078" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2078
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2078" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">9</span> <span class="p">:</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_threads</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strtol</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1965" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1965
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<td class="diff-line-num new_line" data-linenumber="2079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2079
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2079" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">8</span> <span class="p">:</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">record_cmd_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1966" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="2080" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2080
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<pre style="margin: 0;">+<span id="LC2080" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">7</span> <span class="p">:</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">force</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1966" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1966
</td>
<td class="diff-line-num new_line" data-linenumber="2081" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2081
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<pre style="margin: 0;"> <span id="LC2081" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'h'</span><span class="p">:</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1967" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1967
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<td class="diff-line-num new_line" data-linenumber="2082" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2082
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2082" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'?'</span><span class="p">:</span> <span class="n" style="color: #333;">usage</span><span class="p">();</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1968" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1968
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<td class="diff-line-num new_line" data-linenumber="2083" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2083
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<pre style="margin: 0;"> <span id="LC2083" class="line" lang="c"> <span class="nl">default:</span> <span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"Unknown argument: %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">optarg</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/bcftools/commit/e439282c1235fa123a822dbcd7dae553cf4cb693#79af080a263b467ea1886b300bde6b2d35c43aa8"><strong>version.sh</strong></a>
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1
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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/sh</span></span>
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2
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<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"></span>
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3
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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Master version, for use in tarballs or non-git source copies</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
4
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<td class="diff-line-num new_line old" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">VERSION</span><span class="o" style="font-weight: 600;">=</span>1.10</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">VERSION</span><span class="o" style="font-weight: 600;">=</span>1.10<span class="idiff left right">.2</span></span>
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5
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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"></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">
6
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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># If we have a git clone, then check against the current tag</span></span>
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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7
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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-e</span> .git <span class="o" style="font-weight: 600;">]</span></span>
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