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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/htslib">Debian Med / htslib</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/htslib/commit/581cbb1d53372055f7118660c992175a536d49bb">581cbb1d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-17T13:37:11Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.10.1</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/htslib/commit/1e5ac9f6fd65d4580d580eb23fc9ff7908beb15c">1e5ac9f6</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-17T13:37:13Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.10.1'
Update to upstream version '1.10.1'
with Debian dir bdfed011fc46b46a73f03e9f40bd476b264ccbf8</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/htslib/commit/c438eba19bf7ef0079a6dd2ac11904da440b1055">c438eba1</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-17T13:37:39Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refresh patches
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/htslib/commit/feed9d294bb5c7075125f8e0c224dea5b365214c">feed9d29</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-17T13:38:35Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix syntax
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/htslib/commit/df4af758e24c513eb9ac898ba9eac395eef8591a">df4af758</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-17T13:48:36Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>16 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
Makefile
</a>
</li>
<li class="file-stats">
<a href="#9f621eb5fd3bcb2fa5c7bd228c9b1ad42edc46c8">
NEWS
</a>
</li>
<li class="file-stats">
<a href="#7700e7ff8d1d8ed0bf46fab4ebbf67c6420609bc">
README.large_positions.md
</a>
</li>
<li class="file-stats">
<a href="#09be8533ff0a6ee5d577f971145ed449399fcda4">
configure
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#9aa2c7e0becab0a54af7d952db76b2d88da8b72a">
debian/patches/fPIC.patch
</a>
</li>
<li class="file-stats">
<a href="#04876df4215a9666af25987a0f1a6eafe80ade3b">
debian/patches/no_git_version
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#23144171ef46270c8d90b6c189ed5dc6d7b18651">
htslib/hts.h
</a>
</li>
<li class="file-stats">
<a href="#e27c3ca50ec2b3bf2269b7757b4b40eda30f4e3c">
<span class="new-file">
+
htslib/hts.h~
</span>
</a>
</li>
<li class="file-stats">
<a href="#029f45b5a6618d3c762af054ae12f411ce704a81">
htslib/vcf.h
</a>
</li>
<li class="file-stats">
<a href="#5e847d99da5403021aca59876ce59c63d3399090">
test/longrefs/index.expected2.vcf
</a>
</li>
<li class="file-stats">
<a href="#81af447140212c3962fab33cc0aa0cf0e188b4dc">
test/longrefs/index.vcf
</a>
</li>
<li class="file-stats">
<a href="#1dafee15289de195cc70f0739a91d5b95f8e8889">
test/test.pl
</a>
</li>
<li class="file-stats">
<a href="#8a0799313a5296dac6779d2110db74c14c759325">
vcf.c
</a>
</li>
<li class="file-stats">
<a href="#79af080a263b467ea1886b300bde6b2d35c43aa8">
version.sh
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
<a href="https://salsa.debian.org/med-team/htslib/compare/61e050b9d3d5e587cb5a4628fa61111b344ee4ed...df4af758e24c513eb9ac898ba9eac395eef8591a#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c"><strong>Makefile</strong></a>
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<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -30,6 +30,8 @@ RANLIB = ranlib</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC30" class="line" lang="make"><span class="nv" style="color: #008080;">htslib_default_libs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-lz</span> <span class="nt" style="color: #000080;">-lm</span> <span class="nt" style="color: #000080;">-lbz2</span> <span class="nt" style="color: #000080;">-llzma</span> <span class="nt" style="color: #000080;">-lcurl</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC31" class="line" lang="make"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC32" class="line" lang="make"><span class="nv" style="color: #008080;">CPPFLAGS</span> <span class="o" style="font-weight: 600;">=</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC33" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># TODO: make the 64-bit support for VCF optional via configure, for now add -DVCF_ALLOW_INT64</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># to CFLAGS manually, here or in config.mk if the latter exists.</span></span>
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<td class="diff-line-num old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># TODO: probably update cram code to make it compile cleanly with -Wc++-compat</span></span>
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<td class="diff-line-num old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600</span></span>
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<td class="diff-line-num new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600</span></span>
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<a href="https://salsa.debian.org/med-team/htslib/compare/61e050b9d3d5e587cb5a4628fa61111b344ee4ed...df4af758e24c513eb9ac898ba9eac395eef8591a#9f621eb5fd3bcb2fa5c7bd228c9b1ad42edc46c8"><strong>NEWS</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Noteworthy changes in release a.b</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Noteworthy changes in release 1.10.1 (17th December 2019)</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">The support for 64-bit coordinates in VCF brought problems for files</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">not conforming to VCF/BCF specification. While previous versions would</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">make out-of-range values silently overflow creating nonsense values</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">but parseable file, the version 1.10 would silently create an invalid BCF.</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"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Noteworthy changes in release 1.10 (6th December 2019)</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/htslib/compare/61e050b9d3d5e587cb5a4628fa61111b344ee4ed...df4af758e24c513eb9ac898ba9eac395eef8591a#7700e7ff8d1d8ed0bf46fab4ebbf67c6420609bc"><strong>README.large_positions.md</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,7 +9,9 @@ which have, or are expected to have, chromosomes longer than two gigabases.</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown">Currently 64 bit positions can only be stored in SAM and VCF format files.</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown">Binary BAM, CRAM and BCF cannot be used due to limitations in the formats</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown">themselves. As SAM and VCF are text formats, they have no limit on the</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="markdown">size of numeric values.</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown">size of numeric values. Note that while 64 bit positions are supported by</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown">default for SAM, for VCF they must be enabled explicitly at compile time</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown">by editing Makefile and adding -DVCF_ALLOW_INT64=1 to CFLAGS.</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"><span class="gh" style="color: #999;"># Compatibility issues to check</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="markdown"></span>
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<a href="https://salsa.debian.org/med-team/htslib/compare/61e050b9d3d5e587cb5a4628fa61111b344ee4ed...df4af758e24c513eb9ac898ba9eac395eef8591a#09be8533ff0a6ee5d577f971145ed449399fcda4"><strong>configure</strong></a>
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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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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Guess values for system-dependent variables and create Makefiles.</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Generated by GNU Autoconf 2.68 for HTSlib 1.10.</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Generated by GNU Autoconf 2.68 for HTSlib 1.10.<span class="idiff left right">1.</span></span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Report bugs to <samtools-help@lists.sourceforge.net>.</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="c" 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">@@ -565,8 +565,8 @@ MAKEFLAGS=</td>
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<pre style="margin: 0;"> <span id="LC565" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Identity of this package.</span></span>
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<pre style="margin: 0;"> <span id="LC566" class="line" lang="shell"><span class="nv" style="color: #008080;">PACKAGE_NAME</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'HTSlib'</span></span>
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<pre style="margin: 0;"> <span id="LC567" class="line" lang="shell"><span class="nv" style="color: #008080;">PACKAGE_TARNAME</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'htslib'</span></span>
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568
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<pre style="margin: 0;">-<span id="LC568" class="line" lang="shell"><span class="nv" style="color: #008080;">PACKAGE_VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'1.10'</span></span>
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<pre style="margin: 0;">-<span id="LC569" class="line" lang="shell"><span class="nv" style="color: #008080;">PACKAGE_STRING</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'HTSlib 1.10'</span></span>
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="shell"><span class="nv" style="color: #008080;">PACKAGE_VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'1.10<span class="idiff left right">.1</span>'</span></span>
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="shell"><span class="nv" style="color: #008080;">PACKAGE_STRING</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'HTSlib 1.10<span class="idiff left right">.1</span>'</span></span>
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570
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<pre style="margin: 0;"> <span id="LC570" class="line" lang="shell"><span class="nv" style="color: #008080;">PACKAGE_BUGREPORT</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'samtools-help@lists.sourceforge.net'</span></span>
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571
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<pre style="margin: 0;"> <span id="LC571" class="line" lang="shell"><span class="nv" style="color: #008080;">PACKAGE_URL</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'http://www.htslib.org/'</span></span>
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572
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<pre style="margin: 0;"> <span id="LC572" class="line" lang="shell"></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">@@ -1245,7 +1245,7 @@ if test "$ac_init_help" = "long"; then</td>
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1245
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<pre style="margin: 0;"> <span id="LC1245" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Omit some internal or obsolete options to make the list less imposing.</span></span>
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1246
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<pre style="margin: 0;"> <span id="LC1246" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># This message is too long to be a string in the A/UX 3.1 sh.</span></span>
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<pre style="margin: 0;"> <span id="LC1247" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: #008080;">_ACEOF</span></span>
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1248
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<pre style="margin: 0;">-<span id="LC1248" class="line" lang="shell"><span class="se" style="color: #d14;">\`</span><span class="sh" style="color: #d14;">configure' configures HTSlib 1.10 to adapt to many kinds of systems.</span></span>
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1248
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<pre style="margin: 0;">+<span id="LC1248" class="line" lang="shell"><span class="se" style="color: #d14;">\`</span><span class="sh" style="color: #d14;">configure' configures HTSlib 1.10<span class="idiff left right">.1</span> to adapt to many kinds of systems.</span></span>
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1249
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1249
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<pre style="margin: 0;"> <span id="LC1249" class="line" lang="shell"></span>
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1250
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<pre style="margin: 0;"> <span id="LC1250" class="line" lang="shell"><span class="sh" style="color: #d14;">Usage: </span><span class="nv" style="color: #008080;">$0</span><span class="sh" style="color: #d14;"> [OPTION]... [VAR=VALUE]...</span></span>
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1251
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<pre style="margin: 0;"> <span id="LC1251" class="line" lang="shell"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1306,7 +1306,7 @@ fi</td>
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1306
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<pre style="margin: 0;"> <span id="LC1306" class="line" lang="shell"></span>
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1307
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<pre style="margin: 0;"> <span id="LC1307" class="line" lang="shell"><span class="k" style="font-weight: 600;">if </span><span class="nb" style="color: #0086b3;">test</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$ac_init_help</span><span class="s2" style="color: #d14;">"</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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1308
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<pre style="margin: 0;"> <span id="LC1308" class="line" lang="shell"><span class="k" style="font-weight: 600;"> case</span> <span class="nv" style="color: #008080;">$ac_init_help</span> <span class="k" style="font-weight: 600;">in</span></span>
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1309
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<pre style="margin: 0;">-<span id="LC1309" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>short <span class="p">|</span> recursive <span class="p">)</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Configuration of HTSlib 1.10:"</span><span class="p">;;</span></span>
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1309
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<pre style="margin: 0;">+<span id="LC1309" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>short <span class="p">|</span> recursive <span class="p">)</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Configuration of HTSlib 1.10<span class="idiff left right">.1</span>:"</span><span class="p">;;</span></span>
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1310
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1310
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<pre style="margin: 0;"> <span id="LC1310" class="line" lang="shell"> <span class="k" style="font-weight: 600;">esac</span></span>
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1311
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1311
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<pre style="margin: 0;"> <span id="LC1311" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="sh" style="color: #d14;">\</span><span class="no" style="color: #008080;">_ACEOF</span></span>
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1312
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1312
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<pre style="margin: 0;"> <span id="LC1312" class="line" lang="shell"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1413" style="width: 35px; color: rgba(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="1413" style="width: 35px; color: rgba(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">@@ -1413,7 +1413,7 @@ fi</td>
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1413
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1413
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<pre style="margin: 0;"> <span id="LC1413" class="line" lang="shell"><span class="nb" style="color: #0086b3;">test</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$ac_init_help</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">exit</span> <span class="nv" style="color: #008080;">$ac_status</span></span>
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1414
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1414
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<pre style="margin: 0;"> <span id="LC1414" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="nv" style="color: #008080;">$ac_init_version</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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1415
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1415
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<pre style="margin: 0;"> <span id="LC1415" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="sh" style="color: #d14;">\</span><span class="no" style="color: #008080;">_ACEOF</span></span>
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1416
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<pre style="margin: 0;">-<span id="LC1416" class="line" lang="shell"><span class="sh" style="color: #d14;">HTSlib configure 1.10</span></span>
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1416
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<pre style="margin: 0;">+<span id="LC1416" class="line" lang="shell"><span class="sh" style="color: #d14;">HTSlib configure 1.10<span class="idiff left right">.1</span></span></span>
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1417
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1417
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<pre style="margin: 0;"> <span id="LC1417" class="line" lang="shell"><span class="sh" style="color: #d14;">generated by GNU Autoconf 2.68</span></span>
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1418
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1418
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<pre style="margin: 0;"> <span id="LC1418" class="line" lang="shell"></span>
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1419
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<pre style="margin: 0;"> <span id="LC1419" class="line" lang="shell"><span class="sh" style="color: #d14;">Copyright (C) 2010 Free Software Foundation, Inc.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1742" style="width: 35px; color: rgba(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">@@ -1742,7 +1742,7 @@ cat >config.log <<_ACEOF</td>
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1742
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1742
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<pre style="margin: 0;"> <span id="LC1742" class="line" lang="shell"><span class="sh" style="color: #d14;">This file contains any messages produced by compilers while</span></span>
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1743
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1743
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<pre style="margin: 0;"> <span id="LC1743" class="line" lang="shell"><span class="sh" style="color: #d14;">running configure, to aid debugging if configure makes a mistake.</span></span>
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1744
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1744
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<pre style="margin: 0;"> <span id="LC1744" class="line" lang="shell"></span>
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1745
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<pre style="margin: 0;">-<span id="LC1745" class="line" lang="shell"><span class="sh" style="color: #d14;">It was created by HTSlib </span><span class="nv" style="color: #008080;">$as_me</span><span class="sh" style="color: #d14;"> 1.10, which was</span></span>
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1745
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<pre style="margin: 0;">+<span id="LC1745" class="line" lang="shell"><span class="sh" style="color: #d14;">It was created by HTSlib </span><span class="nv" style="color: #008080;">$as_me</span><span class="sh" style="color: #d14;"> 1.10<span class="idiff left right">.1</span>, which was</span></span>
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1746
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1746
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<pre style="margin: 0;"> <span id="LC1746" class="line" lang="shell"><span class="sh" style="color: #d14;">generated by GNU Autoconf 2.68. Invocation command line was</span></span>
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1747
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1747
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<pre style="margin: 0;"> <span id="LC1747" class="line" lang="shell"></span>
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1748
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1748
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<pre style="margin: 0;"> <span id="LC1748" class="line" lang="shell"><span class="sh" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$ $0</span><span class="sh" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$@</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5804" style="width: 35px; color: rgba(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">@@ -5804,7 +5804,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1</td>
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5804
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5804
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<pre style="margin: 0;"> <span id="LC5804" class="line" lang="shell"><span class="sh" style="color: #d14;"># report actual input values of CONFIG_FILES etc. instead of their</span></span>
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5805
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5805
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<pre style="margin: 0;"> <span id="LC5805" class="line" lang="shell"><span class="sh" style="color: #d14;"># values after options handling.</span></span>
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5806
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5806
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<pre style="margin: 0;"> <span id="LC5806" class="line" lang="shell"><span class="sh" style="color: #d14;">ac_log="</span></span>
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5807
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<pre style="margin: 0;">-<span id="LC5807" class="line" lang="shell"><span class="sh" style="color: #d14;">This file was extended by HTSlib </span><span class="nv" style="color: #008080;">$as_me</span><span class="sh" style="color: #d14;"> 1.10, which was</span></span>
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<pre style="margin: 0;">+<span id="LC5807" class="line" lang="shell"><span class="sh" style="color: #d14;">This file was extended by HTSlib </span><span class="nv" style="color: #008080;">$as_me</span><span class="sh" style="color: #d14;"> 1.10<span class="idiff left right">.1</span>, which was</span></span>
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5808
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5808
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<pre style="margin: 0;"> <span id="LC5808" class="line" lang="shell"><span class="sh" style="color: #d14;">generated by GNU Autoconf 2.68. Invocation command line was</span></span>
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5809
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5809
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<pre style="margin: 0;"> <span id="LC5809" class="line" lang="shell"></span>
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5810
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5810
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<pre style="margin: 0;"> <span id="LC5810" class="line" lang="shell"><span class="sh" style="color: #d14;"> CONFIG_FILES = </span><span class="nv" style="color: #008080;">$CONFIG_FILES</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5867" style="width: 35px; color: rgba(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">@@ -5867,7 +5867,7 @@ _ACEOF</td>
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5867
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5867
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<pre style="margin: 0;"> <span id="LC5867" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;">>></span><span class="nv" style="color: #008080;">$CONFIG_STATUS</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: #008080;">_ACEOF</span><span class="sh" style="color: #d14;"> || ac_write_fail=1</span></span>
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5868
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5868
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<pre style="margin: 0;"> <span id="LC5868" class="line" lang="shell"><span class="sh" style="color: #d14;">ac_cs_config="`</span><span class="nv" style="color: #008080;">$as_echo</span><span class="sh" style="color: #d14;"> "</span><span class="nv" style="color: #008080;">$ac_configure_args</span><span class="sh" style="color: #d14;">" | sed 's/^ //; s/[</span><span class="se" style="color: #d14;">\\</span><span class="sh" style="color: #d14;">""</span><span class="se" style="color: #d14;">\`\$</span><span class="sh" style="color: #d14;">]/</span><span class="se" style="color: #d14;">\\\\</span><span class="sh" style="color: #d14;">&/g'`"</span></span>
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5869
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5869
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<pre style="margin: 0;"> <span id="LC5869" class="line" lang="shell"><span class="sh" style="color: #d14;">ac_cs_version="</span><span class="se" style="color: #d14;">\\</span></span>
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5870
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<pre style="margin: 0;">-<span id="LC5870" class="line" lang="shell"><span class="sh" style="color: #d14;">HTSlib config.status 1.10</span></span>
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<pre style="margin: 0;">+<span id="LC5870" class="line" lang="shell"><span class="sh" style="color: #d14;">HTSlib config.status 1.10<span class="idiff left right">.1</span></span></span>
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5871
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5871
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<pre style="margin: 0;"> <span id="LC5871" class="line" lang="shell"><span class="sh" style="color: #d14;">configured by </span><span class="nv" style="color: #008080;">$0</span><span class="sh" style="color: #d14;">, generated by GNU Autoconf 2.68,</span></span>
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5872
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<pre style="margin: 0;"> <span id="LC5872" class="line" lang="shell"><span class="sh" style="color: #d14;"> with options </span><span class="se" style="color: #d14;">\\</span><span class="sh" style="color: #d14;">"</span><span class="se" style="color: #d14;">\$</span><span class="sh" style="color: #d14;">ac_cs_config</span><span class="se" style="color: #d14;">\\</span><span class="sh" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC5873" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="mosel"><span class="n" style="color: #333;">htslib</span> <span class="p">(</span><span class="m" style="color: #099;">1.10</span><span class="p"><span class="idiff left">-</span></span><span class="m" 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 right">UNRELEASED</span></span><span class="p">;</span> <span class="n" style="color: #333;">urgency</span><span class="p">=</span><span class="n" style="color: #333;">medium</span></span>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="mosel"><span class="n" style="color: #333;">htslib</span> <span class="p">(</span><span class="m" style="color: #099;">1.10<span class="idiff left">.1</span></span><span class="p"><span class="idiff">-</span></span><span class="m" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">unstable</span></span><span class="p">;</span> <span class="n" style="color: #333;">urgency</span><span class="p">=</span><span class="n" style="color: #333;">medium</span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="mosel"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">New</span> <span class="n" style="color: #333;">upstream</span> <span class="k" style="font-weight: 600;">version</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">some</span> <span class="n" style="color: #333;">very</span> <span class="n" style="color: #333;">strange</span> <span class="n" style="color: #333;">reason</span> <span class="p">/</span><span class="n" style="color: #333;">usr</span><span class="p">/</span><span class="k" style="font-weight: 600;">include</span><span class="p">/</span><span class="n" style="color: #333;">htslib</span><span class="p">/</span><span class="n" style="color: #333;">cram</span><span class="p">/</span><span class="n" style="color: #333;">cram</span><span class="p">.</span><span class="n" style="color: #333;">h</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">the</span></span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="mosel"> <span class="n" style="color: #333;">private</span> <span class="n" style="color: #333;">interface</span> <span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">h</span><span class="p">.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">provided</span> <span class="n" style="color: #333;">now</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span></span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="mosel"> <span class="n" style="color: #333;">libhts</span><span class="p">-</span><span class="n" style="color: #333;">private</span><span class="p">-</span><span class="n" style="color: #333;">dev</span> <span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">rather</span> <span class="n" style="color: #333;">than</span> <span class="n" style="color: #333;">htslib</span><span class="p">-</span><span class="n" style="color: #333;">test</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,7 +11,7 @@ htslib (1.10-3) UNRELEASED; urgency=medium</td>
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10
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Fix</span> <span class="n" style="color: #333;">Perl</span> <span class="n" style="color: #333;">interpreter</span> <span class="n" style="color: #333;">path</span></span>
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11
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Fix</span> <span class="n" style="color: #333;">permissions</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">script</span></span>
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12
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
13
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<td class="diff-line-num new_line old" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="mosel"> <span class="p">--</span> <span class="n" style="color: #333;">Andreas</span> <span class="n" style="color: #333;">Tille</span> <span class="p"><</span><span class="n" style="color: #333;">tille</span><span class="p">@</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">></span> <span class="n" style="color: #333;">Tue</span><span class="p">,</span> <span class="m" style="color: #099;">17</span> <span class="n" style="color: #333;">Dec</span> <span class="m" style="color: #099;">2019</span> <span class="m" style="color: #099;">1<span class="idiff left">1</span></span><span class="p"><span class="idiff">:</span></span><span class="m" style="color: #099;"><span class="idiff">31</span></span><span class="p"><span class="idiff">:</span></span><span class="m" style="color: #099;"><span class="idiff right">46</span></span> <span class="p">+</span><span class="m" style="color: #099;">0100</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="mosel"> <span class="p">--</span> <span class="n" style="color: #333;">Andreas</span> <span class="n" style="color: #333;">Tille</span> <span class="p"><</span><span class="n" style="color: #333;">tille</span><span class="p">@</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">></span> <span class="n" style="color: #333;">Tue</span><span class="p">,</span> <span class="m" style="color: #099;">17</span> <span class="n" style="color: #333;">Dec</span> <span class="m" style="color: #099;">2019</span> <span class="m" style="color: #099;">1<span class="idiff left">4</span></span><span class="p"><span class="idiff">:</span></span><span class="m" style="color: #099;"><span class="idiff">38</span></span><span class="p"><span class="idiff">:</span></span><span class="m" style="color: #099;"><span class="idiff right">13</span></span> <span class="p">+</span><span class="m" style="color: #099;">0100</span></span>
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14
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="mosel"></span>
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15
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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="mosel"><span class="n" style="color: #333;">htslib</span> <span class="p">(</span><span class="m" style="color: #099;">1.10</span><span class="p">-</span><span class="m" style="color: #099;">2</span><span class="p">)</span> <span class="n" style="color: #333;">unstable</span><span class="p">;</span> <span class="n" style="color: #333;">urgency</span><span class="p">=</span><span class="n" style="color: #333;">medium</span></span>
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16
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="mosel"></span>
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<li id="9aa2c7e0becab0a54af7d952db76b2d88da8b72a">
<a href="https://salsa.debian.org/med-team/htslib/compare/61e050b9d3d5e587cb5a4628fa61111b344ee4ed...df4af758e24c513eb9ac898ba9eac395eef8591a#9aa2c7e0becab0a54af7d952db76b2d88da8b72a"><strong>debian/patches/fPIC.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,9 +3,9 @@ Description: Build with -fPIC instead of -fpic</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"> linking the library on s390x and sparc64.</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="p">Author: Adrian Bunk <bunk@debian.org></span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff">--- <span class="idiff left right">htslib.orig</span>/Makefile</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">htsli</span>b/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="p">@@ -3<span class="idiff left right">4,7 +34,7 @@</span></span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">--- <span class="idiff left right">a</span>/Makefile</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -3<span class="idiff left">6,7 +36,7 @@</span></span><span class="idiff right"> CPPFLAGS =</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> # For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> #CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> CFLAGS = -g -Wall -O2 -fvisibility=hidden</span>
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<a href="https://salsa.debian.org/med-team/htslib/compare/61e050b9d3d5e587cb5a4628fa61111b344ee4ed...df4af758e24c513eb9ac898ba9eac395eef8591a#04876df4215a9666af25987a0f1a6eafe80ade3b"><strong>debian/patches/no_git_version</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Description: Don't check git tags for versioning</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">htslib.orig</span>/version.sh</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">htsli</span>b/version.sh</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- <span class="idiff left right">a</span>/version.sh</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/version.sh</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="p">@@ -27,11 +27,11 @@</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"> VERSION=1.10</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> VERSION=1.10<span class="idiff left right">.1</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> # If we have a git clone, then check against the current tag</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if [ -e .git ]</span></span>
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<a href="https://salsa.debian.org/med-team/htslib/compare/61e050b9d3d5e587cb5a4628fa61111b344ee4ed...df4af758e24c513eb9ac898ba9eac395eef8591a#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -85,7 +85,7 @@ override_dh_link:</td>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="plaintext"> find debian/htslib-test -name header.h</span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="plaintext"> dh_link -phtslib-test usr/include/htslib/cram/header.h usr/share/htslib-test/header.h</span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="plaintext">override_dh_fixperms</span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">override_dh_fixperms<span class="idiff left right">:</span></span>
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="plaintext"> dh_fixperms</span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="plaintext"> find debian -name simple_test_driver.sh -exec chmod +x \{\} \;</span>
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<a href="https://salsa.debian.org/med-team/htslib/compare/61e050b9d3d5e587cb5a4628fa61111b344ee4ed...df4af758e24c513eb9ac898ba9eac395eef8591a#23144171ef46270c8d90b6c189ed5dc6d7b18651"><strong>htslib/hts.h</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">@@ -421,7 +421,7 @@ const char *hts_version(void);</td>
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// Immediately after release, bump ZZ to 90 to distinguish in-development</span></span>
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// Git repository builds from the release; you may wish to increment this</span></span>
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// further when significant features are merged.</span></span>
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<pre style="margin: 0;">-<span id="LC424" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define HTS_VERSION 10100<span class="idiff left right">0</span></span></span>
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define HTS_VERSION 10100<span class="idiff left right">1</span></span></span>
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*!</span></span>
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> @abstract Determine format by peeking at the start of a file</span></span>
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<a href="https://salsa.debian.org/med-team/htslib/compare/61e050b9d3d5e587cb5a4628fa61111b344ee4ed...df4af758e24c513eb9ac898ba9eac395eef8591a#e27c3ca50ec2b3bf2269b7757b4b40eda30f4e3c"><strong>htslib/hts.h~</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">/// @file htslib/hts.h</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">/// Format-neutral I/O, indexing, and iterator API functions.</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">/*</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Copyright (C) 2012-2019 Genome Research Ltd.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Copyright (C) 2010, 2012 Broad Institute.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> Portions copyright (C) 2003-2006, 2008-2010 by Heng Li <lh3@live.co.uk></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> Author: Heng Li <lh3@sanger.ac.uk></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Permission is hereby granted, free of charge, to any person obtaining a copy</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">of this software and associated documentation files (the "Software"), to deal</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">in the Software without restriction, including without limitation the rights</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">to use, copy, modify, merge, publish, distribute, sublicense, and/or sell</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">copies of the Software, and to permit persons to whom the Software is</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">furnished to do so, subject to the following conditions:</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">The above copyright notice and this permission notice shall be included in</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">all copies or substantial portions of the Software.</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">DEALINGS IN THE SOFTWARE. */</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">#ifndef HTSLIB_HTS_H</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">#define HTSLIB_HTS_H</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">#include <stddef.h></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">#include <stdint.h></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">#include <inttypes.h></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">#include "hts_defs.h"</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">#include "hts_log.h"</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">#ifdef __cplusplus</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">extern "C" {</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">#endif</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">// Separator used to split HTS_PATH (for plugins); REF_PATH (cram references)</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">#if defined(_WIN32) || defined(__MSYS__)</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">#define HTS_PATH_SEPARATOR_CHAR ';'</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">#define HTS_PATH_SEPARATOR_STR ";"</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">#else</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">#define HTS_PATH_SEPARATOR_CHAR ':'</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">#define HTS_PATH_SEPARATOR_STR ":"</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">#endif</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">#ifndef HTS_BGZF_TYPEDEF</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">typedef struct BGZF BGZF;</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">#define HTS_BGZF_TYPEDEF</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">#endif</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">struct cram_fd;</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">struct hFILE;</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">struct hts_tpool;</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">struct sam_hdr_t;</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">#ifndef KSTRING_T</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">#define KSTRING_T kstring_t</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">typedef struct kstring_t {</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> size_t l, m;</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> char *s;</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">} kstring_t;</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">#endif</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">#ifndef kroundup32</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">#endif</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">/**</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"> * @hideinitializer</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"> * Deprecated macro to expand a dynamic array of a given type</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"> *</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"> * @param type_t The type of the array elements</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"> * @param[in] n Requested number of elements of type type_t</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"> * @param[in,out] m Size of memory allocated</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"> * @param[in,out] ptr Pointer to the array</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"> *</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"> * @discussion</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext"> * Do not use this macro. Use hts_resize() instead as allows allocation</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext"> * failures to be handled more gracefully.</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext"> *</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext"> * The array *ptr will be expanded if necessary so that it can hold @p n</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext"> * or more elements. If the array is expanded then the new size will be</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext"> * written to @p m and the value in @p ptr may change.</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext"> *</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext"> * It must be possible to take the address of @p ptr and @p m must be usable</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext"> * as an lvalue.</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext"> *</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext"> * @bug</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext"> * If the memory allocation fails, this will call exit(1). This is</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext"> * not ideal behaviour in a library.</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext"> */</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">#define hts_expand(type_t, n, m, ptr) do { \</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext"> if ((n) > (m)) { \</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext"> size_t hts_realloc_or_die(size_t, size_t, size_t, size_t, \</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext"> int, void **, const char *); \</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext"> (m) = hts_realloc_or_die((n) >= 1 ? (n) : 1, (m), sizeof(m), \</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext"> sizeof(type_t), 0, \</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext"> (void **)&(ptr), __func__); \</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext"> } \</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext"> } while (0)</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext"></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">/**</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext"> * @hideinitializer</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext"> * Macro to expand a dynamic array, zeroing any newly-allocated memory</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext"> *</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext"> * @param type_t The type of the array elements</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext"> * @param[in] n Requested number of elements of type type_t</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext"> * @param[in,out] m Size of memory allocated</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext"> * @param[in,out] ptr Pointer to the array</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext"> *</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext"> * @discussion</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext"> * Do not use this macro. Use hts_resize() instead as allows allocation</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext"> * failures to be handled more gracefully.</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext"> *</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext"> * As for hts_expand(), except the bytes that make up the array elements</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext"> * between the old and new values of @p m are set to zero using memset().</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext"> *</span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext"> * @bug</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext"> * If the memory allocation fails, this will call exit(1). This is</span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext"> * not ideal behaviour in a library.</span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext"> */</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext"></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext"></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext">#define hts_expand0(type_t, n, m, ptr) do { \</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext"> if ((n) > (m)) { \</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext"> size_t hts_realloc_or_die(size_t, size_t, size_t, size_t, \</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext"> int, void **, const char *); \</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext"> (m) = hts_realloc_or_die((n) >= 1 ? (n) : 1, (m), sizeof(m), \</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext"> sizeof(type_t), 1, \</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext"> (void **)&(ptr), __func__); \</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext"> } \</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext"> } while (0)</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext"></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext">// For internal use (by hts_resize()) only</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext">int hts_resize_array_(size_t, size_t, size_t, void *, void **, int,</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext"> const char *);</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext"></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext">#define HTS_RESIZE_CLEAR 1</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext"></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext">/**</span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext"> * @hideinitializer</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext"> * Macro to expand a dynamic array of a given type</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext"> *</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext"> * @param type_t The type of the array elements</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext"> * @param[in] num Requested number of elements of type type_t</span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext"> * @param[in,out] size_ptr Pointer to where the size (in elements) of the</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext"> array is stored.</span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext"> * @param[in,out] ptr Location of the pointer to the array</span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext"> * @param[in] flags Option flags</span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext"> *</span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="plaintext"> * @return 0 for success, or negative if an error occurred.</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="plaintext"> *</span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext"> * @discussion</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="plaintext"> * The array *ptr will be expanded if necessary so that it can hold @p num</span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="plaintext"> * or more elements. If the array is expanded then the new size will be</span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext"> * written to @p *size_ptr and the value in @p *ptr may change.</span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext"> *</span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext"> * If ( @p flags & HTS_RESIZE_CLEAR ) is set, any newly allocated memory will</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext"> * be cleared.</span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext"> */</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext"></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext">#define hts_resize(type_t, num, size_ptr, ptr, flags) \</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext"> ((num) > (*(size_ptr)) \</span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="plaintext"> ? hts_resize_array_(sizeof(type_t), (num), \</span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="plaintext"> sizeof(*(size_ptr)), (size_ptr), \</span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="plaintext"> (void **)(ptr), (flags), __func__) \</span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="plaintext"> : 0)</span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="plaintext"></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext">/**</span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="plaintext"> * Wrapper function for free(). Enables memory deallocation across DLL</span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="plaintext"> * boundary. Should be used by all applications, which are compiled</span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="plaintext"> * with a different standard library than htslib and call htslib</span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="plaintext"> * methods that return dynamically allocated data.</span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="plaintext"> */</span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext">void hts_free(void *ptr);</span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext"></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext">/************</span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext"> * File I/O *</span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="plaintext"> ************/</span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext"></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext">// Add new entries only at the end (but before the *_maximum entry)</span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="plaintext">// of these enums, as their numbering is part of the htslib ABI.</span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="plaintext"></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext">enum htsFormatCategory {</span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext"> unknown_category,</span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="plaintext"> sequence_data, // Sequence data -- SAM, BAM, CRAM, etc</span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext"> variant_data, // Variant calling data -- VCF, BCF, etc</span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext"> index_file, // Index file associated with some data file</span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="plaintext"> region_list, // Coordinate intervals or regions -- BED, etc</span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="plaintext"> category_maximum = 32767</span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="plaintext">};</span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="plaintext"></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="plaintext">enum htsExactFormat {</span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="plaintext"> unknown_format,</span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="plaintext"> binary_format, text_format,</span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="plaintext"> sam, bam, bai, cram, crai, vcf, bcf, csi, gzi, tbi, bed,</span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="plaintext"> htsget,</span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="plaintext"> json HTS_DEPRECATED_ENUM("Use htsExactFormat 'htsget' instead") = htsget,</span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="plaintext"> empty_format, // File is empty (or empty after decompression)</span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="plaintext"> fasta_format, fastq_format, fai_format, fqi_format,</span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="plaintext"> format_maximum = 32767</span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="plaintext">};</span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="plaintext"></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="plaintext">enum htsCompression {</span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="plaintext"> no_compression, gzip, bgzf, custom, bzip2_compression,</span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="plaintext"> compression_maximum = 32767</span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="plaintext">};</span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="plaintext"></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="plaintext">typedef struct htsFormat {</span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="plaintext"> enum htsFormatCategory category;</span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="plaintext"> enum htsExactFormat format;</span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="plaintext"> struct { short major, minor; } version;</span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="plaintext"> enum htsCompression compression;</span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="plaintext"> short compression_level; // currently unused</span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="plaintext"> void *specific; // format specific options; see struct hts_opt.</span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="plaintext">} htsFormat;</span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="plaintext">struct __hts_idx_t;</span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="plaintext">typedef struct __hts_idx_t hts_idx_t;</span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="plaintext"></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="plaintext">// Maintainers note htsFile cannot be an opaque structure because some of its</span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="plaintext">// fields are part of libhts.so's ABI (hence these fields must not be moved):</span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="plaintext">// - fp is used in the public sam_itr_next()/etc macros</span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="plaintext">// - is_bin is used directly in samtools <= 1.1 and bcftools <= 1.1</span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="plaintext">// - is_write and is_cram are used directly in samtools <= 1.1</span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="plaintext">// - fp is used directly in samtools (up to and including current develop)</span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="plaintext">// - line is used directly in bcftools (up to and including current develop)</span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="plaintext">typedef struct {</span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="plaintext"> uint32_t is_bin:1, is_write:1, is_be:1, is_cram:1, is_bgzf:1, dummy:27;</span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="plaintext"> int64_t lineno;</span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="plaintext"> kstring_t line;</span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="plaintext"> char *fn, *fn_aux;</span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="plaintext"> union {</span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="plaintext"> BGZF *bgzf;</span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="plaintext"> struct cram_fd *cram;</span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="plaintext"> struct hFILE *hfile;</span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="plaintext"> } fp;</span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="plaintext"> void *state; // format specific state information</span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="plaintext"> htsFormat format;</span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="plaintext"> hts_idx_t *idx;</span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="plaintext"> const char *fnidx;</span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="plaintext"> struct sam_hdr_t *bam_header;</span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="plaintext">} htsFile;</span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="plaintext"></span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="plaintext">// A combined thread pool and queue allocation size.</span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="plaintext">// The pool should already be defined, but qsize may be zero to</span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="plaintext">// indicate an appropriate queue size is taken from the pool.</span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="plaintext">//</span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="plaintext">// Reasons for explicitly setting it could be where many more file</span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="plaintext">// descriptors are in use than threads, so keeping memory low is</span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="plaintext">// important.</span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="plaintext">typedef struct {</span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="plaintext"> struct hts_tpool *pool; // The shared thread pool itself</span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="plaintext"> int qsize; // Size of I/O queue to use for this fp</span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="plaintext">} htsThreadPool;</span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="plaintext"></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="plaintext">// REQUIRED_FIELDS</span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="plaintext">enum sam_fields {</span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="plaintext"> SAM_QNAME = 0x00000001,</span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="plaintext"> SAM_FLAG = 0x00000002,</span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="plaintext"> SAM_RNAME = 0x00000004,</span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="plaintext"> SAM_POS = 0x00000008,</span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="plaintext"> SAM_MAPQ = 0x00000010,</span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="plaintext"> SAM_CIGAR = 0x00000020,</span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="plaintext"> SAM_RNEXT = 0x00000040,</span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="plaintext"> SAM_PNEXT = 0x00000080,</span>
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<td class="diff-line-num new new_line" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="plaintext"> SAM_TLEN = 0x00000100,</span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="plaintext"> SAM_SEQ = 0x00000200,</span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="plaintext"> SAM_QUAL = 0x00000400,</span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="plaintext"> SAM_AUX = 0x00000800,</span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="plaintext"> SAM_RGAUX = 0x00001000,</span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="plaintext">};</span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="plaintext"></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="plaintext">// Mostly CRAM only, but this could also include other format options</span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="plaintext">enum hts_fmt_option {</span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="plaintext"> // CRAM specific</span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="plaintext"> CRAM_OPT_DECODE_MD,</span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="plaintext"> CRAM_OPT_PREFIX,</span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="plaintext"> CRAM_OPT_VERBOSITY, // obsolete, use hts_set_log_level() instead</span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="plaintext"> CRAM_OPT_SEQS_PER_SLICE,</span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="plaintext"> CRAM_OPT_SLICES_PER_CONTAINER,</span>
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<td class="diff-line-num new new_line" data-linenumber="288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="plaintext"> CRAM_OPT_RANGE,</span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="plaintext"> CRAM_OPT_VERSION, // rename to cram_version?</span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="plaintext"> CRAM_OPT_EMBED_REF,</span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="plaintext"> CRAM_OPT_IGNORE_MD5,</span>
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<td class="diff-line-num new new_line" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="plaintext"> CRAM_OPT_REFERENCE, // make general</span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="plaintext"> CRAM_OPT_MULTI_SEQ_PER_SLICE,</span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="plaintext"> CRAM_OPT_NO_REF,</span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="plaintext"> CRAM_OPT_USE_BZIP2,</span>
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<td class="diff-line-num new new_line" data-linenumber="296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="plaintext"> CRAM_OPT_SHARED_REF,</span>
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<td class="diff-line-num new new_line" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="plaintext"> CRAM_OPT_NTHREADS, // deprecated, use HTS_OPT_NTHREADS</span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="plaintext"> CRAM_OPT_THREAD_POOL,// make general</span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="plaintext"> CRAM_OPT_USE_LZMA,</span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="plaintext"> CRAM_OPT_USE_RANS,</span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="plaintext"> CRAM_OPT_REQUIRED_FIELDS,</span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="plaintext"> CRAM_OPT_LOSSY_NAMES,</span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="plaintext"> CRAM_OPT_BASES_PER_SLICE,</span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="plaintext"> CRAM_OPT_STORE_MD,</span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="plaintext"> CRAM_OPT_STORE_NM,</span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="plaintext"></span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="plaintext"> // General purpose</span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="plaintext"> HTS_OPT_COMPRESSION_LEVEL = 100,</span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="plaintext"> HTS_OPT_NTHREADS,</span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="plaintext"> HTS_OPT_THREAD_POOL,</span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="plaintext"> HTS_OPT_CACHE_SIZE,</span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="plaintext"> HTS_OPT_BLOCK_SIZE,</span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="plaintext">};</span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="plaintext"></span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="plaintext">// For backwards compatibility</span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="plaintext">#define cram_option hts_fmt_option</span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="plaintext"></span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="plaintext">typedef struct hts_opt {</span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="plaintext"> char *arg; // string form, strdup()ed</span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="plaintext"> enum hts_fmt_option opt; // tokenised key</span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="plaintext"> union { // ... and value</span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="plaintext"> int i;</span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="plaintext"> char *s;</span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="plaintext"> } val;</span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="plaintext"> struct hts_opt *next;</span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="plaintext">} hts_opt;</span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="plaintext">#define HTS_FILE_OPTS_INIT {{0},0}</span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="plaintext"></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="plaintext">/*</span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="plaintext"> * Explicit index file name delimiter, see below</span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="plaintext"> */</span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="plaintext">#define HTS_IDX_DELIM "##idx##"</span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="plaintext"></span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="plaintext"></span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="plaintext">/**********************</span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="plaintext"> * Exported functions *</span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="plaintext"> **********************/</span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="plaintext"></span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="plaintext">/*</span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="plaintext"> * Parses arg and appends it to the option list.</span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="plaintext"> *</span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="plaintext"> * Returns 0 on success;</span>
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344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="plaintext"> * -1 on failure.</span>
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345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="plaintext"> */</span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="plaintext">int hts_opt_add(hts_opt **opts, const char *c_arg);</span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="plaintext"></span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="plaintext">/*</span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="plaintext"> * Applies an hts_opt option list to a given htsFile.</span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="plaintext"> *</span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="plaintext"> * Returns 0 on success</span>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="plaintext"> * -1 on failure</span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="plaintext"> */</span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="plaintext">int hts_opt_apply(htsFile *fp, hts_opt *opts);</span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="plaintext"></span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="plaintext">/*</span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="plaintext"> * Frees an hts_opt list.</span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="plaintext"> */</span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="plaintext">void hts_opt_free(hts_opt *opts);</span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="plaintext"></span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="plaintext">/*</span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="plaintext"> * Accepts a string file format (sam, bam, cram, vcf, bam) optionally</span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="plaintext"> * followed by a comma separated list of key=value options and splits</span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="plaintext"> * these up into the fields of htsFormat struct.</span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="plaintext"> *</span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="plaintext"> * Returns 0 on success</span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="plaintext"> * -1 on failure.</span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="plaintext"> */</span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="plaintext">int hts_parse_format(htsFormat *opt, const char *str);</span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="plaintext"></span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="plaintext">/*</span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="plaintext"> * Tokenise options as (key(=value)?,)*(key(=value)?)?</span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="plaintext"> * NB: No provision for ',' appearing in the value!</span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="plaintext"> * Add backslashing rules?</span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="plaintext"> *</span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="plaintext"> * This could be used as part of a general command line option parser or</span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="plaintext"> * as a string concatenated onto the file open mode.</span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="plaintext"> *</span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="plaintext"> * Returns 0 on success</span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="plaintext"> * -1 on failure.</span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="plaintext"> */</span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="plaintext">int hts_parse_opt_list(htsFormat *opt, const char *str);</span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="plaintext"></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="plaintext">/*! @abstract Table for converting a nucleotide character to 4-bit encoding.</span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="plaintext">The input character may be either an IUPAC ambiguity code, '=' for 0, or</span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="plaintext">'0'/'1'/'2'/'3' for a result of 1/2/4/8. The result is encoded as 1/2/4/8</span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="plaintext">for A/C/G/T or combinations of these bits for ambiguous bases.</span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="plaintext">*/</span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="plaintext">extern const unsigned char seq_nt16_table[256];</span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="plaintext"></span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="plaintext">/*! @abstract Table for converting a 4-bit encoded nucleotide to an IUPAC</span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="plaintext">ambiguity code letter (or '=' when given 0).</span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="plaintext">*/</span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="plaintext">extern const char seq_nt16_str[];</span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="plaintext"></span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="plaintext">/*! @abstract Table for converting a 4-bit encoded nucleotide to about 2 bits.</span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="plaintext">Returns 0/1/2/3 for 1/2/4/8 (i.e., A/C/G/T), or 4 otherwise (0 or ambiguous).</span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="plaintext">*/</span>
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="plaintext">extern const int seq_nt16_int[];</span>
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="plaintext">/*!</span>
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="plaintext"> @abstract Get the htslib version number</span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="plaintext"> @return For released versions, a string like "N.N[.N]"; or git describe</span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="plaintext"> output if using a library built within a Git repository.</span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="plaintext">*/</span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="plaintext">const char *hts_version(void);</span>
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="plaintext">/*!</span>
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="plaintext"> @abstract Compile-time HTSlib version number, for use in #if checks</span>
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="plaintext"> @return For released versions X.Y[.Z], an integer of the form XYYYZZ;</span>
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="plaintext"> useful for preprocessor conditionals such as</span>
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="plaintext"> #if HTS_VERSION >= 101000 // Check for v1.10 or later</span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="plaintext">*/</span>
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="plaintext">// Maintainers: Bump this in the final stage of preparing a new release.</span>
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="plaintext">// Immediately after release, bump ZZ to 90 to distinguish in-development</span>
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="plaintext">// Git repository builds from the release; you may wish to increment this</span>
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="plaintext">// further when significant features are merged.</span>
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="plaintext">#define HTS_VERSION 101000</span>
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="plaintext">/*!</span>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="plaintext"> @abstract Determine format by peeking at the start of a file</span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="plaintext"> @param fp File opened for reading, positioned at the beginning</span>
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="plaintext"> @param fmt Format structure that will be filled out on return</span>
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430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="plaintext"> @return 0 for success, or negative if an error occurred.</span>
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="plaintext">*/</span>
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432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="plaintext">int hts_detect_format(struct hFILE *fp, htsFormat *fmt);</span>
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434
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="plaintext"></span>
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435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="plaintext">/*!</span>
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436
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="plaintext"> @abstract Get a human-readable description of the file format</span>
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437
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="plaintext"> @param fmt Format structure holding type, version, compression, etc.</span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="plaintext"> @return Description string, to be freed by the caller after use.</span>
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439
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="plaintext">*/</span>
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440
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="plaintext">char *hts_format_description(const htsFormat *format);</span>
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442
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="plaintext"></span>
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443
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="plaintext">/*!</span>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="plaintext"> @abstract Open a sequence data (SAM/BAM/CRAM) or variant data (VCF/BCF)</span>
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445
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="plaintext"> or possibly-compressed textual line-orientated file</span>
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446
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="plaintext"> @param fn The file name or "-" for stdin/stdout. For indexed files</span>
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="plaintext"> with a non-standard naming, the file name can include the</span>
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448
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="plaintext"> name of the index file delimited with HTS_IDX_DELIM</span>
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449
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="plaintext"> @param mode Mode matching / [rwa][bceguxz0-9]* /</span>
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450
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="plaintext"> @discussion</span>
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451
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="plaintext"> With 'r' opens for reading; any further format mode letters are ignored</span>
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452
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="plaintext"> as the format is detected by checking the first few bytes or BGZF blocks</span>
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453
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="plaintext"> of the file. With 'w' or 'a' opens for writing or appending, with format</span>
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454
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="plaintext"> specifier letters:</span>
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455
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="plaintext"> b binary format (BAM, BCF, etc) rather than text (SAM, VCF, etc)</span>
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456
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="plaintext"> c CRAM format</span>
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457
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="plaintext"> g gzip compressed</span>
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458
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="plaintext"> u uncompressed</span>
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459
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="plaintext"> z bgzf compressed</span>
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460
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="plaintext"> [0-9] zlib compression level</span>
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461
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="plaintext"> and with non-format option letters (for any of 'r'/'w'/'a'):</span>
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462
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="plaintext"> e close the file on exec(2) (opens with O_CLOEXEC, where supported)</span>
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463
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="plaintext"> x create the file exclusively (opens with O_EXCL, where supported)</span>
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464
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="plaintext"> Note that there is a distinction between 'u' and '0': the first yields</span>
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465
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="plaintext"> plain uncompressed output whereas the latter outputs uncompressed data</span>
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466
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="plaintext"> wrapped in the zlib format.</span>
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467
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="plaintext"> @example</span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="plaintext"> [rw]b .. compressed BCF, BAM, FAI</span>
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469
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="plaintext"> [rw]bu .. uncompressed BCF</span>
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470
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="plaintext"> [rw]z .. compressed VCF</span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="plaintext"> [rw] .. uncompressed VCF</span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="plaintext">*/</span>
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473
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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474
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="plaintext">htsFile *hts_open(const char *fn, const char *mode);</span>
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475
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="plaintext"></span>
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476
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="plaintext">/*!</span>
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477
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="plaintext"> @abstract Open a SAM/BAM/CRAM/VCF/BCF/etc file</span>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="plaintext"> @param fn The file name or "-" for stdin/stdout</span>
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479
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="plaintext"> @param mode Open mode, as per hts_open()</span>
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480
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="plaintext"> @param fmt Optional format specific parameters</span>
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481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="plaintext"> @discussion</span>
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482
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="plaintext"> See hts_open() for description of fn and mode.</span>
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483
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="plaintext"> // TODO Update documentation for s/opts/fmt/</span>
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484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="plaintext"> Opts contains a format string (sam, bam, cram, vcf, bcf) which will,</span>
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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="plaintext"> if defined, override mode. Opts also contains a linked list of hts_opt</span>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="plaintext"> structures to apply to the open file handle. These can contain things</span>
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487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="plaintext"> like pointers to the reference or information on compression levels,</span>
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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="plaintext"> block sizes, etc.</span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="plaintext">*/</span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="plaintext">htsFile *hts_open_format(const char *fn, const char *mode, const htsFormat *fmt);</span>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="plaintext"></span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="plaintext">/*!</span>
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494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="plaintext"> @abstract Open an existing stream as a SAM/BAM/CRAM/VCF/BCF/etc file</span>
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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="plaintext"> @param fn The already-open file handle</span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="plaintext"> @param mode Open mode, as per hts_open()</span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="plaintext">*/</span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="plaintext">htsFile *hts_hopen(struct hFILE *fp, const char *fn, const char *mode);</span>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="plaintext"></span>
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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="plaintext">/*!</span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="plaintext"> @abstract Close a file handle, flushing buffered data for output streams</span>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="plaintext"> @param fp The file handle to be closed</span>
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504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="plaintext"> @return 0 for success, or negative if an error occurred.</span>
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505
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="plaintext">*/</span>
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506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="plaintext">int hts_close(htsFile *fp);</span>
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="plaintext"></span>
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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="plaintext">/*!</span>
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510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="plaintext"> @abstract Returns the file's format information</span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="plaintext"> @param fp The file handle</span>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="plaintext"> @return Read-only pointer to the file's htsFormat.</span>
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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="plaintext">*/</span>
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514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="plaintext">const htsFormat *hts_get_format(htsFile *fp);</span>
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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="plaintext"></span>
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517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="plaintext">/*!</span>
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518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="plaintext"> @ abstract Returns a string containing the file format extension.</span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="plaintext"> @ param format Format structure containing the file type.</span>
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520
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="plaintext"> @ return A string ("sam", "bam", etc) or "?" for unknown formats.</span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="plaintext"> */</span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="plaintext">const char *hts_format_file_extension(const htsFormat *format);</span>
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524
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="plaintext"></span>
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525
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="plaintext">/*!</span>
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526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="plaintext"> @abstract Sets a specified CRAM option on the open file handle.</span>
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527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="plaintext"> @param fp The file handle open the open file.</span>
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528
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="plaintext"> @param opt The CRAM_OPT_* option.</span>
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529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="plaintext"> @param ... Optional arguments, dependent on the option used.</span>
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530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="plaintext"> @return 0 for success, or negative if an error occurred.</span>
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531
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="plaintext">*/</span>
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532
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="plaintext">int hts_set_opt(htsFile *fp, enum hts_fmt_option opt, ...);</span>
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534
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="plaintext"></span>
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535
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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536
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="plaintext">int hts_getline(htsFile *fp, int delimiter, kstring_t *str);</span>
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537
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="plaintext">char **hts_readlines(const char *fn, int *_n);</span>
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539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="plaintext">/*!</span>
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540
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="plaintext"> @abstract Parse comma-separated list or read list from a file</span>
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541
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="plaintext"> @param list File name or comma-separated list</span>
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542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="plaintext"> @param is_file</span>
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543
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="plaintext"> @param _n Size of the output array (number of items read)</span>
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544
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="plaintext"> @return NULL on failure or pointer to newly allocated array of</span>
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545
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="plaintext"> strings</span>
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546
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="plaintext">*/</span>
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547
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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548
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="plaintext">char **hts_readlist(const char *fn, int is_file, int *_n);</span>
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549
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="plaintext"></span>
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550
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="plaintext">/*!</span>
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551
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="plaintext"> @abstract Create extra threads to aid compress/decompression for this file</span>
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552
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="plaintext"> @param fp The file handle</span>
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553
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="plaintext"> @param n The number of worker threads to create</span>
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554
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="plaintext"> @return 0 for success, or negative if an error occurred.</span>
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555
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="plaintext"> @notes This function creates non-shared threads for use solely by fp.</span>
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556
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="plaintext"> The hts_set_thread_pool function is the recommended alternative.</span>
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557
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="plaintext">*/</span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="plaintext">int hts_set_threads(htsFile *fp, int n);</span>
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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="plaintext"></span>
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561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="plaintext">/*!</span>
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562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="plaintext"> @abstract Create extra threads to aid compress/decompression for this file</span>
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563
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="plaintext"> @param fp The file handle</span>
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564
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="plaintext"> @param p A pool of worker threads, previously allocated by hts_create_threads().</span>
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565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="plaintext"> @return 0 for success, or negative if an error occurred.</span>
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566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="plaintext">*/</span>
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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="plaintext">int hts_set_thread_pool(htsFile *fp, htsThreadPool *p);</span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="plaintext"></span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="plaintext">/*!</span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="plaintext"> @abstract Adds a cache of decompressed blocks, potentially speeding up seeks.</span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="plaintext"> This may not work for all file types (currently it is bgzf only).</span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="plaintext"> @param fp The file handle</span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="plaintext"> @param n The size of cache, in bytes</span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="plaintext">*/</span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="plaintext">void hts_set_cache_size(htsFile *fp, int n);</span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="plaintext"></span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="plaintext">/*!</span>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="plaintext"> @abstract Set .fai filename for a file opened for reading</span>
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581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="plaintext"> @return 0 for success, negative on failure</span>
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582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="plaintext"> @discussion</span>
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583
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="plaintext"> Called before *_hdr_read(), this provides the name of a .fai file</span>
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584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="plaintext"> used to provide a reference list if the htsFile contains no @SQ headers.</span>
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585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="plaintext">*/</span>
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586
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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587
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="plaintext">int hts_set_fai_filename(htsFile *fp, const char *fn_aux);</span>
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588
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="plaintext"></span>
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589
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="plaintext"></span>
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590
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="plaintext">/*!</span>
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591
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="plaintext"> @abstract Determine whether a given htsFile contains a valid EOF block</span>
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592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="plaintext"> @return 3 for a non-EOF checkable filetype;</span>
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593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="plaintext"> 2 for an unseekable file type where EOF cannot be checked;</span>
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594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="plaintext"> 1 for a valid EOF block;</span>
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595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="plaintext"> 0 for if the EOF marker is absent when it should be present;</span>
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596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="plaintext"> -1 (with errno set) on failure</span>
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597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="plaintext"> @discussion</span>
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598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="plaintext"> Check if the BGZF end-of-file (EOF) marker is present</span>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="plaintext">*/</span>
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600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="plaintext">int hts_check_EOF(htsFile *fp);</span>
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602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="plaintext"></span>
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603
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="plaintext">/************</span>
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604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="plaintext"> * Indexing *</span>
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605
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="plaintext"> ************/</span>
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606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="plaintext"></span>
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607
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="plaintext">/*!</span>
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608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="plaintext">These HTS_IDX_* macros are used as special tid values for hts_itr_query()/etc,</span>
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609
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="plaintext">producing iterators operating as follows:</span>
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610
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="plaintext"> - HTS_IDX_NOCOOR iterates over unmapped reads sorted at the end of the file</span>
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611
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="plaintext"> - HTS_IDX_START iterates over the entire file</span>
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612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="plaintext"> - HTS_IDX_REST iterates from the current position to the end of the file</span>
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613
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="plaintext"> - HTS_IDX_NONE always returns "no more alignment records"</span>
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614
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="plaintext">When one of these special tid values is used, beg and end are ignored.</span>
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615
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="plaintext">When REST or NONE is used, idx is also ignored and may be NULL.</span>
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616
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="plaintext">*/</span>
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617
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="plaintext">#define HTS_IDX_NOCOOR (-2)</span>
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618
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="plaintext">#define HTS_IDX_START (-3)</span>
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619
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="plaintext">#define HTS_IDX_REST (-4)</span>
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620
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="plaintext">#define HTS_IDX_NONE (-5)</span>
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621
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="plaintext"></span>
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622
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="plaintext">#define HTS_FMT_CSI 0</span>
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623
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="plaintext">#define HTS_FMT_BAI 1</span>
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624
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="plaintext">#define HTS_FMT_TBI 2</span>
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625
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="plaintext">#define HTS_FMT_CRAI 3</span>
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626
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="plaintext"></span>
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627
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="plaintext">// Almost INT64_MAX, but when cast into a 32-bit int it's</span>
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628
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="plaintext">// also INT_MAX instead of -1. This avoids bugs with old code</span>
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629
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="plaintext">// using the new hts_pos_t data type.</span>
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630
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="plaintext">#define HTS_POS_MAX ((((int64_t)INT_MAX)<<32)|INT_MAX)</span>
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631
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="plaintext">#define HTS_POS_MIN INT64_MIN</span>
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632
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="plaintext">#define PRIhts_pos PRId64</span>
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633
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="plaintext">typedef int64_t hts_pos_t;</span>
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634
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="plaintext">// For comparison with previous release:</span>
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="plaintext">//</span>
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="plaintext">// #define HTS_POS_MAX INT_MAX</span>
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638
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="plaintext">// #define HTS_POS_MIN INT_MIN</span>
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="plaintext">// #define PRIhts_pos PRId32</span>
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640
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="plaintext">// typedef int32_t hts_pos_t;</span>
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="plaintext">typedef struct {</span>
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="plaintext"> hts_pos_t beg, end;</span>
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="plaintext">} hts_pair_pos_t;</span>
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="plaintext">typedef hts_pair_pos_t hts_pair32_t; // For backwards compatibility</span>
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="plaintext">typedef struct {</span>
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="plaintext"> uint64_t u, v;</span>
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="plaintext">} hts_pair64_t;</span>
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="plaintext">typedef struct {</span>
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="plaintext"> uint64_t u, v;</span>
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="plaintext"> uint64_t max;</span>
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="plaintext">} hts_pair64_max_t;</span>
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<pre style="margin: 0;">+<span id="LC656" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="plaintext">typedef struct {</span>
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="plaintext"> const char *reg;</span>
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659
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="plaintext"> hts_pair_pos_t *intervals;</span>
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="plaintext"> int tid;</span>
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661
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<pre style="margin: 0;">+<span id="LC661" class="line" lang="plaintext"> uint32_t count;</span>
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="plaintext"> hts_pos_t min_beg, max_end;</span>
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="plaintext">} hts_reglist_t;</span>
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="plaintext">typedef int hts_readrec_func(BGZF *fp, void *data, void *r, int *tid, hts_pos_t *beg, hts_pos_t *end);</span>
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="plaintext">typedef int hts_seek_func(void *fp, int64_t offset, int where);</span>
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="plaintext">typedef int64_t hts_tell_func(void *fp);</span>
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="plaintext">typedef struct {</span>
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="plaintext"> uint32_t read_rest:1, finished:1, is_cram:1, nocoor:1, multi:1, dummy:27;</span>
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="plaintext"> int tid, n_off, i, n_reg;</span>
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="plaintext"> hts_pos_t beg, end;</span>
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="plaintext"> hts_reglist_t *reg_list;</span>
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="plaintext"> int curr_tid, curr_reg, curr_intv;</span>
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="plaintext"> hts_pos_t curr_beg, curr_end;</span>
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="plaintext"> uint64_t curr_off, nocoor_off;</span>
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="plaintext"> hts_pair64_max_t *off;</span>
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="plaintext"> hts_readrec_func *readrec;</span>
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="plaintext"> hts_seek_func *seek;</span>
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="plaintext"> hts_tell_func *tell;</span>
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="plaintext"> struct {</span>
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="plaintext"> int n, m;</span>
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="plaintext"> int *a;</span>
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="plaintext"> } bins;</span>
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="plaintext">} hts_itr_t;</span>
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="plaintext">typedef struct {</span>
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="plaintext"> int key;</span>
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689
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="plaintext"> uint64_t min_off, max_off;</span>
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690
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="plaintext">} aux_key_t;</span>
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691
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="plaintext"></span>
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692
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="plaintext">typedef hts_itr_t hts_itr_multi_t;</span>
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693
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="plaintext"></span>
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694
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="plaintext"> #define hts_bin_first(l) (((1<<(((l)<<1) + (l))) - 1) / 7)</span>
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695
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="plaintext"> #define hts_bin_parent(l) (((l) - 1) >> 3)</span>
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696
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<pre style="margin: 0;">+<span id="LC696" class="line" lang="plaintext"></span>
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697
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="plaintext">///////////////////////////////////////////////////////////</span>
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698
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="plaintext">// Low-level API for building indexes.</span>
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699
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="plaintext"></span>
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700
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<pre style="margin: 0;">+<span id="LC700" class="line" lang="plaintext">/// Create a BAI/CSI/TBI type index structure</span>
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701
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<pre style="margin: 0;">+<span id="LC701" class="line" lang="plaintext">/** @param n Initial number of targets</span>
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702
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="plaintext"> @param fmt Format, one of HTS_FMT_CSI, HTS_FMT_BAI or HTS_FMT_TBI</span>
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703
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="plaintext"> @param offset0 Initial file offset</span>
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704
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="plaintext"> @param min_shift Number of bits for the minimal interval</span>
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705
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="plaintext"> @param n_lvls Number of levels in the binning index</span>
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706
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="plaintext"> @return An initialised hts_idx_t struct on success; NULL on failure</span>
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707
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="plaintext"></span>
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708
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="plaintext">The struct returned by a successful call should be freed via hts_idx_destroy()</span>
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709
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="plaintext">when it is no longer needed.</span>
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710
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="plaintext">*/</span>
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711
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<pre style="margin: 0;">+<span id="LC711" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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712
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="plaintext">hts_idx_t *hts_idx_init(int n, int fmt, uint64_t offset0, int min_shift, int n_lvls);</span>
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713
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="plaintext"></span>
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714
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="plaintext">/// Free a BAI/CSI/TBI type index</span>
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715
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="plaintext">/** @param idx Index structure to free</span>
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716
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="plaintext"> */</span>
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717
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="plaintext">void hts_idx_destroy(hts_idx_t *idx);</span>
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719
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="plaintext"></span>
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720
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="plaintext">/// Push an index entry</span>
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721
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="plaintext">/** @param idx Index</span>
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722
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<pre style="margin: 0;">+<span id="LC722" class="line" lang="plaintext"> @param tid Target id</span>
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723
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="plaintext"> @param beg Range start (zero-based)</span>
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724
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<pre style="margin: 0;">+<span id="LC724" class="line" lang="plaintext"> @param end Range end (zero-based, half-open)</span>
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725
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<pre style="margin: 0;">+<span id="LC725" class="line" lang="plaintext"> @param offset File offset</span>
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726
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<pre style="margin: 0;">+<span id="LC726" class="line" lang="plaintext"> @param is_mapped Range corresponds to a mapped read</span>
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727
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<pre style="margin: 0;">+<span id="LC727" class="line" lang="plaintext"> @return 0 on success; -1 on failure</span>
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728
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="plaintext"></span>
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729
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="plaintext">The @p is_mapped parameter is used to update the n_mapped / n_unmapped counts</span>
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730
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="plaintext">stored in the meta-data bin.</span>
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731
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="plaintext"> */</span>
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732
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<pre style="margin: 0;">+<span id="LC732" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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733
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<pre style="margin: 0;">+<span id="LC733" class="line" lang="plaintext">int hts_idx_push(hts_idx_t *idx, int tid, hts_pos_t beg, hts_pos_t end, uint64_t offset, int is_mapped);</span>
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734
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<pre style="margin: 0;">+<span id="LC734" class="line" lang="plaintext"></span>
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735
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<pre style="margin: 0;">+<span id="LC735" class="line" lang="plaintext">/// Finish building an index</span>
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736
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="plaintext">/** @param idx Index</span>
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737
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="plaintext"> @param final_offset Last file offset</span>
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738
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="plaintext"> @return 0 on success; non-zero on failure.</span>
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739
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="plaintext">*/</span>
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<pre style="margin: 0;">+<span id="LC740" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="plaintext">int hts_idx_finish(hts_idx_t *idx, uint64_t final_offset);</span>
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="plaintext">/// Returns index format</span>
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744
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="plaintext">/** @param idx Index</span>
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="plaintext"> @return One of HTS_FMT_CSI, HTS_FMT_BAI or HTS_FMT_TBI</span>
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746
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<pre style="margin: 0;">+<span id="LC746" class="line" lang="plaintext">*/</span>
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747
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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<pre style="margin: 0;">+<span id="LC748" class="line" lang="plaintext">int hts_idx_fmt(hts_idx_t *idx);</span>
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749
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<pre style="margin: 0;">+<span id="LC749" class="line" lang="plaintext"></span>
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750
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<pre style="margin: 0;">+<span id="LC750" class="line" lang="plaintext">/// Add name to TBI index meta-data</span>
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<pre style="margin: 0;">+<span id="LC751" class="line" lang="plaintext">/** @param idx Index</span>
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<pre style="margin: 0;">+<span id="LC752" class="line" lang="plaintext"> @param tid Target identifier</span>
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<pre style="margin: 0;">+<span id="LC753" class="line" lang="plaintext"> @param name Target name</span>
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="plaintext"> @return Index number of name in names list on success; -1 on failure.</span>
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<pre style="margin: 0;">+<span id="LC755" class="line" lang="plaintext">*/</span>
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<pre style="margin: 0;">+<span id="LC756" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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<pre style="margin: 0;">+<span id="LC757" class="line" lang="plaintext">int hts_idx_tbi_name(hts_idx_t *idx, int tid, const char *name);</span>
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758
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<pre style="margin: 0;">+<span id="LC758" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC759" class="line" lang="plaintext">// Index loading and saving</span>
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760
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<pre style="margin: 0;">+<span id="LC760" class="line" lang="plaintext"></span>
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761
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<pre style="margin: 0;">+<span id="LC761" class="line" lang="plaintext">/// Save an index to a file</span>
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762
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<pre style="margin: 0;">+<span id="LC762" class="line" lang="plaintext">/** @param idx Index to be written</span>
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763
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<pre style="margin: 0;">+<span id="LC763" class="line" lang="plaintext"> @param fn Input BAM/BCF/etc filename, to which .bai/.csi/etc will be added</span>
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764
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<pre style="margin: 0;">+<span id="LC764" class="line" lang="plaintext"> @param fmt One of the HTS_FMT_* index formats</span>
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765
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<pre style="margin: 0;">+<span id="LC765" class="line" lang="plaintext"> @return 0 if successful, or negative if an error occurred.</span>
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<pre style="margin: 0;">+<span id="LC766" class="line" lang="plaintext">*/</span>
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767
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<pre style="margin: 0;">+<span id="LC767" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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768
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<pre style="margin: 0;">+<span id="LC768" class="line" lang="plaintext">int hts_idx_save(const hts_idx_t *idx, const char *fn, int fmt) HTS_RESULT_USED;</span>
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769
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<pre style="margin: 0;">+<span id="LC769" class="line" lang="plaintext"></span>
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770
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<pre style="margin: 0;">+<span id="LC770" class="line" lang="plaintext">/// Save an index to a specific file</span>
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771
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<pre style="margin: 0;">+<span id="LC771" class="line" lang="plaintext">/** @param idx Index to be written</span>
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772
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="plaintext"> @param fn Input BAM/BCF/etc filename</span>
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773
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<pre style="margin: 0;">+<span id="LC773" class="line" lang="plaintext"> @param fnidx Output filename, or NULL to add .bai/.csi/etc to @a fn</span>
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<pre style="margin: 0;">+<span id="LC774" class="line" lang="plaintext"> @param fmt One of the HTS_FMT_* index formats</span>
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775
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="plaintext"> @return 0 if successful, or negative if an error occurred.</span>
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776
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<pre style="margin: 0;">+<span id="LC776" class="line" lang="plaintext">*/</span>
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777
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<pre style="margin: 0;">+<span id="LC777" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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<pre style="margin: 0;">+<span id="LC778" class="line" lang="plaintext">int hts_idx_save_as(const hts_idx_t *idx, const char *fn, const char *fnidx, int fmt) HTS_RESULT_USED;</span>
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779
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<pre style="margin: 0;">+<span id="LC779" class="line" lang="plaintext"></span>
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780
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<pre style="margin: 0;">+<span id="LC780" class="line" lang="plaintext">/// Load an index file</span>
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781
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<pre style="margin: 0;">+<span id="LC781" class="line" lang="plaintext">/** @param fn BAM/BCF/etc filename, to which .bai/.csi/etc will be added or</span>
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782
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<pre style="margin: 0;">+<span id="LC782" class="line" lang="plaintext"> the extension substituted, to search for an existing index file.</span>
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783
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<pre style="margin: 0;">+<span id="LC783" class="line" lang="plaintext"> In case of a non-standard naming, the file name can include the</span>
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784
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<pre style="margin: 0;">+<span id="LC784" class="line" lang="plaintext"> name of the index file delimited with HTS_IDX_DELIM.</span>
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785
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<pre style="margin: 0;">+<span id="LC785" class="line" lang="plaintext"> @param fmt One of the HTS_FMT_* index formats</span>
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786
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<pre style="margin: 0;">+<span id="LC786" class="line" lang="plaintext"> @return The index, or NULL if an error occurred.</span>
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787
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="plaintext"></span>
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788
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<pre style="margin: 0;">+<span id="LC788" class="line" lang="plaintext">If @p fn contains the string "##idx##" (HTS_IDX_DELIM), the part before</span>
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789
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<pre style="margin: 0;">+<span id="LC789" class="line" lang="plaintext">the delimiter will be used as the name of the data file and the part after</span>
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790
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<pre style="margin: 0;">+<span id="LC790" class="line" lang="plaintext">it will be used as the name of the index.</span>
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791
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<pre style="margin: 0;">+<span id="LC791" class="line" lang="plaintext"></span>
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792
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<pre style="margin: 0;">+<span id="LC792" class="line" lang="plaintext">Otherwise, this function tries to work out the index name as follows:</span>
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793
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<pre style="margin: 0;">+<span id="LC793" class="line" lang="plaintext"></span>
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794
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<pre style="margin: 0;">+<span id="LC794" class="line" lang="plaintext"> It will try appending ".csi" to @p fn</span>
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795
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="plaintext"> It will try substituting an existing suffix (e.g. .bam, .vcf) with ".csi"</span>
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796
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<pre style="margin: 0;">+<span id="LC796" class="line" lang="plaintext"> Then, if @p fmt is HTS_FMT_BAI:</span>
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797
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<pre style="margin: 0;">+<span id="LC797" class="line" lang="plaintext"> It will try appending ".bai" to @p fn</span>
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798
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<pre style="margin: 0;">+<span id="LC798" class="line" lang="plaintext"> To will substituting the existing suffix (e.g. .bam) with ".bai"</span>
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799
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<pre style="margin: 0;">+<span id="LC799" class="line" lang="plaintext"> else if @p fmt is HTS_FMT_TBI:</span>
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800
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<pre style="margin: 0;">+<span id="LC800" class="line" lang="plaintext"> It will try appending ".tbi" to @p fn</span>
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801
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<pre style="margin: 0;">+<span id="LC801" class="line" lang="plaintext"> To will substituting the existing suffix (e.g. .vcf) with ".tbi"</span>
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802
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<pre style="margin: 0;">+<span id="LC802" class="line" lang="plaintext"></span>
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803
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<pre style="margin: 0;">+<span id="LC803" class="line" lang="plaintext">If the index file is remote (served over a protocol like https), first a check</span>
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804
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<pre style="margin: 0;">+<span id="LC804" class="line" lang="plaintext">is made to see is a locally cached copy is available. This is done for all</span>
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805
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<pre style="margin: 0;">+<span id="LC805" class="line" lang="plaintext">of the possible names listed above. If a cached copy is not available then</span>
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806
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<pre style="margin: 0;">+<span id="LC806" class="line" lang="plaintext">the index will be downloaded and stored in the current working directory,</span>
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807
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<pre style="margin: 0;">+<span id="LC807" class="line" lang="plaintext">with the same name as the remote index.</span>
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808
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<pre style="margin: 0;">+<span id="LC808" class="line" lang="plaintext"></span>
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809
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<pre style="margin: 0;">+<span id="LC809" class="line" lang="plaintext"> Equivalent to hts_idx_load3(fn, NULL, fmt, HTS_IDX_SAVE_REMOTE);</span>
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810
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<pre style="margin: 0;">+<span id="LC810" class="line" lang="plaintext">*/</span>
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811
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<pre style="margin: 0;">+<span id="LC811" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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812
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<pre style="margin: 0;">+<span id="LC812" class="line" lang="plaintext">hts_idx_t *hts_idx_load(const char *fn, int fmt);</span>
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813
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<pre style="margin: 0;">+<span id="LC813" class="line" lang="plaintext"></span>
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814
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<pre style="margin: 0;">+<span id="LC814" class="line" lang="plaintext">/// Load a specific index file</span>
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815
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<pre style="margin: 0;">+<span id="LC815" class="line" lang="plaintext">/** @param fn Input BAM/BCF/etc filename</span>
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816
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<pre style="margin: 0;">+<span id="LC816" class="line" lang="plaintext"> @param fnidx The input index filename</span>
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<pre style="margin: 0;">+<span id="LC817" class="line" lang="plaintext"> @return The index, or NULL if an error occurred.</span>
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818
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<pre style="margin: 0;">+<span id="LC818" class="line" lang="plaintext"></span>
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819
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<pre style="margin: 0;">+<span id="LC819" class="line" lang="plaintext"> Equivalent to hts_idx_load3(fn, fnidx, 0, 0);</span>
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820
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<pre style="margin: 0;">+<span id="LC820" class="line" lang="plaintext"></span>
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821
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<pre style="margin: 0;">+<span id="LC821" class="line" lang="plaintext"> This function will not attempt to save index files locally.</span>
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822
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<pre style="margin: 0;">+<span id="LC822" class="line" lang="plaintext">*/</span>
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823
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<pre style="margin: 0;">+<span id="LC823" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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824
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<pre style="margin: 0;">+<span id="LC824" class="line" lang="plaintext">hts_idx_t *hts_idx_load2(const char *fn, const char *fnidx);</span>
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825
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<pre style="margin: 0;">+<span id="LC825" class="line" lang="plaintext"></span>
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826
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<pre style="margin: 0;">+<span id="LC826" class="line" lang="plaintext">/// Load a specific index file</span>
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827
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<pre style="margin: 0;">+<span id="LC827" class="line" lang="plaintext">/** @param fn Input BAM/BCF/etc filename</span>
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828
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<pre style="margin: 0;">+<span id="LC828" class="line" lang="plaintext"> @param fnidx The input index filename</span>
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829
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<pre style="margin: 0;">+<span id="LC829" class="line" lang="plaintext"> @param fmt One of the HTS_FMT_* index formats</span>
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830
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<pre style="margin: 0;">+<span id="LC830" class="line" lang="plaintext"> @param flags Flags to alter behaviour (see description)</span>
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831
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<pre style="margin: 0;">+<span id="LC831" class="line" lang="plaintext"> @return The index, or NULL if an error occurred.</span>
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832
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<pre style="margin: 0;">+<span id="LC832" class="line" lang="plaintext"></span>
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833
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<pre style="margin: 0;">+<span id="LC833" class="line" lang="plaintext"> If @p fnidx is NULL, the index name will be derived from @p fn in the</span>
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834
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<pre style="margin: 0;">+<span id="LC834" class="line" lang="plaintext"> same way as hts_idx_load().</span>
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835
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<pre style="margin: 0;">+<span id="LC835" class="line" lang="plaintext"></span>
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836
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<pre style="margin: 0;">+<span id="LC836" class="line" lang="plaintext"> If @p fnidx is not NULL, @p fmt is ignored.</span>
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837
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<pre style="margin: 0;">+<span id="LC837" class="line" lang="plaintext"></span>
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838
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<pre style="margin: 0;">+<span id="LC838" class="line" lang="plaintext"> The @p flags parameter can be set to a combination of the following</span>
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839
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<pre style="margin: 0;">+<span id="LC839" class="line" lang="plaintext"> values:</span>
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840
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<pre style="margin: 0;">+<span id="LC840" class="line" lang="plaintext"></span>
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841
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<pre style="margin: 0;">+<span id="LC841" class="line" lang="plaintext"> HTS_IDX_SAVE_REMOTE Save a local copy of any remote indexes</span>
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842
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<pre style="margin: 0;">+<span id="LC842" class="line" lang="plaintext"> HTS_IDX_SILENT_FAIL Fail silently if the index is not present</span>
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843
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<pre style="margin: 0;">+<span id="LC843" class="line" lang="plaintext"></span>
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844
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<pre style="margin: 0;">+<span id="LC844" class="line" lang="plaintext"> The index struct returned by a successful call should be freed</span>
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845
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<pre style="margin: 0;">+<span id="LC845" class="line" lang="plaintext"> via hts_idx_destroy() when it is no longer needed.</span>
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846
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<pre style="margin: 0;">+<span id="LC846" class="line" lang="plaintext">*/</span>
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847
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<pre style="margin: 0;">+<span id="LC847" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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848
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<pre style="margin: 0;">+<span id="LC848" class="line" lang="plaintext">hts_idx_t *hts_idx_load3(const char *fn, const char *fnidx, int fmt, int flags);</span>
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849
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<pre style="margin: 0;">+<span id="LC849" class="line" lang="plaintext"></span>
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850
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<pre style="margin: 0;">+<span id="LC850" class="line" lang="plaintext">/// Flags for hts_idx_load3() ( and also sam_idx_load3(), tbx_idx_load3() )</span>
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851
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<pre style="margin: 0;">+<span id="LC851" class="line" lang="plaintext">#define HTS_IDX_SAVE_REMOTE 1</span>
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852
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<pre style="margin: 0;">+<span id="LC852" class="line" lang="plaintext">#define HTS_IDX_SILENT_FAIL 2</span>
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853
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<pre style="margin: 0;">+<span id="LC853" class="line" lang="plaintext"></span>
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854
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<pre style="margin: 0;">+<span id="LC854" class="line" lang="plaintext">///////////////////////////////////////////////////////////</span>
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855
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<pre style="margin: 0;">+<span id="LC855" class="line" lang="plaintext">// Functions for accessing meta-data stored in indexes</span>
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856
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<pre style="margin: 0;">+<span id="LC856" class="line" lang="plaintext"></span>
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857
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<pre style="margin: 0;">+<span id="LC857" class="line" lang="plaintext">/// Get extra index meta-data</span>
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858
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<pre style="margin: 0;">+<span id="LC858" class="line" lang="plaintext">/** @param idx The index</span>
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859
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<pre style="margin: 0;">+<span id="LC859" class="line" lang="plaintext"> @param l_meta Pointer to where the length of the extra data is stored</span>
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860
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<pre style="margin: 0;">+<span id="LC860" class="line" lang="plaintext"> @return Pointer to the extra data if present; NULL otherwise</span>
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861
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<pre style="margin: 0;">+<span id="LC861" class="line" lang="plaintext"></span>
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862
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<pre style="margin: 0;">+<span id="LC862" class="line" lang="plaintext"> Indexes (both .tbi and .csi) made by tabix include extra data about</span>
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863
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<pre style="margin: 0;">+<span id="LC863" class="line" lang="plaintext"> the indexed file. The returns a pointer to this data. Note that the</span>
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864
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<pre style="margin: 0;">+<span id="LC864" class="line" lang="plaintext"> data is stored exactly as it is in the index. Callers need to interpret</span>
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865
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<pre style="margin: 0;">+<span id="LC865" class="line" lang="plaintext"> the results themselves, including knowing what sort of data to expect;</span>
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866
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<pre style="margin: 0;">+<span id="LC866" class="line" lang="plaintext"> byte swapping etc.</span>
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867
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<pre style="margin: 0;">+<span id="LC867" class="line" lang="plaintext">*/</span>
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868
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<pre style="margin: 0;">+<span id="LC868" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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869
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<pre style="margin: 0;">+<span id="LC869" class="line" lang="plaintext">uint8_t *hts_idx_get_meta(hts_idx_t *idx, uint32_t *l_meta);</span>
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870
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<pre style="margin: 0;">+<span id="LC870" class="line" lang="plaintext"></span>
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871
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<pre style="margin: 0;">+<span id="LC871" class="line" lang="plaintext">/// Set extra index meta-data</span>
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872
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<pre style="margin: 0;">+<span id="LC872" class="line" lang="plaintext">/** @param idx The index</span>
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873
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<pre style="margin: 0;">+<span id="LC873" class="line" lang="plaintext"> @param l_meta Length of data</span>
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874
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<pre style="margin: 0;">+<span id="LC874" class="line" lang="plaintext"> @param meta Pointer to the extra data</span>
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875
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<pre style="margin: 0;">+<span id="LC875" class="line" lang="plaintext"> @param is_copy If not zero, a copy of the data is taken</span>
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876
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<pre style="margin: 0;">+<span id="LC876" class="line" lang="plaintext"> @return 0 on success; -1 on failure (out of memory).</span>
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877
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<pre style="margin: 0;">+<span id="LC877" class="line" lang="plaintext"></span>
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878
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<pre style="margin: 0;">+<span id="LC878" class="line" lang="plaintext"> Sets the data that is returned by hts_idx_get_meta().</span>
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879
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<pre style="margin: 0;">+<span id="LC879" class="line" lang="plaintext"></span>
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880
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<pre style="margin: 0;">+<span id="LC880" class="line" lang="plaintext"> If is_copy != 0, a copy of the input data is taken. If not, ownership of</span>
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881
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<pre style="margin: 0;">+<span id="LC881" class="line" lang="plaintext"> the data pointed to by *meta passes to the index.</span>
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882
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<pre style="margin: 0;">+<span id="LC882" class="line" lang="plaintext">*/</span>
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883
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<pre style="margin: 0;">+<span id="LC883" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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884
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<pre style="margin: 0;">+<span id="LC884" class="line" lang="plaintext">int hts_idx_set_meta(hts_idx_t *idx, uint32_t l_meta, uint8_t *meta, int is_copy);</span>
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885
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<pre style="margin: 0;">+<span id="LC885" class="line" lang="plaintext"></span>
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886
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<pre style="margin: 0;">+<span id="LC886" class="line" lang="plaintext">/// Get number of mapped and unmapped reads from an index</span>
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887
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<pre style="margin: 0;">+<span id="LC887" class="line" lang="plaintext">/** @param idx Index</span>
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888
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<pre style="margin: 0;">+<span id="LC888" class="line" lang="plaintext"> @param tid Target ID</span>
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889
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<pre style="margin: 0;">+<span id="LC889" class="line" lang="plaintext"> @param[out] mapped Location to store number of mapped reads</span>
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890
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<pre style="margin: 0;">+<span id="LC890" class="line" lang="plaintext"> @param[out] unmapped Location to store number of unmapped reads</span>
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891
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<pre style="margin: 0;">+<span id="LC891" class="line" lang="plaintext"> @return 0 on success; -1 on failure (data not available)</span>
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892
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<pre style="margin: 0;">+<span id="LC892" class="line" lang="plaintext"></span>
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893
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<pre style="margin: 0;">+<span id="LC893" class="line" lang="plaintext"> BAI and CSI indexes store information on the number of reads for each</span>
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894
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<pre style="margin: 0;">+<span id="LC894" class="line" lang="plaintext"> target that were mapped or unmapped (unmapped reads will generally have</span>
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895
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<pre style="margin: 0;">+<span id="LC895" class="line" lang="plaintext"> a paired read that is mapped to the target). This function returns this</span>
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896
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<pre style="margin: 0;">+<span id="LC896" class="line" lang="plaintext"> infomation if it is available.</span>
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897
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<pre style="margin: 0;">+<span id="LC897" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC898" class="line" lang="plaintext"> @note Cram CRAI indexes do not include this information.</span>
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899
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<pre style="margin: 0;">+<span id="LC899" class="line" lang="plaintext">*/</span>
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900
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<pre style="margin: 0;">+<span id="LC900" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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<pre style="margin: 0;">+<span id="LC901" class="line" lang="plaintext">int hts_idx_get_stat(const hts_idx_t* idx, int tid, uint64_t* mapped, uint64_t* unmapped);</span>
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902
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<pre style="margin: 0;">+<span id="LC902" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC903" class="line" lang="plaintext">/// Return the number of unplaced reads from an index</span>
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<pre style="margin: 0;">+<span id="LC904" class="line" lang="plaintext">/** @param idx Index</span>
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<pre style="margin: 0;">+<span id="LC905" class="line" lang="plaintext"> @return Unplaced reads count</span>
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906
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<pre style="margin: 0;">+<span id="LC906" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC907" class="line" lang="plaintext"> Unplaced reads are not linked to any reference (e.g. RNAME is '*' in SAM</span>
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908
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<pre style="margin: 0;">+<span id="LC908" class="line" lang="plaintext"> files).</span>
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909
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<pre style="margin: 0;">+<span id="LC909" class="line" lang="plaintext">*/</span>
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910
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<pre style="margin: 0;">+<span id="LC910" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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<pre style="margin: 0;">+<span id="LC911" class="line" lang="plaintext">uint64_t hts_idx_get_n_no_coor(const hts_idx_t* idx);</span>
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912
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<pre style="margin: 0;">+<span id="LC912" class="line" lang="plaintext"></span>
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913
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<pre style="margin: 0;">+<span id="LC913" class="line" lang="plaintext">///////////////////////////////////////////////////////////</span>
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914
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<pre style="margin: 0;">+<span id="LC914" class="line" lang="plaintext">// Region parsing</span>
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915
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<pre style="margin: 0;">+<span id="LC915" class="line" lang="plaintext"></span>
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916
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<pre style="margin: 0;">+<span id="LC916" class="line" lang="plaintext">#define HTS_PARSE_THOUSANDS_SEP 1 ///< Ignore ',' separators within numbers</span>
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917
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<pre style="margin: 0;">+<span id="LC917" class="line" lang="plaintext">#define HTS_PARSE_ONE_COORD 2 ///< chr:pos means chr:pos-pos and not chr:pos-end</span>
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918
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<pre style="margin: 0;">+<span id="LC918" class="line" lang="plaintext">#define HTS_PARSE_LIST 4 ///< Expect a comma separated list of regions. (Disables HTS_PARSE_THOUSANDS_SEP)</span>
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919
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<pre style="margin: 0;">+<span id="LC919" class="line" lang="plaintext"></span>
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920
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<pre style="margin: 0;">+<span id="LC920" class="line" lang="plaintext">/// Parse a numeric string</span>
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<td class="diff-line-num new new_line" data-linenumber="921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
921
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<pre style="margin: 0;">+<span id="LC921" class="line" lang="plaintext">/** The number may be expressed in scientific notation, and optionally may</span>
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<td class="diff-line-num new new_line" data-linenumber="922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
922
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<pre style="margin: 0;">+<span id="LC922" class="line" lang="plaintext"> contain commas in the integer part (before any decimal point or E notation).</span>
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923
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<pre style="margin: 0;">+<span id="LC923" class="line" lang="plaintext"> @param str String to be parsed</span>
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924
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<pre style="margin: 0;">+<span id="LC924" class="line" lang="plaintext"> @param strend If non-NULL, set on return to point to the first character</span>
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925
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<pre style="margin: 0;">+<span id="LC925" class="line" lang="plaintext"> in @a str after those forming the parsed number</span>
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926
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<pre style="margin: 0;">+<span id="LC926" class="line" lang="plaintext"> @param flags Or'ed-together combination of HTS_PARSE_* flags</span>
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<td class="diff-line-num new new_line" data-linenumber="927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
927
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<pre style="margin: 0;">+<span id="LC927" class="line" lang="plaintext"> @return Converted value of the parsed number.</span>
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928
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<pre style="margin: 0;">+<span id="LC928" class="line" lang="plaintext"></span>
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929
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<pre style="margin: 0;">+<span id="LC929" class="line" lang="plaintext"> When @a strend is NULL, a warning will be printed (if hts_verbose is HTS_LOG_WARNING</span>
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930
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<pre style="margin: 0;">+<span id="LC930" class="line" lang="plaintext"> or more) if there are any trailing characters after the number.</span>
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931
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<pre style="margin: 0;">+<span id="LC931" class="line" lang="plaintext">*/</span>
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932
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<pre style="margin: 0;">+<span id="LC932" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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933
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<pre style="margin: 0;">+<span id="LC933" class="line" lang="plaintext">long long hts_parse_decimal(const char *str, char **strend, int flags);</span>
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934
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<pre style="margin: 0;">+<span id="LC934" class="line" lang="plaintext"></span>
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935
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<pre style="margin: 0;">+<span id="LC935" class="line" lang="plaintext">typedef int (*hts_name2id_f)(void*, const char*);</span>
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936
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<pre style="margin: 0;">+<span id="LC936" class="line" lang="plaintext">typedef const char *(*hts_id2name_f)(void*, int);</span>
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937
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<pre style="margin: 0;">+<span id="LC937" class="line" lang="plaintext"></span>
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938
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<pre style="margin: 0;">+<span id="LC938" class="line" lang="plaintext">/// Parse a "CHR:START-END"-style region string</span>
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<td class="diff-line-num new new_line" data-linenumber="939" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
939
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<pre style="margin: 0;">+<span id="LC939" class="line" lang="plaintext">/** @param str String to be parsed</span>
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940
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<pre style="margin: 0;">+<span id="LC940" class="line" lang="plaintext"> @param beg Set on return to the 0-based start of the region</span>
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941
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<pre style="margin: 0;">+<span id="LC941" class="line" lang="plaintext"> @param end Set on return to the 1-based end of the region</span>
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942
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<pre style="margin: 0;">+<span id="LC942" class="line" lang="plaintext"> @return Pointer to the colon or '\0' after the reference sequence name,</span>
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<td class="diff-line-num new new_line" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
943
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<pre style="margin: 0;">+<span id="LC943" class="line" lang="plaintext"> or NULL if @a str could not be parsed.</span>
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944
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<pre style="margin: 0;">+<span id="LC944" class="line" lang="plaintext"></span>
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945
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<pre style="margin: 0;">+<span id="LC945" class="line" lang="plaintext"> NOTE: For compatibility with hts_parse_reg only.</span>
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946
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<pre style="margin: 0;">+<span id="LC946" class="line" lang="plaintext"> Please use hts_parse_region instead.</span>
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947
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<pre style="margin: 0;">+<span id="LC947" class="line" lang="plaintext">*/</span>
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948
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<pre style="margin: 0;">+<span id="LC948" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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949
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<pre style="margin: 0;">+<span id="LC949" class="line" lang="plaintext">const char *hts_parse_reg64(const char *str, hts_pos_t *beg, hts_pos_t *end);</span>
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950
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<pre style="margin: 0;">+<span id="LC950" class="line" lang="plaintext"></span>
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951
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<pre style="margin: 0;">+<span id="LC951" class="line" lang="plaintext">/// Parse a "CHR:START-END"-style region string</span>
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952
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<pre style="margin: 0;">+<span id="LC952" class="line" lang="plaintext">/** @param str String to be parsed</span>
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953
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<pre style="margin: 0;">+<span id="LC953" class="line" lang="plaintext"> @param beg Set on return to the 0-based start of the region</span>
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954
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<pre style="margin: 0;">+<span id="LC954" class="line" lang="plaintext"> @param end Set on return to the 1-based end of the region</span>
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955
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<pre style="margin: 0;">+<span id="LC955" class="line" lang="plaintext"> @return Pointer to the colon or '\0' after the reference sequence name,</span>
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956
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<pre style="margin: 0;">+<span id="LC956" class="line" lang="plaintext"> or NULL if @a str could not be parsed.</span>
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957
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<pre style="margin: 0;">+<span id="LC957" class="line" lang="plaintext">*/</span>
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958
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<pre style="margin: 0;">+<span id="LC958" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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<pre style="margin: 0;">+<span id="LC959" class="line" lang="plaintext">const char *hts_parse_reg(const char *str, int *beg, int *end);</span>
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960
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<pre style="margin: 0;">+<span id="LC960" class="line" lang="plaintext"></span>
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961
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<pre style="margin: 0;">+<span id="LC961" class="line" lang="plaintext">/// Parse a "CHR:START-END"-style region string</span>
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962
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<pre style="margin: 0;">+<span id="LC962" class="line" lang="plaintext">/** @param str String to be parsed</span>
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963
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<pre style="margin: 0;">+<span id="LC963" class="line" lang="plaintext"> @param tid Set on return (if not NULL) to be reference index (-1 if invalid)</span>
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964
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<pre style="margin: 0;">+<span id="LC964" class="line" lang="plaintext"> @param beg Set on return to the 0-based start of the region</span>
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965
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<pre style="margin: 0;">+<span id="LC965" class="line" lang="plaintext"> @param end Set on return to the 1-based end of the region</span>
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966
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<pre style="margin: 0;">+<span id="LC966" class="line" lang="plaintext"> @param getid Function pointer. Called if not NULL to set tid.</span>
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967
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<pre style="margin: 0;">+<span id="LC967" class="line" lang="plaintext"> @param hdr Caller data passed to getid.</span>
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968
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<pre style="margin: 0;">+<span id="LC968" class="line" lang="plaintext"> @param flags Bitwise HTS_PARSE_* flags listed above.</span>
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969
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<pre style="margin: 0;">+<span id="LC969" class="line" lang="plaintext"> @return Pointer to the byte after the end of the entire region</span>
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970
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<pre style="margin: 0;">+<span id="LC970" class="line" lang="plaintext"> specifier (including any trailing comma) on success,</span>
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971
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<pre style="margin: 0;">+<span id="LC971" class="line" lang="plaintext"> or NULL if @a str could not be parsed.</span>
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972
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<pre style="margin: 0;">+<span id="LC972" class="line" lang="plaintext"></span>
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973
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<pre style="margin: 0;">+<span id="LC973" class="line" lang="plaintext"> A variant of hts_parse_reg which is reference-id aware. It uses</span>
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974
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<pre style="margin: 0;">+<span id="LC974" class="line" lang="plaintext"> the iterator name2id callbacks to validate the region tokenisation works.</span>
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975
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<pre style="margin: 0;">+<span id="LC975" class="line" lang="plaintext"></span>
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976
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<pre style="margin: 0;">+<span id="LC976" class="line" lang="plaintext"> This is necessary due to GRCh38 HLA additions which have reference names</span>
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977
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<pre style="margin: 0;">+<span id="LC977" class="line" lang="plaintext"> like "HLA-DRB1*12:17".</span>
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978
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<pre style="margin: 0;">+<span id="LC978" class="line" lang="plaintext"></span>
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979
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<pre style="margin: 0;">+<span id="LC979" class="line" lang="plaintext"> To work around ambiguous parsing issues, eg both "chr1" and "chr1:100-200"</span>
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980
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<pre style="margin: 0;">+<span id="LC980" class="line" lang="plaintext"> are reference names, quote using curly braces.</span>
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981
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<pre style="margin: 0;">+<span id="LC981" class="line" lang="plaintext"> Thus "{chr1}:100-200" and "{chr1:100-200}" disambiguate the above example.</span>
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982
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<pre style="margin: 0;">+<span id="LC982" class="line" lang="plaintext"></span>
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983
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<pre style="margin: 0;">+<span id="LC983" class="line" lang="plaintext"> Flags are used to control how parsing works, and can be one of the below.</span>
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984
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<pre style="margin: 0;">+<span id="LC984" class="line" lang="plaintext"></span>
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985
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<pre style="margin: 0;">+<span id="LC985" class="line" lang="plaintext"> HTS_PARSE_THOUSANDS_SEP:</span>
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986
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<pre style="margin: 0;">+<span id="LC986" class="line" lang="plaintext"> Ignore commas in numbers. For example with this flag 1,234,567</span>
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987
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<pre style="margin: 0;">+<span id="LC987" class="line" lang="plaintext"> is interpreted as 1234567.</span>
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988
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<pre style="margin: 0;">+<span id="LC988" class="line" lang="plaintext"></span>
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989
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<pre style="margin: 0;">+<span id="LC989" class="line" lang="plaintext"> HTS_PARSE_LIST:</span>
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990
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<pre style="margin: 0;">+<span id="LC990" class="line" lang="plaintext"> If present, the region is assmed to be a comma separated list and</span>
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991
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<pre style="margin: 0;">+<span id="LC991" class="line" lang="plaintext"> position parsing will not contain commas (this implicitly</span>
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992
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<pre style="margin: 0;">+<span id="LC992" class="line" lang="plaintext"> clears HTS_PARSE_THOUSANDS_SEP in the call to hts_parse_decimal).</span>
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993
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<pre style="margin: 0;">+<span id="LC993" class="line" lang="plaintext"> On success the return pointer will be the start of the next region, ie</span>
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994
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<pre style="margin: 0;">+<span id="LC994" class="line" lang="plaintext"> the character after the comma. (If *ret != '\0' then the caller can</span>
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995
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<pre style="margin: 0;">+<span id="LC995" class="line" lang="plaintext"> assume another region is present in the list.)</span>
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996
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<pre style="margin: 0;">+<span id="LC996" class="line" lang="plaintext"></span>
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997
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<pre style="margin: 0;">+<span id="LC997" class="line" lang="plaintext"> If not set then positions may contain commas. In this case the return</span>
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998
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<pre style="margin: 0;">+<span id="LC998" class="line" lang="plaintext"> value should point to the end of the string, or NULL on failure.</span>
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999
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<pre style="margin: 0;">+<span id="LC999" class="line" lang="plaintext"></span>
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1000
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<pre style="margin: 0;">+<span id="LC1000" class="line" lang="plaintext"> HTS_PARSE_ONE_COORD:</span>
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1001
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<pre style="margin: 0;">+<span id="LC1001" class="line" lang="plaintext"> If present, X:100 is treated as the single base pair region X:100-100.</span>
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1002
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<pre style="margin: 0;">+<span id="LC1002" class="line" lang="plaintext"> In this case X:-100 is shorthand for X:1-100 and X:100- is X:100-<end>.</span>
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1003
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<pre style="margin: 0;">+<span id="LC1003" class="line" lang="plaintext"> (This is the standard bcftools region convention.)</span>
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1004
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<pre style="margin: 0;">+<span id="LC1004" class="line" lang="plaintext"></span>
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1005
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<pre style="margin: 0;">+<span id="LC1005" class="line" lang="plaintext"> When not set X:100 is considered to be X:100-<end> where <end> is</span>
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1006
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<pre style="margin: 0;">+<span id="LC1006" class="line" lang="plaintext"> the end of chromosome X (set to INT_MAX here). X:100- and X:-100 are</span>
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1007
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<pre style="margin: 0;">+<span id="LC1007" class="line" lang="plaintext"> invalid.</span>
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1008
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<pre style="margin: 0;">+<span id="LC1008" class="line" lang="plaintext"> (This is the standard samtools region convention.)</span>
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1009
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<pre style="margin: 0;">+<span id="LC1009" class="line" lang="plaintext"></span>
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1010
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<pre style="margin: 0;">+<span id="LC1010" class="line" lang="plaintext"> Note the supplied string expects 1 based inclusive coordinates, but the</span>
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1011
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<pre style="margin: 0;">+<span id="LC1011" class="line" lang="plaintext"> returned coordinates start from 0 and are half open, so pos0 is valid</span>
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1012
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<pre style="margin: 0;">+<span id="LC1012" class="line" lang="plaintext"> for use in e.g. "for (pos0 = beg; pos0 < end; pos0++) {...}"</span>
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1013
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<pre style="margin: 0;">+<span id="LC1013" class="line" lang="plaintext"></span>
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1014
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<pre style="margin: 0;">+<span id="LC1014" class="line" lang="plaintext"> If NULL is returned, the value in tid mat give additional information</span>
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1015
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<pre style="margin: 0;">+<span id="LC1015" class="line" lang="plaintext"> about the error:</span>
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1016
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<pre style="margin: 0;">+<span id="LC1016" class="line" lang="plaintext"></span>
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1017
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<pre style="margin: 0;">+<span id="LC1017" class="line" lang="plaintext"> -2 Failed to parse @p hdr; or out of memory</span>
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1018
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<pre style="margin: 0;">+<span id="LC1018" class="line" lang="plaintext"> -1 The reference in @p str has mismatched braces, or does not</span>
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1019
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<pre style="margin: 0;">+<span id="LC1019" class="line" lang="plaintext"> exist in @p hdr</span>
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1020
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<pre style="margin: 0;">+<span id="LC1020" class="line" lang="plaintext"> >= 0 The specified range in @p str could not be parsed</span>
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1021
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<pre style="margin: 0;">+<span id="LC1021" class="line" lang="plaintext">*/</span>
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1022
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<pre style="margin: 0;">+<span id="LC1022" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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<td class="diff-line-num new new_line" data-linenumber="1023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1023
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<pre style="margin: 0;">+<span id="LC1023" class="line" lang="plaintext">const char *hts_parse_region(const char *s, int *tid, hts_pos_t *beg,</span>
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1024
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<pre style="margin: 0;">+<span id="LC1024" class="line" lang="plaintext"> hts_pos_t *end, hts_name2id_f getid, void *hdr,</span>
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1025
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<pre style="margin: 0;">+<span id="LC1025" class="line" lang="plaintext"> int flags);</span>
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1026
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<pre style="margin: 0;">+<span id="LC1026" class="line" lang="plaintext"></span>
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1027
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<pre style="margin: 0;">+<span id="LC1027" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="1028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1028
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<pre style="margin: 0;">+<span id="LC1028" class="line" lang="plaintext">///////////////////////////////////////////////////////////</span>
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<td class="diff-line-num new new_line" data-linenumber="1029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1029
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<pre style="margin: 0;">+<span id="LC1029" class="line" lang="plaintext">// Generic iterators</span>
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1030
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<pre style="margin: 0;">+<span id="LC1030" class="line" lang="plaintext">//</span>
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<td class="diff-line-num new new_line" data-linenumber="1031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1031
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<pre style="margin: 0;">+<span id="LC1031" class="line" lang="plaintext">// These functions provide the low-level infrastructure for iterators.</span>
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<td class="diff-line-num new new_line" data-linenumber="1032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1032
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<pre style="margin: 0;">+<span id="LC1032" class="line" lang="plaintext">// Wrappers around these are used to make iterators for specific file types.</span>
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1033
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<pre style="margin: 0;">+<span id="LC1033" class="line" lang="plaintext">// See:</span>
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<td class="diff-line-num new new_line" data-linenumber="1034" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1034
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<pre style="margin: 0;">+<span id="LC1034" class="line" lang="plaintext">// htslib/sam.h for SAM/BAM/CRAM iterators</span>
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1035
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<pre style="margin: 0;">+<span id="LC1035" class="line" lang="plaintext">// htslib/vcf.h for VCF/BCF iterators</span>
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1036
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<pre style="margin: 0;">+<span id="LC1036" class="line" lang="plaintext">// htslib/tbx.h for files indexed by tabix</span>
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1037
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<pre style="margin: 0;">+<span id="LC1037" class="line" lang="plaintext"></span>
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1038
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<pre style="margin: 0;">+<span id="LC1038" class="line" lang="plaintext">/// Create a single-region iterator</span>
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1039
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<pre style="margin: 0;">+<span id="LC1039" class="line" lang="plaintext">/** @param idx Index</span>
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1040
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<pre style="margin: 0;">+<span id="LC1040" class="line" lang="plaintext"> @param tid Target ID</span>
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1041
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<pre style="margin: 0;">+<span id="LC1041" class="line" lang="plaintext"> @param beg Start of region</span>
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1042
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<pre style="margin: 0;">+<span id="LC1042" class="line" lang="plaintext"> @param end End of region</span>
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1043
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<pre style="margin: 0;">+<span id="LC1043" class="line" lang="plaintext"> @param readrec Callback to read a record from the input file</span>
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1044
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<pre style="margin: 0;">+<span id="LC1044" class="line" lang="plaintext"> @return An iterator on success; NULL on failure</span>
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1045
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<pre style="margin: 0;">+<span id="LC1045" class="line" lang="plaintext"></span>
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1046
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<pre style="margin: 0;">+<span id="LC1046" class="line" lang="plaintext"> The iterator struct returned by a successful call should be freed</span>
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<td class="diff-line-num new new_line" data-linenumber="1047" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1047
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<pre style="margin: 0;">+<span id="LC1047" class="line" lang="plaintext"> via hts_itr_destroy() when it is no longer needed.</span>
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<td class="diff-line-num new new_line" data-linenumber="1048" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1048
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<pre style="margin: 0;">+<span id="LC1048" class="line" lang="plaintext"> */</span>
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<td class="diff-line-num new new_line" data-linenumber="1049" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1049
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<pre style="margin: 0;">+<span id="LC1049" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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<td class="diff-line-num new new_line" data-linenumber="1050" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1050
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<pre style="margin: 0;">+<span id="LC1050" class="line" lang="plaintext">hts_itr_t *hts_itr_query(const hts_idx_t *idx, int tid, hts_pos_t beg, hts_pos_t end, hts_readrec_func *readrec);</span>
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<td class="diff-line-num new new_line" data-linenumber="1051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1051
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<pre style="margin: 0;">+<span id="LC1051" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="1052" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1052
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<pre style="margin: 0;">+<span id="LC1052" class="line" lang="plaintext">/// Free an iterator</span>
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<td class="diff-line-num new new_line" data-linenumber="1053" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1053
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<pre style="margin: 0;">+<span id="LC1053" class="line" lang="plaintext">/** @param iter Iterator to free</span>
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<td class="diff-line-num new new_line" data-linenumber="1054" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1054
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<pre style="margin: 0;">+<span id="LC1054" class="line" lang="plaintext"> */</span>
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<td class="diff-line-num new new_line" data-linenumber="1055" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1055
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<pre style="margin: 0;">+<span id="LC1055" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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<td class="diff-line-num new new_line" data-linenumber="1056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1056
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<pre style="margin: 0;">+<span id="LC1056" class="line" lang="plaintext">void hts_itr_destroy(hts_itr_t *iter);</span>
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<td class="diff-line-num new new_line" data-linenumber="1057" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1057
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<pre style="margin: 0;">+<span id="LC1057" class="line" lang="plaintext"></span>
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1058
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<pre style="margin: 0;">+<span id="LC1058" class="line" lang="plaintext">typedef hts_itr_t *hts_itr_query_func(const hts_idx_t *idx, int tid, hts_pos_t beg, hts_pos_t end, hts_readrec_func *readrec);</span>
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<td class="diff-line-num new new_line" data-linenumber="1059" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1059
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<pre style="margin: 0;">+<span id="LC1059" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="1060" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1060
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<pre style="margin: 0;">+<span id="LC1060" class="line" lang="plaintext">/// Create a single-region iterator from a text region specification</span>
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<td class="diff-line-num new new_line" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1061
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<pre style="margin: 0;">+<span id="LC1061" class="line" lang="plaintext">/** @param idx Index</span>
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<td class="diff-line-num new new_line" data-linenumber="1062" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1062
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<pre style="margin: 0;">+<span id="LC1062" class="line" lang="plaintext"> @param reg Region specifier</span>
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<td class="diff-line-num new new_line" data-linenumber="1063" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1063
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<pre style="margin: 0;">+<span id="LC1063" class="line" lang="plaintext"> @param getid Callback function to return the target ID for a name</span>
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<td class="diff-line-num new new_line" data-linenumber="1064" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1064
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<pre style="margin: 0;">+<span id="LC1064" class="line" lang="plaintext"> @param hdr Input file header</span>
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<td class="diff-line-num new new_line" data-linenumber="1065" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1065
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<pre style="margin: 0;">+<span id="LC1065" class="line" lang="plaintext"> @param itr_query Callback function returning an iterator for a numeric tid,</span>
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<td class="diff-line-num new new_line" data-linenumber="1066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1066
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<pre style="margin: 0;">+<span id="LC1066" class="line" lang="plaintext"> start and end position</span>
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<td class="diff-line-num new new_line" data-linenumber="1067" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1067
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<pre style="margin: 0;">+<span id="LC1067" class="line" lang="plaintext"> @param readrec Callback to read a record from the input file</span>
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<td class="diff-line-num new new_line" data-linenumber="1068" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1068
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<pre style="margin: 0;">+<span id="LC1068" class="line" lang="plaintext"> @return An iterator on success; NULL on error</span>
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1069
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<pre style="margin: 0;">+<span id="LC1069" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="1070" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1070
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<pre style="margin: 0;">+<span id="LC1070" class="line" lang="plaintext"> The iterator struct returned by a successful call should be freed</span>
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<td class="diff-line-num new new_line" data-linenumber="1071" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1071
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<pre style="margin: 0;">+<span id="LC1071" class="line" lang="plaintext"> via hts_itr_destroy() when it is no longer needed.</span>
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1072
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<pre style="margin: 0;">+<span id="LC1072" class="line" lang="plaintext"> */</span>
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1073
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<pre style="margin: 0;">+<span id="LC1073" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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<td class="diff-line-num new new_line" data-linenumber="1074" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1074
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<pre style="margin: 0;">+<span id="LC1074" class="line" lang="plaintext">hts_itr_t *hts_itr_querys(const hts_idx_t *idx, const char *reg, hts_name2id_f getid, void *hdr, hts_itr_query_func *itr_query, hts_readrec_func *readrec);</span>
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1075
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<pre style="margin: 0;">+<span id="LC1075" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="1076" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1076
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<pre style="margin: 0;">+<span id="LC1076" class="line" lang="plaintext">/// Return the next record from an iterator</span>
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<td class="diff-line-num new new_line" data-linenumber="1077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1077
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<pre style="margin: 0;">+<span id="LC1077" class="line" lang="plaintext">/** @param fp Input file handle</span>
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<td class="diff-line-num new new_line" data-linenumber="1078" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1078
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<pre style="margin: 0;">+<span id="LC1078" class="line" lang="plaintext"> @param iter Iterator</span>
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<td class="diff-line-num new new_line" data-linenumber="1079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1079
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<pre style="margin: 0;">+<span id="LC1079" class="line" lang="plaintext"> @param r Pointer to record placeholder</span>
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<td class="diff-line-num new new_line" data-linenumber="1080" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1080
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<pre style="margin: 0;">+<span id="LC1080" class="line" lang="plaintext"> @param data Data passed to the readrec callback</span>
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1081
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<pre style="margin: 0;">+<span id="LC1081" class="line" lang="plaintext"> @return >= 0 on success, -1 when there is no more data, < -1 on error</span>
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1082
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<pre style="margin: 0;">+<span id="LC1082" class="line" lang="plaintext"> */</span>
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1083
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<pre style="margin: 0;">+<span id="LC1083" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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1084
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<pre style="margin: 0;">+<span id="LC1084" class="line" lang="plaintext">int hts_itr_next(BGZF *fp, hts_itr_t *iter, void *r, void *data) HTS_RESULT_USED;</span>
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1085
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<pre style="margin: 0;">+<span id="LC1085" class="line" lang="plaintext"></span>
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1086
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<pre style="margin: 0;">+<span id="LC1086" class="line" lang="plaintext">/// Return a list of target names from an index</span>
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1087
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<pre style="margin: 0;">+<span id="LC1087" class="line" lang="plaintext">/** @param idx Index</span>
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<td class="diff-line-num new new_line" data-linenumber="1088" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1088
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<pre style="margin: 0;">+<span id="LC1088" class="line" lang="plaintext"> @param[out] n Location to store the number of targets</span>
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1089
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<pre style="margin: 0;">+<span id="LC1089" class="line" lang="plaintext"> @param getid Callback function to get the name for a target ID</span>
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1090
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<pre style="margin: 0;">+<span id="LC1090" class="line" lang="plaintext"> @param hdr Header from indexed file</span>
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1091
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<pre style="margin: 0;">+<span id="LC1091" class="line" lang="plaintext"> @return An array of pointers to the names on success; NULL on failure</span>
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1092
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<pre style="margin: 0;">+<span id="LC1092" class="line" lang="plaintext"></span>
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1093
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<pre style="margin: 0;">+<span id="LC1093" class="line" lang="plaintext"> @note The names are pointers into the header data structure. When cleaning</span>
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1094
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<pre style="margin: 0;">+<span id="LC1094" class="line" lang="plaintext"> up, only the array should be freed, not the names.</span>
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1095
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<pre style="margin: 0;">+<span id="LC1095" class="line" lang="plaintext"> */</span>
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1096
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<pre style="margin: 0;">+<span id="LC1096" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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1097
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<pre style="margin: 0;">+<span id="LC1097" class="line" lang="plaintext">const char **hts_idx_seqnames(const hts_idx_t *idx, int *n, hts_id2name_f getid, void *hdr); // free only the array, not the values</span>
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1098
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<pre style="margin: 0;">+<span id="LC1098" class="line" lang="plaintext"></span>
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1099
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<pre style="margin: 0;">+<span id="LC1099" class="line" lang="plaintext">/**********************************</span>
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1100
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<pre style="margin: 0;">+<span id="LC1100" class="line" lang="plaintext"> * Iterator with multiple regions *</span>
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1101
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<pre style="margin: 0;">+<span id="LC1101" class="line" lang="plaintext"> **********************************/</span>
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1102
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<pre style="margin: 0;">+<span id="LC1102" class="line" lang="plaintext"></span>
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1103
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<pre style="margin: 0;">+<span id="LC1103" class="line" lang="plaintext">typedef int hts_itr_multi_query_func(const hts_idx_t *idx, hts_itr_t *itr);</span>
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1104
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<pre style="margin: 0;">+<span id="LC1104" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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1105
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<pre style="margin: 0;">+<span id="LC1105" class="line" lang="plaintext">int hts_itr_multi_bam(const hts_idx_t *idx, hts_itr_t *iter);</span>
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1106
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<pre style="margin: 0;">+<span id="LC1106" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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1107
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<pre style="margin: 0;">+<span id="LC1107" class="line" lang="plaintext">int hts_itr_multi_cram(const hts_idx_t *idx, hts_itr_t *iter);</span>
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1108
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<pre style="margin: 0;">+<span id="LC1108" class="line" lang="plaintext"></span>
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1109
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<pre style="margin: 0;">+<span id="LC1109" class="line" lang="plaintext">/// Create a multi-region iterator from a region list</span>
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1110
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<pre style="margin: 0;">+<span id="LC1110" class="line" lang="plaintext">/** @param idx Index</span>
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1111
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<pre style="margin: 0;">+<span id="LC1111" class="line" lang="plaintext"> @param reglist Region list</span>
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1112
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<pre style="margin: 0;">+<span id="LC1112" class="line" lang="plaintext"> @param count Number of items in region list</span>
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1113
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<pre style="margin: 0;">+<span id="LC1113" class="line" lang="plaintext"> @param getid Callback to convert names to target IDs</span>
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1114
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<pre style="margin: 0;">+<span id="LC1114" class="line" lang="plaintext"> @param hdr Indexed file header (passed to getid)</span>
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1115
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<pre style="margin: 0;">+<span id="LC1115" class="line" lang="plaintext"> @param itr_specific Filetype-specific callback function</span>
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1116
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<pre style="margin: 0;">+<span id="LC1116" class="line" lang="plaintext"> @param readrec Callback to read an input file record</span>
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1117
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<pre style="margin: 0;">+<span id="LC1117" class="line" lang="plaintext"> @param seek Callback to seek in the input file</span>
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1118
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<pre style="margin: 0;">+<span id="LC1118" class="line" lang="plaintext"> @param tell Callback to return current input file location</span>
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<td class="diff-line-num new new_line" data-linenumber="1119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1119
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<pre style="margin: 0;">+<span id="LC1119" class="line" lang="plaintext"> @return An iterator on success; NULL on failure</span>
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1120
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<pre style="margin: 0;">+<span id="LC1120" class="line" lang="plaintext"></span>
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1121
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<pre style="margin: 0;">+<span id="LC1121" class="line" lang="plaintext"> The iterator struct returned by a successful call should be freed</span>
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1122
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<pre style="margin: 0;">+<span id="LC1122" class="line" lang="plaintext"> via hts_itr_destroy() when it is no longer needed.</span>
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1123
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<pre style="margin: 0;">+<span id="LC1123" class="line" lang="plaintext"> */</span>
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<td class="diff-line-num new new_line" data-linenumber="1124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1124
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<pre style="margin: 0;">+<span id="LC1124" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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<td class="diff-line-num new new_line" data-linenumber="1125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1125
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<pre style="margin: 0;">+<span id="LC1125" class="line" lang="plaintext">hts_itr_t *hts_itr_regions(const hts_idx_t *idx, hts_reglist_t *reglist, int count, hts_name2id_f getid, void *hdr, hts_itr_multi_query_func *itr_specific, hts_readrec_func *readrec, hts_seek_func *seek, hts_tell_func *tell);</span>
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1126
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<pre style="margin: 0;">+<span id="LC1126" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="1127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1127
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<pre style="margin: 0;">+<span id="LC1127" class="line" lang="plaintext">/// Return the next record from an iterator</span>
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<td class="diff-line-num new new_line" data-linenumber="1128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1128
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<pre style="margin: 0;">+<span id="LC1128" class="line" lang="plaintext">/** @param fp Input file handle</span>
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1129
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<pre style="margin: 0;">+<span id="LC1129" class="line" lang="plaintext"> @param iter Iterator</span>
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<td class="diff-line-num new new_line" data-linenumber="1130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1130
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<pre style="margin: 0;">+<span id="LC1130" class="line" lang="plaintext"> @param r Pointer to record placeholder</span>
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<td class="diff-line-num new new_line" data-linenumber="1131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1131
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<pre style="margin: 0;">+<span id="LC1131" class="line" lang="plaintext"> @return >= 0 on success, -1 when there is no more data, < -1 on error</span>
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<td class="diff-line-num new new_line" data-linenumber="1132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1132
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<pre style="margin: 0;">+<span id="LC1132" class="line" lang="plaintext"> */</span>
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1133
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<pre style="margin: 0;">+<span id="LC1133" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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<td class="diff-line-num new new_line" data-linenumber="1134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1134
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<pre style="margin: 0;">+<span id="LC1134" class="line" lang="plaintext">int hts_itr_multi_next(htsFile *fd, hts_itr_t *iter, void *r);</span>
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1135
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<pre style="margin: 0;">+<span id="LC1135" class="line" lang="plaintext"></span>
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1136
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<pre style="margin: 0;">+<span id="LC1136" class="line" lang="plaintext">/// Create a region list from a char array</span>
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1137
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<pre style="margin: 0;">+<span id="LC1137" class="line" lang="plaintext">/** @param argv Char array of target:interval elements, e.g. chr1:2500-3600, chr1:5100, chr2</span>
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1138
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<pre style="margin: 0;">+<span id="LC1138" class="line" lang="plaintext"> @param argc Number of items in the array</span>
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<td class="diff-line-num new new_line" data-linenumber="1139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1139
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<pre style="margin: 0;">+<span id="LC1139" class="line" lang="plaintext"> @param r_count Pointer to the number of items in the resulting region list</span>
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1140
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<pre style="margin: 0;">+<span id="LC1140" class="line" lang="plaintext"> @param hdr Header for the sam/bam/cram file</span>
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1141
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<pre style="margin: 0;">+<span id="LC1141" class="line" lang="plaintext"> @param getid Callback to convert target names to target ids.</span>
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1142
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<pre style="margin: 0;">+<span id="LC1142" class="line" lang="plaintext"> @return A region list on success, NULL on failure</span>
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1143
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<pre style="margin: 0;">+<span id="LC1143" class="line" lang="plaintext"></span>
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1144
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<pre style="margin: 0;">+<span id="LC1144" class="line" lang="plaintext"> The hts_reglist_t struct returned by a successful call should be freed</span>
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<td class="diff-line-num new new_line" data-linenumber="1145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1145
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<pre style="margin: 0;">+<span id="LC1145" class="line" lang="plaintext"> via hts_reglist_free() when it is no longer needed.</span>
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1146
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<pre style="margin: 0;">+<span id="LC1146" class="line" lang="plaintext"> */</span>
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1147
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<pre style="margin: 0;">+<span id="LC1147" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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1148
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<pre style="margin: 0;">+<span id="LC1148" class="line" lang="plaintext">hts_reglist_t *hts_reglist_create(char **argv, int argc, int *r_count, void *hdr, hts_name2id_f getid);</span>
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1149
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<pre style="margin: 0;">+<span id="LC1149" class="line" lang="plaintext"></span>
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1150
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<pre style="margin: 0;">+<span id="LC1150" class="line" lang="plaintext">/// Free a region list</span>
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1151
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<pre style="margin: 0;">+<span id="LC1151" class="line" lang="plaintext">/** @param reglist Region list</span>
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1152
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<pre style="margin: 0;">+<span id="LC1152" class="line" lang="plaintext"> @param count Number of items in the list</span>
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1153
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<pre style="margin: 0;">+<span id="LC1153" class="line" lang="plaintext"> */</span>
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1154
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<pre style="margin: 0;">+<span id="LC1154" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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1155
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<pre style="margin: 0;">+<span id="LC1155" class="line" lang="plaintext">void hts_reglist_free(hts_reglist_t *reglist, int count);</span>
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1156
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<pre style="margin: 0;">+<span id="LC1156" class="line" lang="plaintext"></span>
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1157
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<pre style="margin: 0;">+<span id="LC1157" class="line" lang="plaintext">/// Free a multi-region iterator</span>
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1158
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<pre style="margin: 0;">+<span id="LC1158" class="line" lang="plaintext">/** @param iter Iterator to free</span>
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1159
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<pre style="margin: 0;">+<span id="LC1159" class="line" lang="plaintext"> */</span>
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1160
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<pre style="margin: 0;">+<span id="LC1160" class="line" lang="plaintext">#define hts_itr_multi_destroy(iter) hts_itr_destroy(iter)</span>
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1161
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<pre style="margin: 0;">+<span id="LC1161" class="line" lang="plaintext"></span>
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1162
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<pre style="margin: 0;">+<span id="LC1162" class="line" lang="plaintext"></span>
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1163
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<pre style="margin: 0;">+<span id="LC1163" class="line" lang="plaintext"> /**</span>
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1164
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<pre style="margin: 0;">+<span id="LC1164" class="line" lang="plaintext"> * hts_file_type() - Convenience function to determine file type</span>
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1165
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<pre style="margin: 0;">+<span id="LC1165" class="line" lang="plaintext"> * DEPRECATED: This function has been replaced by hts_detect_format().</span>
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1166
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<pre style="margin: 0;">+<span id="LC1166" class="line" lang="plaintext"> * It and these FT_* macros will be removed in a future HTSlib release.</span>
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1167
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<pre style="margin: 0;">+<span id="LC1167" class="line" lang="plaintext"> */</span>
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1168
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<pre style="margin: 0;">+<span id="LC1168" class="line" lang="plaintext"> #define FT_UNKN 0</span>
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1169
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<pre style="margin: 0;">+<span id="LC1169" class="line" lang="plaintext"> #define FT_GZ 1</span>
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1170
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<pre style="margin: 0;">+<span id="LC1170" class="line" lang="plaintext"> #define FT_VCF 2</span>
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1171
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<pre style="margin: 0;">+<span id="LC1171" class="line" lang="plaintext"> #define FT_VCF_GZ (FT_GZ|FT_VCF)</span>
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1172
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<pre style="margin: 0;">+<span id="LC1172" class="line" lang="plaintext"> #define FT_BCF (1<<2)</span>
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1173
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<pre style="margin: 0;">+<span id="LC1173" class="line" lang="plaintext"> #define FT_BCF_GZ (FT_GZ|FT_BCF)</span>
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1174
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<pre style="margin: 0;">+<span id="LC1174" class="line" lang="plaintext"> #define FT_STDIN (1<<3)</span>
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1175
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<pre style="margin: 0;">+<span id="LC1175" class="line" lang="plaintext"> HTSLIB_EXPORT</span>
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1176
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<pre style="margin: 0;">+<span id="LC1176" class="line" lang="plaintext"> int hts_file_type(const char *fname);</span>
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1177
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<pre style="margin: 0;">+<span id="LC1177" class="line" lang="plaintext"></span>
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1178
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<pre style="margin: 0;">+<span id="LC1178" class="line" lang="plaintext"></span>
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1179
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<pre style="margin: 0;">+<span id="LC1179" class="line" lang="plaintext">/***************************</span>
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1180
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<pre style="margin: 0;">+<span id="LC1180" class="line" lang="plaintext"> * Revised MAQ error model *</span>
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1181
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<pre style="margin: 0;">+<span id="LC1181" class="line" lang="plaintext"> ***************************/</span>
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1182
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<pre style="margin: 0;">+<span id="LC1182" class="line" lang="plaintext"></span>
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1183
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<pre style="margin: 0;">+<span id="LC1183" class="line" lang="plaintext">struct errmod_t;</span>
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1184
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<pre style="margin: 0;">+<span id="LC1184" class="line" lang="plaintext">typedef struct errmod_t errmod_t;</span>
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1185
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<pre style="margin: 0;">+<span id="LC1185" class="line" lang="plaintext"></span>
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1186
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<pre style="margin: 0;">+<span id="LC1186" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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1187
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<pre style="margin: 0;">+<span id="LC1187" class="line" lang="plaintext">errmod_t *errmod_init(double depcorr);</span>
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1188
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<pre style="margin: 0;">+<span id="LC1188" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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1189
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<pre style="margin: 0;">+<span id="LC1189" class="line" lang="plaintext">void errmod_destroy(errmod_t *em);</span>
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1190
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<pre style="margin: 0;">+<span id="LC1190" class="line" lang="plaintext"></span>
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1191
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<pre style="margin: 0;">+<span id="LC1191" class="line" lang="plaintext">/*</span>
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1192
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<pre style="margin: 0;">+<span id="LC1192" class="line" lang="plaintext"> n: number of bases</span>
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1193
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<pre style="margin: 0;">+<span id="LC1193" class="line" lang="plaintext"> m: maximum base</span>
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1194
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<pre style="margin: 0;">+<span id="LC1194" class="line" lang="plaintext"> bases[i]: qual:6, strand:1, base:4</span>
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1195
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<pre style="margin: 0;">+<span id="LC1195" class="line" lang="plaintext"> q[i*m+j]: phred-scaled likelihood of (i,j)</span>
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1196
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<pre style="margin: 0;">+<span id="LC1196" class="line" lang="plaintext"> */</span>
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1197
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<pre style="margin: 0;">+<span id="LC1197" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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1198
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<pre style="margin: 0;">+<span id="LC1198" class="line" lang="plaintext">int errmod_cal(const errmod_t *em, int n, int m, uint16_t *bases, float *q);</span>
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1199
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<pre style="margin: 0;">+<span id="LC1199" class="line" lang="plaintext"></span>
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1200
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<pre style="margin: 0;">+<span id="LC1200" class="line" lang="plaintext"></span>
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1201
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<pre style="margin: 0;">+<span id="LC1201" class="line" lang="plaintext">/*****************************************************</span>
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1202
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<pre style="margin: 0;">+<span id="LC1202" class="line" lang="plaintext"> * Probabilistic banded glocal alignment *</span>
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1203
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<pre style="margin: 0;">+<span id="LC1203" class="line" lang="plaintext"> * See https://doi.org/10.1093/bioinformatics/btr076 *</span>
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1204
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<pre style="margin: 0;">+<span id="LC1204" class="line" lang="plaintext"> *****************************************************/</span>
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1205
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<pre style="margin: 0;">+<span id="LC1205" class="line" lang="plaintext"></span>
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1206
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<pre style="margin: 0;">+<span id="LC1206" class="line" lang="plaintext">typedef struct probaln_par_t {</span>
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1207
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<pre style="margin: 0;">+<span id="LC1207" class="line" lang="plaintext"> float d, e;</span>
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1208
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<pre style="margin: 0;">+<span id="LC1208" class="line" lang="plaintext"> int bw;</span>
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1209
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<pre style="margin: 0;">+<span id="LC1209" class="line" lang="plaintext">} probaln_par_t;</span>
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1210
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<pre style="margin: 0;">+<span id="LC1210" class="line" lang="plaintext"></span>
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1211
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<pre style="margin: 0;">+<span id="LC1211" class="line" lang="plaintext">/// Perform probabilistic banded glocal alignment</span>
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1212
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<pre style="margin: 0;">+<span id="LC1212" class="line" lang="plaintext">/** @param ref Reference sequence</span>
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<pre style="margin: 0;">+<span id="LC1213" class="line" lang="plaintext"> @param l_ref Length of reference</span>
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<pre style="margin: 0;">+<span id="LC1214" class="line" lang="plaintext"> @param query Query sequence</span>
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<pre style="margin: 0;">+<span id="LC1215" class="line" lang="plaintext"> @param l_query Length of query sequence</span>
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<pre style="margin: 0;">+<span id="LC1216" class="line" lang="plaintext"> @param iqual Query base qualities</span>
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<pre style="margin: 0;">+<span id="LC1217" class="line" lang="plaintext"> @param c Alignment parameters</span>
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<pre style="margin: 0;">+<span id="LC1218" class="line" lang="plaintext"> @param[out] state Output alignment</span>
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<pre style="margin: 0;">+<span id="LC1219" class="line" lang="plaintext"> @param[out] q Phred scaled posterior probability of state[i] being wrong</span>
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1220
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<pre style="margin: 0;">+<span id="LC1220" class="line" lang="plaintext"> @return Phred-scaled likelihood score, or INT_MIN on failure.</span>
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1221
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<pre style="margin: 0;">+<span id="LC1221" class="line" lang="plaintext"></span>
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1222
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<pre style="margin: 0;">+<span id="LC1222" class="line" lang="plaintext">The reference and query sequences are coded using integers 0,1,2,3,4 for</span>
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<pre style="margin: 0;">+<span id="LC1223" class="line" lang="plaintext">bases A,C,G,T,N respectively (N here is for any ambiguity code).</span>
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<pre style="margin: 0;">+<span id="LC1224" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC1225" class="line" lang="plaintext">On output, state and q are arrays of length l_query. The higher 30</span>
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1226
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<pre style="margin: 0;">+<span id="LC1226" class="line" lang="plaintext">bits give the reference position the query base is matched to and the</span>
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1227
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<pre style="margin: 0;">+<span id="LC1227" class="line" lang="plaintext">lower two bits can be 0 (an alignment match) or 1 (an</span>
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1228
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<pre style="margin: 0;">+<span id="LC1228" class="line" lang="plaintext">insertion). q[i] gives the phred scaled posterior probability of</span>
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1229
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<pre style="margin: 0;">+<span id="LC1229" class="line" lang="plaintext">state[i] being wrong.</span>
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1230
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<pre style="margin: 0;">+<span id="LC1230" class="line" lang="plaintext"></span>
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1231
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<pre style="margin: 0;">+<span id="LC1231" class="line" lang="plaintext">On failure, errno will be set to EINVAL if the values of l_ref or l_query</span>
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1232
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<pre style="margin: 0;">+<span id="LC1232" class="line" lang="plaintext">were invalid; or ENOMEM if a memory allocation failed.</span>
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1233
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<pre style="margin: 0;">+<span id="LC1233" class="line" lang="plaintext">*/</span>
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1234
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<pre style="margin: 0;">+<span id="LC1234" class="line" lang="plaintext"></span>
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1235
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<pre style="margin: 0;">+<span id="LC1235" class="line" lang="plaintext">HTSLIB_EXPORT</span>
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1236
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<pre style="margin: 0;">+<span id="LC1236" class="line" lang="plaintext">int probaln_glocal(const uint8_t *ref, int l_ref, const uint8_t *query, int l_query, const uint8_t *iqual, const probaln_par_t *c, int *state, uint8_t *q);</span>
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1237
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<pre style="margin: 0;">+<span id="LC1237" class="line" lang="plaintext"></span>
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1238
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<pre style="margin: 0;">+<span id="LC1238" class="line" lang="plaintext"></span>
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1239
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<pre style="margin: 0;">+<span id="LC1239" class="line" lang="plaintext"> /**********************</span>
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1240
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<pre style="margin: 0;">+<span id="LC1240" class="line" lang="plaintext"> * MD5 implementation *</span>
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1241
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<pre style="margin: 0;">+<span id="LC1241" class="line" lang="plaintext"> **********************/</span>
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1242
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<pre style="margin: 0;">+<span id="LC1242" class="line" lang="plaintext"></span>
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1243
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<pre style="margin: 0;">+<span id="LC1243" class="line" lang="plaintext"> struct hts_md5_context;</span>
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1244
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<pre style="margin: 0;">+<span id="LC1244" class="line" lang="plaintext"> typedef struct hts_md5_context hts_md5_context;</span>
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1245
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<pre style="margin: 0;">+<span id="LC1245" class="line" lang="plaintext"></span>
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1246
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<pre style="margin: 0;">+<span id="LC1246" class="line" lang="plaintext"> /*! @abstract Intialises an MD5 context.</span>
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1247
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<pre style="margin: 0;">+<span id="LC1247" class="line" lang="plaintext"> * @discussion</span>
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1248
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<pre style="margin: 0;">+<span id="LC1248" class="line" lang="plaintext"> * The expected use is to allocate an hts_md5_context using</span>
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1249
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<pre style="margin: 0;">+<span id="LC1249" class="line" lang="plaintext"> * hts_md5_init(). This pointer is then passed into one or more calls</span>
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1250
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<pre style="margin: 0;">+<span id="LC1250" class="line" lang="plaintext"> * of hts_md5_update() to compute successive internal portions of the</span>
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<pre style="margin: 0;">+<span id="LC1251" class="line" lang="plaintext"> * MD5 sum, which can then be externalised as a full 16-byte MD5sum</span>
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<td class="diff-line-num new new_line" data-linenumber="1252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1252
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<pre style="margin: 0;">+<span id="LC1252" class="line" lang="plaintext"> * calculation by calling hts_md5_final(). This can then be turned</span>
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1253
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<pre style="margin: 0;">+<span id="LC1253" class="line" lang="plaintext"> * into ASCII via hts_md5_hex().</span>
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1254
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<pre style="margin: 0;">+<span id="LC1254" class="line" lang="plaintext"> *</span>
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<td class="diff-line-num new new_line" data-linenumber="1255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1255
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<pre style="margin: 0;">+<span id="LC1255" class="line" lang="plaintext"> * To dealloate any resources created by hts_md5_init() call the</span>
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1256
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<pre style="margin: 0;">+<span id="LC1256" class="line" lang="plaintext"> * hts_md5_destroy() function.</span>
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1257
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<pre style="margin: 0;">+<span id="LC1257" class="line" lang="plaintext"> *</span>
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1258
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<pre style="margin: 0;">+<span id="LC1258" class="line" lang="plaintext"> * @return hts_md5_context pointer on success, NULL otherwise.</span>
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1259
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<pre style="margin: 0;">+<span id="LC1259" class="line" lang="plaintext"> */</span>
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1260
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<pre style="margin: 0;">+<span id="LC1260" class="line" lang="plaintext"> HTSLIB_EXPORT</span>
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1261
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<pre style="margin: 0;">+<span id="LC1261" class="line" lang="plaintext"> hts_md5_context *hts_md5_init(void);</span>
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1262
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<pre style="margin: 0;">+<span id="LC1262" class="line" lang="plaintext"></span>
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1263
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<pre style="margin: 0;">+<span id="LC1263" class="line" lang="plaintext"> /*! @abstract Updates the context with the MD5 of the data. */</span>
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1264
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<pre style="margin: 0;">+<span id="LC1264" class="line" lang="plaintext"> HTSLIB_EXPORT</span>
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1265
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<pre style="margin: 0;">+<span id="LC1265" class="line" lang="plaintext"> void hts_md5_update(hts_md5_context *ctx, const void *data, unsigned long size);</span>
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1266
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<pre style="margin: 0;">+<span id="LC1266" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="1267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1267
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<pre style="margin: 0;">+<span id="LC1267" class="line" lang="plaintext"> /*! @abstract Computes the final 128-bit MD5 hash from the given context */</span>
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<td class="diff-line-num new new_line" data-linenumber="1268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1268
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<pre style="margin: 0;">+<span id="LC1268" class="line" lang="plaintext"> HTSLIB_EXPORT</span>
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<td class="diff-line-num new new_line" data-linenumber="1269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1269
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<pre style="margin: 0;">+<span id="LC1269" class="line" lang="plaintext"> void hts_md5_final(unsigned char *digest, hts_md5_context *ctx);</span>
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1270
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<pre style="margin: 0;">+<span id="LC1270" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="1271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1271
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<pre style="margin: 0;">+<span id="LC1271" class="line" lang="plaintext"> /*! @abstract Resets an md5_context to the initial state, as returned</span>
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<td class="diff-line-num new new_line" data-linenumber="1272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1272
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<pre style="margin: 0;">+<span id="LC1272" class="line" lang="plaintext"> * by hts_md5_init().</span>
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<td class="diff-line-num new new_line" data-linenumber="1273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1273
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<pre style="margin: 0;">+<span id="LC1273" class="line" lang="plaintext"> */</span>
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<td class="diff-line-num new new_line" data-linenumber="1274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1274
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<pre style="margin: 0;">+<span id="LC1274" class="line" lang="plaintext"> HTSLIB_EXPORT</span>
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1275
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<pre style="margin: 0;">+<span id="LC1275" class="line" lang="plaintext"> void hts_md5_reset(hts_md5_context *ctx);</span>
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1276
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<pre style="margin: 0;">+<span id="LC1276" class="line" lang="plaintext"></span>
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1277
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<pre style="margin: 0;">+<span id="LC1277" class="line" lang="plaintext"> /*! @abstract Converts a 128-bit MD5 hash into a 33-byte nul-termninated</span>
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1278
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<pre style="margin: 0;">+<span id="LC1278" class="line" lang="plaintext"> * hex string.</span>
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1279
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<pre style="margin: 0;">+<span id="LC1279" class="line" lang="plaintext"> */</span>
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1280
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<pre style="margin: 0;">+<span id="LC1280" class="line" lang="plaintext"> HTSLIB_EXPORT</span>
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<td class="diff-line-num new new_line" data-linenumber="1281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1281
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<pre style="margin: 0;">+<span id="LC1281" class="line" lang="plaintext"> void hts_md5_hex(char *hex, const unsigned char *digest);</span>
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1282
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<pre style="margin: 0;">+<span id="LC1282" class="line" lang="plaintext"></span>
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1283
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<pre style="margin: 0;">+<span id="LC1283" class="line" lang="plaintext"> /*! @abstract Deallocates any memory allocated by hts_md5_init. */</span>
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1284
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<pre style="margin: 0;">+<span id="LC1284" class="line" lang="plaintext"> HTSLIB_EXPORT</span>
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1285
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<pre style="margin: 0;">+<span id="LC1285" class="line" lang="plaintext"> void hts_md5_destroy(hts_md5_context *ctx);</span>
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1286
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<pre style="margin: 0;">+<span id="LC1286" class="line" lang="plaintext"></span>
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1287
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<pre style="margin: 0;">+<span id="LC1287" class="line" lang="plaintext">static inline int hts_reg2bin(hts_pos_t beg, hts_pos_t end, int min_shift, int n_lvls)</span>
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1288
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<pre style="margin: 0;">+<span id="LC1288" class="line" lang="plaintext">{</span>
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1289
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<pre style="margin: 0;">+<span id="LC1289" class="line" lang="plaintext"> int l, s = min_shift, t = ((1<<((n_lvls<<1) + n_lvls)) - 1) / 7;</span>
</pre>
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1290
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<pre style="margin: 0;">+<span id="LC1290" class="line" lang="plaintext"> for (--end, l = n_lvls; l > 0; --l, s += 3, t -= 1<<((l<<1)+l))</span>
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1291
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<pre style="margin: 0;">+<span id="LC1291" class="line" lang="plaintext"> if (beg>>s == end>>s) return t + (beg>>s);</span>
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1292
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<pre style="margin: 0;">+<span id="LC1292" class="line" lang="plaintext"> return 0;</span>
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1293
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<pre style="margin: 0;">+<span id="LC1293" class="line" lang="plaintext">}</span>
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1294
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<pre style="margin: 0;">+<span id="LC1294" class="line" lang="plaintext"></span>
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1295
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<pre style="margin: 0;">+<span id="LC1295" class="line" lang="plaintext">static inline int hts_bin_bot(int bin, int n_lvls)</span>
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1296
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<pre style="margin: 0;">+<span id="LC1296" class="line" lang="plaintext">{</span>
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1297
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<pre style="margin: 0;">+<span id="LC1297" class="line" lang="plaintext"> int l, b;</span>
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1298
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<pre style="margin: 0;">+<span id="LC1298" class="line" lang="plaintext"> for (l = 0, b = bin; b; ++l, b = hts_bin_parent(b)); // compute the level of bin</span>
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1299
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<pre style="margin: 0;">+<span id="LC1299" class="line" lang="plaintext"> return (bin - hts_bin_first(l)) << (n_lvls - l) * 3;</span>
</pre>
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1300
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<pre style="margin: 0;">+<span id="LC1300" class="line" lang="plaintext">}</span>
</pre>
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1301
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<pre style="margin: 0;">+<span id="LC1301" class="line" lang="plaintext"></span>
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1302
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<pre style="margin: 0;">+<span id="LC1302" class="line" lang="plaintext">/**************</span>
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<td class="diff-line-num new new_line" data-linenumber="1303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1303
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<pre style="margin: 0;">+<span id="LC1303" class="line" lang="plaintext"> * Endianness *</span>
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<td class="diff-line-num new new_line" data-linenumber="1304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1304
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<pre style="margin: 0;">+<span id="LC1304" class="line" lang="plaintext"> **************/</span>
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<td class="diff-line-num new new_line" data-linenumber="1305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1305
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<pre style="margin: 0;">+<span id="LC1305" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="1306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1306
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<pre style="margin: 0;">+<span id="LC1306" class="line" lang="plaintext">static inline int ed_is_big(void)</span>
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<td class="diff-line-num new new_line" data-linenumber="1307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1307
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<pre style="margin: 0;">+<span id="LC1307" class="line" lang="plaintext">{</span>
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<td class="diff-line-num new new_line" data-linenumber="1308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1308
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<pre style="margin: 0;">+<span id="LC1308" class="line" lang="plaintext"> long one= 1;</span>
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<td class="diff-line-num new new_line" data-linenumber="1309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1309
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<pre style="margin: 0;">+<span id="LC1309" class="line" lang="plaintext"> return !(*((char *)(&one)));</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1310
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<pre style="margin: 0;">+<span id="LC1310" class="line" lang="plaintext">}</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1311
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<pre style="margin: 0;">+<span id="LC1311" class="line" lang="plaintext">static inline uint16_t ed_swap_2(uint16_t v)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1312
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<pre style="margin: 0;">+<span id="LC1312" class="line" lang="plaintext">{</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1313
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<pre style="margin: 0;">+<span id="LC1313" class="line" lang="plaintext"> return (uint16_t)(((v & 0x00FF00FFU) << 8) | ((v & 0xFF00FF00U) >> 8));</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1314
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<pre style="margin: 0;">+<span id="LC1314" class="line" lang="plaintext">}</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1315
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<pre style="margin: 0;">+<span id="LC1315" class="line" lang="plaintext">static inline void *ed_swap_2p(void *x)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1316
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<pre style="margin: 0;">+<span id="LC1316" class="line" lang="plaintext">{</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1317
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<pre style="margin: 0;">+<span id="LC1317" class="line" lang="plaintext"> *(uint16_t*)x = ed_swap_2(*(uint16_t*)x);</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1318
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<pre style="margin: 0;">+<span id="LC1318" class="line" lang="plaintext"> return x;</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1319
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<pre style="margin: 0;">+<span id="LC1319" class="line" lang="plaintext">}</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1320
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<pre style="margin: 0;">+<span id="LC1320" class="line" lang="plaintext">static inline uint32_t ed_swap_4(uint32_t v)</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1321
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<pre style="margin: 0;">+<span id="LC1321" class="line" lang="plaintext">{</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1322
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<pre style="margin: 0;">+<span id="LC1322" class="line" lang="plaintext"> v = ((v & 0x0000FFFFU) << 16) | (v >> 16);</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1323
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<pre style="margin: 0;">+<span id="LC1323" class="line" lang="plaintext"> return ((v & 0x00FF00FFU) << 8) | ((v & 0xFF00FF00U) >> 8);</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1324
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<pre style="margin: 0;">+<span id="LC1324" class="line" lang="plaintext">}</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1325
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<pre style="margin: 0;">+<span id="LC1325" class="line" lang="plaintext">static inline void *ed_swap_4p(void *x)</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1326
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<pre style="margin: 0;">+<span id="LC1326" class="line" lang="plaintext">{</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1327
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<pre style="margin: 0;">+<span id="LC1327" class="line" lang="plaintext"> *(uint32_t*)x = ed_swap_4(*(uint32_t*)x);</span>
</pre>
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1328
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<pre style="margin: 0;">+<span id="LC1328" class="line" lang="plaintext"> return x;</span>
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1329
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<pre style="margin: 0;">+<span id="LC1329" class="line" lang="plaintext">}</span>
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1330
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<pre style="margin: 0;">+<span id="LC1330" class="line" lang="plaintext">static inline uint64_t ed_swap_8(uint64_t v)</span>
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1331
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<pre style="margin: 0;">+<span id="LC1331" class="line" lang="plaintext">{</span>
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1332
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<pre style="margin: 0;">+<span id="LC1332" class="line" lang="plaintext"> v = ((v & 0x00000000FFFFFFFFLLU) << 32) | (v >> 32);</span>
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1333
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<pre style="margin: 0;">+<span id="LC1333" class="line" lang="plaintext"> v = ((v & 0x0000FFFF0000FFFFLLU) << 16) | ((v & 0xFFFF0000FFFF0000LLU) >> 16);</span>
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1334
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<pre style="margin: 0;">+<span id="LC1334" class="line" lang="plaintext"> return ((v & 0x00FF00FF00FF00FFLLU) << 8) | ((v & 0xFF00FF00FF00FF00LLU) >> 8);</span>
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1335
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<pre style="margin: 0;">+<span id="LC1335" class="line" lang="plaintext">}</span>
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1336
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<pre style="margin: 0;">+<span id="LC1336" class="line" lang="plaintext">static inline void *ed_swap_8p(void *x)</span>
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1337
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<pre style="margin: 0;">+<span id="LC1337" class="line" lang="plaintext">{</span>
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1338
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<pre style="margin: 0;">+<span id="LC1338" class="line" lang="plaintext"> *(uint64_t*)x = ed_swap_8(*(uint64_t*)x);</span>
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1339
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<pre style="margin: 0;">+<span id="LC1339" class="line" lang="plaintext"> return x;</span>
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1340
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<pre style="margin: 0;">+<span id="LC1340" class="line" lang="plaintext">}</span>
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1341
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<pre style="margin: 0;">+<span id="LC1341" class="line" lang="plaintext"></span>
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1342
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<pre style="margin: 0;">+<span id="LC1342" class="line" lang="plaintext">#ifdef __cplusplus</span>
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1343
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<pre style="margin: 0;">+<span id="LC1343" class="line" lang="plaintext">}</span>
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1344
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<pre style="margin: 0;">+<span id="LC1344" class="line" lang="plaintext">#endif</span>
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1345
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<pre style="margin: 0;">+<span id="LC1345" class="line" lang="plaintext"></span>
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1346
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<pre style="margin: 0;">+<span id="LC1346" class="line" lang="plaintext">#endif</span></pre>
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<li id="029f45b5a6618d3c762af054ae12f411ce704a81">
<a href="https://salsa.debian.org/med-team/htslib/compare/61e050b9d3d5e587cb5a4628fa61111b344ee4ed...df4af758e24c513eb9ac898ba9eac395eef8591a#029f45b5a6618d3c762af054ae12f411ce704a81"><strong>htslib/vcf.h</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1390" style="width: 35px; color: rgba(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="1390" style="width: 35px; color: rgba(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">@@ -1390,10 +1390,10 @@ static inline int bcf_enc_int1(kstring_t *s, int32_t x)</td>
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1390
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1390
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<pre style="margin: 0;"> <span id="LC1390" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> @param[out] q Location to store an updated value for p</span></span>
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1391
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1391
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<pre style="margin: 0;"> <span id="LC1391" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> @return The integer value, or zero if @p type is not valid.</span></span>
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1392
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1392
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<pre style="margin: 0;"> <span id="LC1392" class="line" lang="c"></span>
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1393
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<pre style="margin: 0;">-<span id="LC1393" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">If @p type is not one of BCF_BT_INT8, BCF_BT_INT16<span class="idiff left right"> or BCF_BT_INT32, zero</span></span></span>
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1394
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<pre style="margin: 0;">-<span id="LC1394" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right">will be returned and @p *q will not be updated. Otherwise, the integer</span></span></span>
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<pre style="margin: 0;">-<span id="LC1395" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right">value will be returned and @p *q will be set to the memory location</span></span></span>
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<pre style="margin: 0;">-<span id="LC1396" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">immediately following the integer value.</span></span>
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<pre style="margin: 0;">+<span id="LC1393" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">If @p type is not one of BCF_BT_INT8, BCF_BT_INT16<span class="idiff left right">, BCF_BT_INT32 or</span></span></span>
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<pre style="margin: 0;">+<span id="LC1394" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right">BCF_BT_INT64, zero will be returned and @p *q will not be updated.</span></span></span>
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<pre style="margin: 0;">+<span id="LC1395" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right">Otherwise, the integer value will be returned and @p *q will be set</span></span></span>
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<pre style="margin: 0;">+<span id="LC1396" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right">to the memory location </span>immediately following the integer value.</span></span>
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1397
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1397
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<pre style="margin: 0;"> <span id="LC1397" class="line" lang="c"></span>
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1398
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<pre style="margin: 0;"> <span id="LC1398" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">Cautious callers can detect invalid type codes by checking that *q has</span></span>
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<pre style="margin: 0;"> <span id="LC1399" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">actually been updated.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1411" style="width: 35px; color: rgba(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">@@ -1411,7 +1411,7 @@ static inline int64_t bcf_dec_int1(const uint8_t *p, int type, uint8_t **q)</td>
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1411
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<pre style="margin: 0;"> <span id="LC1411" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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1412
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1412
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<pre style="margin: 0;"> <span id="LC1412" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">le_to_i32</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">);</span></span>
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1413
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1413
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<pre style="margin: 0;"> <span id="LC1413" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">type</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">BCF_BT_INT64</span><span class="p">)</span> <span class="p">{</span></span>
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1414
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<pre style="margin: 0;">-<span id="LC1414" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;"><span class="idiff left right">4</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1414" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;"><span class="idiff left right">8</span></span><span class="p">;</span></span>
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1415
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1415
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<pre style="margin: 0;"> <span id="LC1415" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">le_to_i64</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">);</span></span>
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1416
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1416
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<pre style="margin: 0;"> <span id="LC1416" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// Invalid type.</span></span>
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1417
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1417
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<pre style="margin: 0;"> <span id="LC1417" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">1 10010000110 . G <DEL> 0 . SVTYPE=DEL;SVLEN=-890;END=10010001000 PL 0,1,45</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">1 10010000110 . G <DEL> 0 . SVTYPE=DEL;SVLEN=-890;END=10010001000<span class="idiff left right">;QS=1,0</span> PL 0,1,45</span></pre>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -213,4 +213,4 @@</td>
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="plaintext">1 10010000107 . G <*> 0 . DP=1;I16=0,1,0,0,33,1089,0,0,29,841,0,0,2,4,0,0;QS=1,0;MQ0F=0 PL 0,3,29</span>
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="plaintext">1 10010000108 . C <*> 0 . DP=1;I16=0,1,0,0,32,1024,0,0,29,841,0,0,1,1,0,0;QS=1,0;MQ0F=0 PL 0,3,29</span>
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="plaintext">1 10010000109 . A <*> 0 . DP=1;I16=0,1,0,0,35,1225,0,0,29,841,0,0,0,0,0,0;QS=1,0;MQ0F=0 PL 0,3,29</span>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="plaintext">1 10010000110 . G <DEL> 0 . SVTYPE=DEL;SVLEN=-890;END=10010001000 PL 0,1,45</span></pre>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="plaintext">1 10010000110 . G <DEL> 0 . SVTYPE=DEL;SVLEN=-890;END=10010001000<span class="idiff left right">;QS=1,0</span> PL 0,1,45</span></pre>
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<a href="https://salsa.debian.org/med-team/htslib/compare/61e050b9d3d5e587cb5a4628fa61111b344ee4ed...df4af758e24c513eb9ac898ba9eac395eef8591a#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">@@ -660,18 +660,19 @@ sub test_view</td>
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<pre style="margin: 0;"> <span id="LC660" class="line" lang="perl"> <span class="nv" style="color: #008080;">testv</span> <span class="nv" style="color: #008080;">$opts</span><span class="p">,</span> <span class="p">"</span><span class="s2" style="color: #d14;">./test_view </span><span class="si" style="color: #d14;">$tv_args</span><span class="s2" style="color: #d14;"> -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110</span><span class="p">";</span></span>
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<pre style="margin: 0;"> <span id="LC661" class="line" lang="perl"> <span class="nv" style="color: #008080;">testv</span> <span class="nv" style="color: #008080;">$opts</span><span class="p">,</span> <span class="p">"</span><span class="s2" style="color: #d14;">./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam</span><span class="p">";</span></span>
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<pre style="margin: 0;"> <span id="LC662" class="line" lang="perl"></span>
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<pre style="margin: 0;">-<span id="LC663" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># VCF round trip</span></span>
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<pre style="margin: 0;">-<span id="LC664" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">unlink</span><span class="p">("</span><span class="s2" style="color: #d14;">longrefs/index.tmp.vcf.gz.csi</span><span class="p">");</span> <span class="c1" style="color: #998; font-style: italic;"># To stop vcf_hdr_read from reading a stale index</span></span>
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<pre style="margin: 0;">-<span id="LC665" class="line" lang="perl"> <span class="nv" style="color: #008080;">testv</span> <span class="nv" style="color: #008080;">$opts</span><span class="p">,</span> <span class="p">"</span><span class="s2" style="color: #d14;">./test_view </span><span class="si" style="color: #d14;">$tv_args</span><span class="s2" style="color: #d14;"> -z -p longrefs/index.tmp.vcf.gz -x longrefs/index.tmp.vcf.gz.csi.otf -m 14 longrefs/index.vcf</span><span class="p">";</span></span>
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<pre style="margin: 0;">-<span id="LC666" class="line" lang="perl"> <span class="nv" style="color: #008080;">testv</span> <span class="nv" style="color: #008080;">$opts</span><span class="p">,</span> <span class="p">"</span><span class="s2" style="color: #d14;">./test_view </span><span class="si" style="color: #d14;">$tv_args</span><span class="s2" style="color: #d14;"> -p longrefs/index.tmp.vcf_ longrefs/index.tmp.vcf.gz</span><span class="p">";</span></span>
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<pre style="margin: 0;">-<span id="LC667" class="line" lang="perl"> <span class="nv" style="color: #008080;">testv</span> <span class="nv" style="color: #008080;">$opts</span><span class="p">,</span> <span class="p">"</span><span class="s2" style="color: #d14;">cmp longrefs/index.vcf longrefs/index.tmp.vcf_</span><span class="p">";</span></span>
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<pre style="margin: 0;">-<span id="LC668" class="line" lang="perl"></span>
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<pre style="margin: 0;">-<span id="LC669" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Build index and compare with on-the-fly one made earlier.</span></span>
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670
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<pre style="margin: 0;">-<span id="LC670" class="line" lang="perl"> <span class="nv" style="color: #008080;">test_compare</span> <span class="nv" style="color: #008080;">$opts</span><span class="p">,</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;">{path}/test_index -c longrefs/index.tmp.vcf.gz</span><span class="p">",</span> <span class="p">"</span><span class="s2" style="color: #d14;">longrefs/index.tmp.vcf.gz.csi.otf</span><span class="p">",</span> <span class="p">"</span><span class="s2" style="color: #d14;">longrefs/index.tmp.vcf.gz.csi</span><span class="p">",</span> <span class="nv" style="color: #008080;">gz</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="LC671" class="line" lang="perl"></span>
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<pre style="margin: 0;">-<span id="LC672" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># test_view can't do indexed look-ups on vcf, but we can use tabix</span></span>
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<pre style="margin: 0;">-<span id="LC673" class="line" lang="perl"> <span class="nv" style="color: #008080;">test_compare</span> <span class="nv" style="color: #008080;">$opts</span><span class="p">,</span> <span class="p">"</span><span class="s2" style="color: #d14;">$</span><span class="si" style="color: #d14;">$opts</span><span class="s2" style="color: #d14;">{bin}/tabix longrefs/index.tmp.vcf.gz 1:10010000100-10010000105 > longrefs/index.tmp.tabix1.vcf</span><span class="p">",</span> <span class="p">"</span><span class="s2" style="color: #d14;">longrefs/index.expected1.vcf</span><span class="p">",</span> <span class="p">"</span><span class="s2" style="color: #d14;">longrefs/index.tmp.tabix1.vcf</span><span class="p">",</span> <span class="nv" style="color: #008080;">fix_newlines</span> <span class="o" style="font-weight: 600;">=></span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC674" class="line" lang="perl"> <span class="nv" style="color: #008080;">test_compare</span> <span class="nv" style="color: #008080;">$opts</span><span class="p">,</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}/tabix longrefs/index.tmp.vcf.gz 1:10010000120-10010000130 > longrefs/index.tmp.tabix2.vcf</span><span class="p">",</span> <span class="p">"</span><span class="s2" style="color: #d14;">longrefs/index.expected2.vcf</span><span class="p">",</span> <span class="p">"</span><span class="s2" style="color: #d14;">longrefs/index.tmp.tabix2.vcf</span><span class="p">",</span> <span class="nv" style="color: #008080;">fix_newlines</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="LC663" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># 64-bit positions are currently not compiled in by default for VCF</span></span>
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664
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># # VCF round trip</span></span>
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665
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># unlink("longrefs/index.tmp.vcf.gz.csi"); # To stop vcf_hdr_read from reading a stale index</span></span>
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666
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># testv $opts, "./test_view $tv_args -z -p longrefs/index.tmp.vcf.gz -x longrefs/index.tmp.vcf.gz.csi.otf -m 14 longrefs/index.vcf";</span></span>
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667
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># testv $opts, "./test_view $tv_args -p longrefs/index.tmp.vcf_ longrefs/index.tmp.vcf.gz";</span></span>
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668
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># testv $opts, "cmp longrefs/index.vcf longrefs/index.tmp.vcf_";</span></span>
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669
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># # Build index and compare with on-the-fly one made earlier.</span></span>
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671
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># test_compare $opts, "$$opts{path}/test_index -c longrefs/index.tmp.vcf.gz", "longrefs/index.tmp.vcf.gz.csi.otf", "longrefs/index.tmp.vcf.gz.csi", gz=>1;</span></span>
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672
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># # test_view can't do indexed look-ups on vcf, but we can use tabix</span></span>
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674
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># test_compare $opts, "$$opts{bin}/tabix longrefs/index.tmp.vcf.gz 1:10010000100-10010000105 > longrefs/index.tmp.tabix1.vcf", "longrefs/index.expected1.vcf", "longrefs/index.tmp.tabix1.vcf", fix_newlines => 1;</span></span>
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675
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># test_compare $opts, "$$opts{bin}/tabix longrefs/index.tmp.vcf.gz 1:10010000120-10010000130 > longrefs/index.tmp.tabix2.vcf", "longrefs/index.expected2.vcf", "longrefs/index.tmp.tabix2.vcf", fix_newlines => 1;</span></span>
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<pre style="margin: 0;"> <span id="LC676" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC677" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$test_view_failures</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC678" class="line" lang="perl"> <span class="nv" style="color: #008080;">passed</span><span class="p">(</span><span class="nv" style="color: #008080;">$opts</span><span class="p">,</span> <span class="p">"</span><span class="s2" style="color: #d14;">large position tests</span><span class="p">");</span></span>
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<a href="https://salsa.debian.org/med-team/htslib/compare/61e050b9d3d5e587cb5a4628fa61111b344ee4ed...df4af758e24c513eb9ac898ba9eac395eef8591a#8a0799313a5296dac6779d2110db74c14c759325"><strong>vcf.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">@@ -59,10 +59,26 @@ HTSLIB_EXPORT</td>
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59
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">bcf_float_vector_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="mh" style="color: #099;">0x7F800002</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="c"><span class="n" style="color: #333;">HTSLIB_EXPORT</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">bcf_type_shift</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;"><span class="idiff left right">0</span></span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">bcf_type_shift</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;"><span class="idiff left right">3</span></span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">};</span></span>
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63
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63
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="c"></span>
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">bcf_idinfo_t</span> <span class="n" style="color: #333;">bcf_idinfo_def</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span> <span class="p">.</span><span class="n" style="color: #333;">info</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span> <span class="mi" style="color: #099;">15</span><span class="p">,</span> <span class="mi" style="color: #099;">15</span><span class="p">,</span> <span class="mi" style="color: #099;">15</span> <span class="p">},</span> <span class="p">.</span><span class="n" style="color: #333;">hrec</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">},</span> <span class="p">.</span><span class="n" style="color: #333;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Partial support for 64-bit POS and Number=1 INFO tags.</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Notes:</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> - the support for 64-bit values is motivated by POS and INFO/END for large genomes</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> - the use of 64-bit values does not conform to the specification</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> - cannot output 64-bit BCF and if it does, it is not compatible with anything</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> - experimental, use at your risk</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef VCF_ALLOW_INT64</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="c"> <span class="cp" style="color: #999; font-weight: 600;">#define BCF_MAX_BT_INT64 (0x7fffffffffffffff) </span><span class="cm" style="color: #998; font-style: italic;">/* INT64_MAX, for internal use only */</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="c"> <span class="cp" style="color: #999; font-weight: 600;">#define BCF_MIN_BT_INT64 -9223372036854775800LL </span><span class="cm" style="color: #998; font-style: italic;">/* INT64_MIN + 8, for internal use only */</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="c"></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define BCF_IS_64BIT (1<<30)</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="nf" style="color: #900; font-weight: 600;">dump_char</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;">buffer</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">c</span><span class="p">)</span></span>
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67
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="c"><span class="p">{</span></span>
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68
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84
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<pre style="margin: 0;"> <span id="LC84" 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 class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1267" style="width: 35px; color: rgba(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">@@ -1251,6 +1267,14 @@ static int bcf_dec_typed_int1_safe(uint8_t *p, uint8_t *end, uint8_t **q,</td>
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1251
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1267
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<pre style="margin: 0;"> <span id="LC1267" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1252
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1268
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<pre style="margin: 0;"> <span id="LC1268" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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1253
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1269
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<pre style="margin: 0;"> <span id="LC1269" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">le_to_i32</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">);</span></span>
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1270
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<pre style="margin: 0;">+<span id="LC1270" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef VCF_ALLOW_INT64</span></span>
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1271
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<pre style="margin: 0;">+<span id="LC1271" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">BCF_BT_INT64</span><span class="p">)</span> <span class="p">{</span></span>
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1272
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<pre style="margin: 0;">+<span id="LC1272" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// This case should never happen because there should be no 64-bit BCFs</span></span>
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1273
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<pre style="margin: 0;">+<span id="LC1273" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// at all, definitely not coming from htslib</span></span>
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1274
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<pre style="margin: 0;">+<span id="LC1274" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">8</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1275
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<pre style="margin: 0;">+<span id="LC1275" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">8</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1276
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<pre style="margin: 0;">+<span id="LC1276" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">le_to_i64</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">);</span></span>
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1277
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<pre style="margin: 0;">+<span id="LC1277" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1254
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<td class="diff-line-num new_line" data-linenumber="1278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1278
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<pre style="margin: 0;"> <span id="LC1278" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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1255
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1279
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<pre style="margin: 0;"> <span id="LC1279" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1256
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1280
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<pre style="margin: 0;"> <span id="LC1280" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1314" style="width: 35px; color: rgba(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">@@ -1290,6 +1314,9 @@ static int bcf_record_check(const bcf_hdr_t *hdr, bcf1_t *rec) {</td>
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1290
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1314
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<pre style="margin: 0;"> <span id="LC1314" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">reports</span><span class="p">;</span></span>
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1291
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1315
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<pre style="margin: 0;"> <span id="LC1315" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">is_integer</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">BCF_BT_INT8</span><span class="p">)</span> <span class="o" style="font-weight: 600;">|</span></span>
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1292
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<td class="diff-line-num new_line" data-linenumber="1316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1316
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<pre style="margin: 0;"> <span id="LC1316" class="line" lang="c"> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">BCF_BT_INT16</span><span class="p">)</span> <span class="o" style="font-weight: 600;">|</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1317
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<pre style="margin: 0;">+<span id="LC1317" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef VCF_ALLOW_INT64</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1318
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<pre style="margin: 0;">+<span id="LC1318" class="line" lang="c"> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">BCF_BT_INT64</span><span class="p">)</span> <span class="o" style="font-weight: 600;">|</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1319
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<pre style="margin: 0;">+<span id="LC1319" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1293
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<td class="diff-line-num new_line" data-linenumber="1320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1320
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<pre style="margin: 0;"> <span id="LC1320" class="line" lang="c"> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">BCF_BT_INT32</span><span class="p">));</span></span>
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1294
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<td class="diff-line-num new_line" data-linenumber="1321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1321
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<pre style="margin: 0;"> <span id="LC1321" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">is_valid_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">is_integer</span> <span class="o" style="font-weight: 600;">|</span></span>
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<td class="diff-line-num old_line" data-linenumber="1295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1295
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<td class="diff-line-num new_line" data-linenumber="1322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1322
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<pre style="margin: 0;"> <span id="LC1322" class="line" lang="c"> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">BCF_BT_NULL</span><span class="p">)</span> <span class="o" style="font-weight: 600;">|</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1728" style="width: 35px; color: rgba(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="1755" style="width: 35px; color: rgba(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">@@ -1728,6 +1755,12 @@ int bcf_write(htsFile *hfp, bcf_hdr_t *h, bcf1_t *v)</td>
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1728
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1755
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<pre style="margin: 0;"> <span id="LC1755" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1729
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1756
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<pre style="margin: 0;"> <span id="LC1756" class="line" lang="c"> <span class="n" style="color: #333;">bcf1_sync</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// check if the BCF record was modified</span></span>
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<td class="diff-line-num old_line" data-linenumber="1730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1730
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1757
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<pre style="margin: 0;"> <span id="LC1757" class="line" lang="c"></span>
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<td class="diff-line-num new new_line" data-linenumber="1758" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1758
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<pre style="margin: 0;">+<span id="LC1758" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">v</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">unpacked</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">BCF_IS_64BIT</span> <span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1759" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1759
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<pre style="margin: 0;">+<span id="LC1759" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1760" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1760
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<pre style="margin: 0;">+<span id="LC1760" class="line" lang="c"> <span class="n" style="color: #333;">hts_log_error</span><span class="p">(</span><span class="s" style="color: #d14;">"Data contains 64-bit values not representable in BCF. Please use VCF instead"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1761
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<pre style="margin: 0;">+<span id="LC1761" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1762
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<pre style="margin: 0;">+<span id="LC1762" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1763
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<pre style="margin: 0;">+<span id="LC1763" class="line" lang="c"></span>
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1731
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1764
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<pre style="margin: 0;"> <span id="LC1764" class="line" lang="c"> <span class="n" style="color: #333;">BGZF</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hfp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fp</span><span class="p">.</span><span class="n" style="color: #333;">bgzf</span><span class="p">;</span></span>
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1732
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<td class="diff-line-num new_line" data-linenumber="1765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1765
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<pre style="margin: 0;"> <span id="LC1765" class="line" lang="c"> <span class="k" style="font-weight: 600;">union</span> <span class="p">{</span></span>
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1733
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1766
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<pre style="margin: 0;"> <span id="LC1766" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2040" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2073" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2040,6 +2073,7 @@ int bcf_enc_vint(kstring_t *s, int n, int32_t *a, int wsize)</td>
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2040
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2073
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<pre style="margin: 0;"> <span id="LC2073" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// FIXME: check for errs in this function</span></span>
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2041
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2074
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<pre style="margin: 0;"> <span id="LC2074" class="line" lang="c"><span class="p">}</span></span>
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2042
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2075
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<pre style="margin: 0;"> <span id="LC2075" class="line" lang="c"></span>
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2076
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<pre style="margin: 0;">+<span id="LC2076" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef VCF_ALLOW_INT64</span></span>
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2043
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<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;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">bcf_enc_long1</span><span class="p">(</span><span class="n" style="color: #333;">kstring_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="p">{</span></span>
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2044
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<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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<pre style="margin: 0;"> <span id="LC2078" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="2045" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2045
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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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<pre style="margin: 0;"> <span id="LC2079" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">BCF_MAX_BT_INT32</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">BCF_MIN_BT_INT32</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2057" style="width: 35px; color: rgba(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="2091" style="width: 35px; color: rgba(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">@@ -2057,6 +2091,7 @@ static int bcf_enc_long1(kstring_t *s, int64_t x) {</td>
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2057
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2091
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<pre style="margin: 0;"> <span id="LC2091" class="line" lang="c"> <span class="p">}</span></span>
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2058
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2092
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<pre style="margin: 0;"> <span id="LC2092" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="2059" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2059
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<td class="diff-line-num new_line" data-linenumber="2093" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2093
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<pre style="margin: 0;"> <span id="LC2093" class="line" lang="c"><span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2094" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2094
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<pre style="margin: 0;">+<span id="LC2094" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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2060
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2095
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<pre style="margin: 0;"> <span id="LC2095" class="line" lang="c"></span>
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<td class="diff-line-num old_line" data-linenumber="2061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2061
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<td class="diff-line-num new_line" data-linenumber="2096" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2096
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<pre style="margin: 0;"> <span id="LC2096" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">serialize_float_array</span><span class="p">(</span><span class="n" style="color: #333;">kstring_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">a</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="2062" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2062
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<td class="diff-line-num new_line" data-linenumber="2097" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2097
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<pre style="margin: 0;"> <span id="LC2097" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">p</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2169" style="width: 35px; color: rgba(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="2204" style="width: 35px; color: rgba(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">@@ -2169,6 +2204,7 @@ static int vcf_parse_format(kstring_t *s, const bcf_hdr_t *h, bcf1_t *v, char *p</td>
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2169
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<td class="diff-line-num new_line" data-linenumber="2204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2204
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<pre style="margin: 0;"> <span id="LC2204" class="line" lang="c"><span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="2170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2170
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<td class="diff-line-num new_line" data-linenumber="2205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2205
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<pre style="margin: 0;"> <span id="LC2205" 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;">bcf_hdr_nsamples</span><span class="p">(</span><span class="n" style="color: #333;">h</span><span class="p">)</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="2171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2171
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<td class="diff-line-num new_line" data-linenumber="2206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2206
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<pre style="margin: 0;"> <span id="LC2206" class="line" lang="c"></span>
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<td class="diff-line-num new old_line" data-linenumber="2172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2207
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<pre style="margin: 0;">+<span id="LC2207" 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;">extreme_int_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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<td class="diff-line-num old_line" data-linenumber="2172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2172
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<td class="diff-line-num new_line" data-linenumber="2208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2208
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<pre style="margin: 0;"> <span id="LC2208" 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;">r</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">t</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="2173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2173
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2209
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<pre style="margin: 0;"> <span id="LC2209" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">g</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="2174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2174
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2210
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<pre style="margin: 0;"> <span id="LC2210" class="line" lang="c"> <span class="n" style="color: #333;">khint_t</span> <span class="n" style="color: #333;">k</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2362,7 +2398,23 @@ static int vcf_parse_format(kstring_t *s, const bcf_hdr_t *h, bcf1_t *v, char *p</td>
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2362
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2398
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<pre style="margin: 0;"> <span id="LC2398" 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;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">)(</span><span class="n" style="color: #333;">z</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">buf</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">z</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">m</span><span class="p">);</span></span>
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2363
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2399
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<pre style="margin: 0;"> <span id="LC2399" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">t</span><span class="p">)</span> <span class="p">{</span></span>
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2364
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2400
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<pre style="margin: 0;"> <span id="LC2400" 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;">t</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'.'</span><span class="p">)</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bcf_int32_missing</span><span class="p">,</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">t</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// ++t to skip "."</span></span>
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2365
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<td class="diff-line-num new_line old" data-linenumber="2401" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC2365" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strtol</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">t</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">);</span></span>
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2401
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<pre style="margin: 0;">+<span id="LC2401" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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2402
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<pre style="margin: 0;">+<span id="LC2402" class="line" lang="c"> <span class="p">{</span></span>
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2403
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<pre style="margin: 0;">+<span id="LC2403" class="line" lang="c"> <span class="n" style="color: #333;">errno</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2404
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<pre style="margin: 0;">+<span id="LC2404" 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;">te</span><span class="p">;</span></span>
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2405
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<pre style="margin: 0;">+<span id="LC2405" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tmp_val</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;">t</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">te</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">);</span></span>
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2406
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<pre style="margin: 0;">+<span id="LC2406" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">te</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">errno</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">tmp_val</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BCF_MIN_BT_INT32</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">tmp_val</span><span class="o" style="font-weight: 600;">></span><span class="n" style="color: #333;">BCF_MAX_BT_INT32</span> <span class="p">)</span></span>
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2407
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<pre style="margin: 0;">+<span id="LC2407" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2408
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<pre style="margin: 0;">+<span id="LC2408" 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;">extreme_int_warned</span> <span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2409
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<pre style="margin: 0;">+<span id="LC2409" class="line" lang="c"> <span class="p">{</span></span>
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2410
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<pre style="margin: 0;">+<span id="LC2410" class="line" lang="c"> <span class="n" style="color: #333;">hts_log_warning</span><span class="p">(</span><span class="s" style="color: #d14;">"Extreme FORMAT/%s value encountered and set to missing at %s:%"</span><span class="n" style="color: #333;">PRIhts_pos</span><span class="p">,</span><span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">[</span><span class="n" style="color: #333;">BCF_DT_ID</span><span class="p">][</span><span class="n" style="color: #333;">fmt</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">key</span><span class="p">].</span><span class="n" style="color: #333;">key</span><span class="p">,</span><span class="n" style="color: #333;">bcf_seqname</span><span class="p">(</span><span class="n" style="color: #333;">h</span><span class="p">,</span><span class="n" style="color: #333;">v</span><span class="p">),</span> <span class="n" style="color: #333;">v</span><span class="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 new new_line" data-linenumber="2411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2411
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<pre style="margin: 0;">+<span id="LC2411" class="line" lang="c"> <span class="n" style="color: #333;">extreme_int_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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2412
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<pre style="margin: 0;">+<span id="LC2412" class="line" lang="c"> <span class="p">}</span></span>
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2413
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<pre style="margin: 0;">+<span id="LC2413" class="line" lang="c"> <span class="n" style="color: #333;">tmp_val</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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<td class="diff-line-num new new_line" data-linenumber="2414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2414
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<pre style="margin: 0;">+<span id="LC2414" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2366" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2415
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<pre style="margin: 0;">+<span id="LC2415" class="line" lang="c"> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp_val</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2416
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<pre style="margin: 0;">+<span id="LC2416" class="line" lang="c"> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">te</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2366" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2417
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<pre style="margin: 0;">+<span id="LC2417" class="line" lang="c"> <span class="p">}</span></span>
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2366
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<td class="diff-line-num new_line" data-linenumber="2418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2418
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<pre style="margin: 0;"> <span id="LC2418" 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;">t</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;">break</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="2367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2367
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<td class="diff-line-num new_line" data-linenumber="2419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2419
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<pre style="margin: 0;"> <span id="LC2419" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="2368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2368
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<td class="diff-line-num new_line" data-linenumber="2420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2420
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<pre style="margin: 0;"> <span id="LC2420" 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;">l</span> <span class="p">)</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bcf_int32_missing</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2469" style="width: 35px; color: rgba(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="2521" style="width: 35px; color: rgba(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">@@ -2469,6 +2521,7 @@ static int vcf_parse_format(kstring_t *s, const bcf_hdr_t *h, bcf1_t *v, char *p</td>
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2469
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<td class="diff-line-num new_line" data-linenumber="2521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2521
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<pre style="margin: 0;"> <span id="LC2521" class="line" lang="c"></span>
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<td class="diff-line-num old_line" data-linenumber="2470" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2470
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<td class="diff-line-num new_line" data-linenumber="2522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2522
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<pre style="margin: 0;"> <span id="LC2522" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">vcf_parse</span><span class="p">(</span><span class="n" style="color: #333;">kstring_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">bcf_hdr_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">h</span><span class="p">,</span> <span class="n" style="color: #333;">bcf1_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">v</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="2471" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2471
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<td class="diff-line-num new_line" data-linenumber="2523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2523
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<pre style="margin: 0;"> <span id="LC2523" class="line" lang="c"><span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2472" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2524
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<pre style="margin: 0;">+<span id="LC2524" 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;">extreme_int_warned</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;">negative_rlen_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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<td class="diff-line-num old_line" data-linenumber="2472" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2472
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<td class="diff-line-num new_line" data-linenumber="2525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2525
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<pre style="margin: 0;"> <span id="LC2525" 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="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="2473" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2473
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<td class="diff-line-num new_line" data-linenumber="2526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2526
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<pre style="margin: 0;"> <span id="LC2526" 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;">p</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">t</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="2474" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2474
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<td class="diff-line-num new_line" data-linenumber="2527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2527
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<pre style="margin: 0;"> <span id="LC2527" class="line" lang="c"> <span class="n" style="color: #333;">kstring_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">str</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2526" style="width: 35px; color: rgba(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="2579" style="width: 35px; color: rgba(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">@@ -2526,6 +2579,8 @@ int vcf_parse(kstring_t *s, const bcf_hdr_t *h, bcf1_t *v)</td>
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2526
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<td class="diff-line-num new_line" data-linenumber="2579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2579
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<pre style="margin: 0;"> <span id="LC2579" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="2527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2527
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<td class="diff-line-num new_line" data-linenumber="2580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2580
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<pre style="margin: 0;"> <span id="LC2580" class="line" lang="c"> <span class="n" style="color: #333;">v</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 old_line" data-linenumber="2528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2528
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<td class="diff-line-num new_line" data-linenumber="2581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2581
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<pre style="margin: 0;"> <span id="LC2581" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2582
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<pre style="margin: 0;">+<span id="LC2582" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">v</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">INT32_MAX</span><span class="p">)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2583
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<pre style="margin: 0;">+<span id="LC2583" class="line" lang="c"> <span class="n" style="color: #333;">v</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">unpacked</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">BCF_IS_64BIT</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="2529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2529
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2584
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<pre style="margin: 0;"> <span id="LC2584" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// ID</span></span>
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2530
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2585
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<pre style="margin: 0;"> <span id="LC2585" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="s" style="color: #d14;">"."</span><span class="p">))</span> <span class="n" style="color: #333;">bcf_enc_vchar</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="p">,</span> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">);</span></span>
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2531
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2586
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<pre style="margin: 0;"> <span id="LC2586" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">bcf_enc_size</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">BCF_BT_CHAR</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2672" style="width: 35px; color: rgba(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="2727" style="width: 35px; color: rgba(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">@@ -2672,31 +2727,77 @@ int vcf_parse(kstring_t *s, const bcf_hdr_t *h, bcf1_t *v)</td>
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2672
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2727
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<pre style="margin: 0;"> <span id="LC2727" class="line" lang="c"> <span class="n" style="color: #333;">val_a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">z</span><span class="p">;</span></span>
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2673
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2728
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<pre style="margin: 0;"> <span id="LC2728" class="line" lang="c"> <span class="p">}</span></span>
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2674
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<td class="diff-line-num new_line" data-linenumber="2729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2729
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<pre style="margin: 0;"> <span id="LC2729" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;">>></span><span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">&</span><span class="mh" style="color: #099;">0xf</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">BCF_HT_INT</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2675
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<pre style="margin: 0;">-<span id="LC2675" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Allow first value only to be 64 bit</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2676
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<pre style="margin: 0;">-<span id="LC2676" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// (for large END value)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2677
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<td class="diff-line-num new_line old" data-linenumber="2730" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC2677" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">v64</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strtoll</span><span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">te</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">);</span></span>
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2678
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<td class="diff-line-num new_line old" data-linenumber="2730" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC2678" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">te</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">val</span> <span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// conversion failed</span></span>
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2679
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<pre style="margin: 0;">-<span id="LC2679" class="line" lang="c"> <span class="n" style="color: #333;">val_a</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bcf_int32_missing</span><span class="p">;</span></span>
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2680
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<pre style="margin: 0;">-<span id="LC2680" class="line" lang="c"> <span class="n" style="color: #333;">v64</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bcf_int64_missing</span><span class="p">;</span></span>
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2681
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<pre style="margin: 0;">-<span id="LC2681" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2682
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<td class="diff-line-num new_line old" data-linenumber="2730" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC2682" class="line" lang="c"> <span class="n" style="color: #333;">val_a</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">v64</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">BCF_MIN_BT_INT32</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">v64</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">BCF_MAX_BT_INT32</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">v64</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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2730
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<pre style="margin: 0;">+<span id="LC2730" class="line" lang="c"> <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;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">val</span><span class="p">;</span></span>
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2731
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<pre style="margin: 0;">+<span id="LC2731" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">val1</span><span class="p">;</span></span>
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2732
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<pre style="margin: 0;">+<span id="LC2732" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef VCF_ALLOW_INT64</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2733
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<pre style="margin: 0;">+<span id="LC2733" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">is_int64</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2734
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<pre style="margin: 0;">+<span id="LC2734" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">n_val</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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2735
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<pre style="margin: 0;">+<span id="LC2735" class="line" lang="c"> <span class="p">{</span></span>
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2736
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<pre style="margin: 0;">+<span id="LC2736" class="line" lang="c"> <span class="n" style="color: #333;">errno</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2737
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<pre style="margin: 0;">+<span id="LC2737" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tmp_val</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strtoll</span><span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">te</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2738
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<pre style="margin: 0;">+<span id="LC2738" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">te</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">val</span> <span class="p">)</span> <span class="n" style="color: #333;">tmp_val</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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<td class="diff-line-num new new_line" data-linenumber="2739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2739
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<pre style="margin: 0;">+<span id="LC2739" 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;">te</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">errno</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">tmp_val</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BCF_MIN_BT_INT64</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">tmp_val</span><span class="o" style="font-weight: 600;">></span><span class="n" style="color: #333;">BCF_MAX_BT_INT64</span> <span class="p">)</span></span>
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2740
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<pre style="margin: 0;">+<span id="LC2740" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2741
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<pre style="margin: 0;">+<span id="LC2741" 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;">extreme_int_warned</span> <span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2742
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<pre style="margin: 0;">+<span id="LC2742" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2743
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<pre style="margin: 0;">+<span id="LC2743" class="line" lang="c"> <span class="n" style="color: #333;">hts_log_warning</span><span class="p">(</span><span class="s" style="color: #d14;">"Extreme INFO/%s value encountered and set to missing at %s:%"</span><span class="n" style="color: #333;">PRIhts_pos</span><span class="p">,</span><span class="n" style="color: #333;">key</span><span class="p">,</span><span class="n" style="color: #333;">bcf_seqname</span><span class="p">(</span><span class="n" style="color: #333;">h</span><span class="p">,</span><span class="n" style="color: #333;">v</span><span class="p">),</span> <span class="n" style="color: #333;">v</span><span class="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 new new_line" data-linenumber="2744" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2744
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<pre style="margin: 0;">+<span id="LC2744" class="line" lang="c"> <span class="n" style="color: #333;">extreme_int_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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2745
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<pre style="margin: 0;">+<span id="LC2745" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2746" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2746
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<pre style="margin: 0;">+<span id="LC2746" class="line" lang="c"> <span class="n" style="color: #333;">tmp_val</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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<td class="diff-line-num new new_line" data-linenumber="2747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2747
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<pre style="margin: 0;">+<span id="LC2747" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2748
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<pre style="margin: 0;">+<span id="LC2748" 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="2749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2749
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<pre style="margin: 0;">+<span id="LC2749" class="line" lang="c"> <span class="n" style="color: #333;">is_int64</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="2750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2750
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<pre style="margin: 0;">+<span id="LC2750" class="line" lang="c"> <span class="n" style="color: #333;">val1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp_val</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2751
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<pre style="margin: 0;">+<span id="LC2751" class="line" lang="c"> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">te</span><span class="p">;</span></span>
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2752
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<pre style="margin: 0;">+<span id="LC2752" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// this is just to avoid adding another nested block...</span></span>
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2683
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2753
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<pre style="margin: 0;"> <span id="LC2753" class="line" lang="c"> <span class="p">}</span></span>
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2684
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<td class="diff-line-num new_line old" data-linenumber="2754" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC2684" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">te</span><span class="p">;</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">','</span><span class="p">;</span> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">++</span><span class="p">);</span></span>
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2685
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<pre style="margin: 0;">-<span id="LC2685" 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;">t</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">','</span><span class="p">)</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">t</span><span class="p">;</span></span>
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2686
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<td class="diff-line-num new_line old" data-linenumber="2754" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC2686" 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;">1</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;">n_val</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">t</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2754" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2754
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<pre style="margin: 0;">+<span id="LC2754" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2755" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2755
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<pre style="margin: 0;">+<span id="LC2755" 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="n" style="color: #333;">n_val</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">t</span><span class="p">)</span></span>
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2687
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<td class="diff-line-num new_line" data-linenumber="2756" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2756
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<pre style="margin: 0;"> <span id="LC2756" class="line" lang="c"> <span class="p">{</span></span>
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2688
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<td class="diff-line-num new_line old" data-linenumber="2757" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC2688" class="line" lang="c"> <span class="n" style="color: #333;">val_a</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;">strtol</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">te</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">);</span></span>
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2689
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<td class="diff-line-num new_line old" data-linenumber="2757" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC2689" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">te</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">t</span> <span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">// conversion failed</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2690
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<td class="diff-line-num new_line old" data-linenumber="2757" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC2690" class="line" lang="c"> <span class="n" style="color: #333;">val_a</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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<td class="diff-line-num new old_line" data-linenumber="2691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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2757
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<pre style="margin: 0;">+<span id="LC2757" class="line" lang="c"> <span class="n" style="color: #333;">errno</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2758" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2758
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<pre style="margin: 0;">+<span id="LC2758" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tmp_val</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;">t</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">te</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2759" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2759
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<pre style="margin: 0;">+<span id="LC2759" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">te</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">t</span> <span class="p">)</span> <span class="n" style="color: #333;">tmp_val</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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<td class="diff-line-num new new_line" data-linenumber="2760" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2760
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<pre style="margin: 0;">+<span id="LC2760" 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;">errno</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">tmp_val</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">BCF_MIN_BT_INT32</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">tmp_val</span><span class="o" style="font-weight: 600;">></span><span class="n" style="color: #333;">BCF_MAX_BT_INT32</span> <span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2761
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<pre style="margin: 0;">+<span id="LC2761" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2762" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2762
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<pre style="margin: 0;">+<span id="LC2762" 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;">extreme_int_warned</span> <span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2763
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<pre style="margin: 0;">+<span id="LC2763" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2764" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2764
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<pre style="margin: 0;">+<span id="LC2764" class="line" lang="c"> <span class="n" style="color: #333;">hts_log_warning</span><span class="p">(</span><span class="s" style="color: #d14;">"Extreme INFO/%s value encountered and set to missing at %s:%"</span><span class="n" style="color: #333;">PRIhts_pos</span><span class="p">,</span><span class="n" style="color: #333;">key</span><span class="p">,</span><span class="n" style="color: #333;">bcf_seqname</span><span class="p">(</span><span class="n" style="color: #333;">h</span><span class="p">,</span><span class="n" style="color: #333;">v</span><span class="p">),</span> <span class="n" style="color: #333;">v</span><span class="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 new new_line" data-linenumber="2765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2765
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<pre style="margin: 0;">+<span id="LC2765" class="line" lang="c"> <span class="n" style="color: #333;">extreme_int_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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<td class="diff-line-num new new_line" data-linenumber="2766" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2766
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<pre style="margin: 0;">+<span id="LC2766" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2767
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<pre style="margin: 0;">+<span id="LC2767" class="line" lang="c"> <span class="n" style="color: #333;">tmp_val</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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2768
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<pre style="margin: 0;">+<span id="LC2768" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2769" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2769
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<pre style="margin: 0;">+<span id="LC2769" class="line" lang="c"> <span class="n" style="color: #333;">val_a</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;">tmp_val</span><span class="p">;</span></span>
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2691
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<td class="diff-line-num new_line" data-linenumber="2770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2770
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<pre style="margin: 0;"> <span id="LC2770" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">te</span><span class="p">;</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">','</span><span class="p">;</span> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">++</span><span class="p">);</span></span>
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2692
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<td class="diff-line-num new_line" data-linenumber="2771" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2771
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<pre style="margin: 0;"> <span id="LC2771" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="2693" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2693
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<td class="diff-line-num new_line" data-linenumber="2772" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2772
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<pre style="margin: 0;"> <span id="LC2772" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">n_val</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2694
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<td class="diff-line-num new_line old" data-linenumber="2773" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC2694" class="line" lang="c"> <span class="n" style="color: #333;">bcf_enc_long1</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="p">,</span> <span class="n" style="color: #333;">v64</span><span class="p">);</span></span>
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2773
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<pre style="margin: 0;">+<span id="LC2773" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef VCF_ALLOW_INT64</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2774" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2774
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<pre style="margin: 0;">+<span id="LC2774" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">is_int64</span> <span class="p">)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2775
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<pre style="margin: 0;">+<span id="LC2775" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2776
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<pre style="margin: 0;">+<span id="LC2776" class="line" lang="c"> <span class="n" style="color: #333;">v</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">unpacked</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">BCF_IS_64BIT</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2777" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2777
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<pre style="margin: 0;">+<span id="LC2777" class="line" lang="c"> <span class="n" style="color: #333;">bcf_enc_long1</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="p">,</span> <span class="n" style="color: #333;">val1</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2778" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2778
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<pre style="margin: 0;">+<span id="LC2778" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2779
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<pre style="margin: 0;">+<span id="LC2779" 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="2780" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2780
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<pre style="margin: 0;">+<span id="LC2780" class="line" lang="c"> <span class="n" style="color: #333;">bcf_enc_int1</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">)</span><span class="n" style="color: #333;">val1</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2781
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<pre style="margin: 0;">+<span id="LC2781" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2782
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<pre style="margin: 0;">+<span id="LC2782" class="line" lang="c"> <span class="n" style="color: #333;">val1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">val_a</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2783
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<pre style="margin: 0;">+<span id="LC2783" class="line" lang="c"> <span class="n" style="color: #333;">bcf_enc_int1</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">)</span><span class="n" style="color: #333;">val1</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2784
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<pre style="margin: 0;">+<span id="LC2784" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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2695
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<td class="diff-line-num new_line" data-linenumber="2785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2785
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<pre style="margin: 0;"> <span id="LC2785" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="2696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2696
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<td class="diff-line-num new_line" data-linenumber="2786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2786
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<pre style="margin: 0;"> <span id="LC2786" class="line" lang="c"> <span class="n" style="color: #333;">bcf_enc_vint</span><span class="p">(</span><span class="n" style="color: #333;">str</span><span class="p">,</span> <span class="n" style="color: #333;">n_val</span><span class="p">,</span> <span class="n" style="color: #333;">val_a</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="2697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2697
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<td class="diff-line-num new_line" data-linenumber="2787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2787
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<pre style="margin: 0;"> <span id="LC2787" class="line" lang="c"> <span class="p">}</span></span>
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2698
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<td class="diff-line-num new_line old" data-linenumber="2788" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC2698" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="s" style="color: #d14;">"END"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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2699
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<pre style="margin: 0;">-<span id="LC2699" class="line" lang="c"> <span class="n" style="color: #333;">v</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">rlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">v64</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">v</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pos</span><span class="p">;</span></span>
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2788
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<pre style="margin: 0;">+<span id="LC2788" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">n_val</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;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="s" style="color: #d14;">"END"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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2789
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<pre style="margin: 0;">+<span id="LC2789" class="line" lang="c"> <span class="p">{</span></span>
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2790
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<pre style="margin: 0;">+<span id="LC2790" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">val1</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">v</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pos</span> <span class="p">)</span></span>
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2791
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<pre style="margin: 0;">+<span id="LC2791" class="line" lang="c"> <span class="p">{</span></span>
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2792
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<pre style="margin: 0;">+<span id="LC2792" 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;">negative_rlen_warned</span> <span class="p">)</span></span>
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2793
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<pre style="margin: 0;">+<span id="LC2793" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2794
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<pre style="margin: 0;">+<span id="LC2794" class="line" lang="c"> <span class="n" style="color: #333;">hts_log_warning</span><span class="p">(</span><span class="s" style="color: #d14;">"INFO/END=%"</span><span class="n" style="color: #333;">PRIhts_pos</span><span class="s" style="color: #d14;">" is smaller than POS at %s:%"</span><span class="n" style="color: #333;">PRIhts_pos</span><span class="p">,</span><span class="n" style="color: #333;">val1</span><span class="p">,</span><span class="n" style="color: #333;">bcf_seqname</span><span class="p">(</span><span class="n" style="color: #333;">h</span><span class="p">,</span><span class="n" style="color: #333;">v</span><span class="p">),</span><span class="n" style="color: #333;">v</span><span class="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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2795
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<pre style="margin: 0;">+<span id="LC2795" class="line" lang="c"> <span class="n" style="color: #333;">negative_rlen_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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2796
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<pre style="margin: 0;">+<span id="LC2796" class="line" lang="c"> <span class="p">}</span></span>
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2797
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<pre style="margin: 0;">+<span id="LC2797" class="line" lang="c"> <span class="p">}</span></span>
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2798
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<pre style="margin: 0;">+<span id="LC2798" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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2799
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<pre style="margin: 0;">+<span id="LC2799" class="line" lang="c"> <span class="n" style="color: #333;">v</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">rlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">val1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">v</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pos</span><span class="p">;</span></span>
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2800
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<pre style="margin: 0;">+<span id="LC2800" class="line" lang="c"> <span class="p">}</span></span>
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2700
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2801
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<pre style="margin: 0;"> <span id="LC2801" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;">>></span><span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">&</span><span class="mh" style="color: #099;">0xf</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">BCF_HT_REAL</span><span class="p">)</span> <span class="p">{</span></span>
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2701
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2802
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<pre style="margin: 0;"> <span id="LC2802" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">val_f</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">val_a</span><span class="p">;</span></span>
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2702
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2803
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<pre style="margin: 0;"> <span id="LC2803" 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;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">val</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;">n_val</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">t</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3835" style="width: 35px; color: rgba(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">@@ -3835,6 +3936,7 @@ int bcf_update_info(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const v</td>
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3835
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3936
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<pre style="margin: 0;"> <span id="LC3936" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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3836
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3937
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<pre style="margin: 0;"> <span id="LC3937" class="line" lang="c"> <span class="n" style="color: #333;">bcf_enc_vchar</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">str</span><span class="p">,</span> <span class="n" style="color: #333;">strlen</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">values</span><span class="p">),</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">values</span><span class="p">);</span></span>
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3837
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3938
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<pre style="margin: 0;"> <span id="LC3938" class="line" lang="c"> <span class="p">}</span></span>
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3939
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<pre style="margin: 0;">+<span id="LC3939" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef VCF_ALLOW_INT64</span></span>
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3838
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3940
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<pre style="margin: 0;"> <span id="LC3940" 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;">type</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">BCF_HT_LONG</span> <span class="p">)</span></span>
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3839
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3941
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<pre style="margin: 0;"> <span id="LC3941" class="line" lang="c"> <span class="p">{</span></span>
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3840
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<td class="diff-line-num new_line" data-linenumber="3942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3942
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<pre style="margin: 0;"> <span id="LC3942" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3843" style="width: 35px; color: rgba(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="3945" style="width: 35px; color: rgba(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">@@ -3843,6 +3945,7 @@ int bcf_update_info(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const v</td>
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3843
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3945
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<pre style="margin: 0;"> <span id="LC3945" class="line" lang="c"> <span class="p">}</span></span>
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3844
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3946
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<pre style="margin: 0;"> <span id="LC3946" class="line" lang="c"> <span class="n" style="color: #333;">bcf_enc_long1</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">str</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">values</span><span class="p">);</span></span>
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3845
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3947
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<pre style="margin: 0;"> <span id="LC3947" class="line" lang="c"> <span class="p">}</span></span>
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3948
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<pre style="margin: 0;">+<span id="LC3948" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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3846
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3949
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<pre style="margin: 0;"> <span id="LC3949" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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3847
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3950
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<pre style="margin: 0;"> <span id="LC3950" class="line" lang="c"> <span class="p">{</span></span>
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3848
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3951
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<pre style="margin: 0;"> <span id="LC3951" class="line" lang="c"> <span class="n" style="color: #333;">hts_log_error</span><span class="p">(</span><span class="s" style="color: #d14;">"The type %d not implemented yet"</span><span class="p">,</span> <span class="n" style="color: #333;">type</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/htslib/compare/61e050b9d3d5e587cb5a4628fa61111b344ee4ed...df4af758e24c513eb9ac898ba9eac395eef8591a#79af080a263b467ea1886b300bde6b2d35c43aa8"><strong>version.sh</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">@@ -24,7 +24,7 @@</td>
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24
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># DEALINGS IN THE SOFTWARE.</span></span>
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25
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="shell"></span>
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26
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26
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<pre style="margin: 0;"> <span id="LC26" 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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27
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<pre style="margin: 0;">-<span id="LC27" 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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27
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<pre style="margin: 0;">+<span id="LC27" 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">.1</span></span>
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28
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="shell"></span>
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29
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29
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<pre style="margin: 0;"> <span id="LC29" 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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<pre style="margin: 0;"> <span id="LC30" 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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