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<h3>
Étienne Mollier pushed to branch master
at <a href="https://salsa.debian.org/med-team/biobambam2">Debian Med / biobambam2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/biobambam2/-/commit/dd4ab7a2bafc47acc0fdd586a34610f68f218c1e">dd4ab7a2</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-08-24T12:48:30+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/biobambam2/-/commit/7709cfd66811220bcee4b01be8a594502fa4fa1e">7709cfd6</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-08-24T12:48:32+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.0.183+ds</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/biobambam2/-/commit/e4daece17fcfd21c7863c9ea13f3a64ce7c104b2">e4daece1</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-08-24T12:48:36+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.0.183+ds'
Update to upstream version '2.0.183+ds'
with Debian dir 7ed9bf23c110557070e8ca797e109e162d1fde8b</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/biobambam2/-/commit/669b5d63a79f7f59823173f978d71895cb14dd37">669b5d63</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-08-24T12:48:36+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.6.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/biobambam2/-/commit/e9fd708ff1a92705fe5c8bc710425a38971fc128">e9fd708f</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-08-24T12:48:45+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove duplicate line from changelog.
Changes-By: lintian-brush
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/biobambam2/-/commit/773f61534410d264409ac666baa24a163614df3a">773f6153</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-08-24T15:47:14+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/control: build depends on libmaus2-dev (>= 2.0.800)
older versions of libmaus2 will cause a configure error at build time.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/biobambam2/-/commit/5b75a6a60a6ca64f4e9dbfc1f737c68e12b0adea">5b75a6a6</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-08-24T16:36:18+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">update changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/biobambam2/-/commit/81dd7b7e23e1dcc763939c7b75df933c6bd84638">81dd7b7e</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-08-24T16:54:23+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
</li>
</ul>
<h4>23 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#00fe7828d56d7a3ee4030d6cea057cf13f50e70c">
ChangeLog
</a>
</li>
<li class="file-stats">
<a href="#87db583be5c13c1f7b3c958b10e03d67b6a2ca06">
configure.ac
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#0815eab16a52d3bd513af16e288f25eb877061dd">
src/biobambam2/ReadHeader.cpp
</a>
</li>
<li class="file-stats">
<a href="#f6d6a44a2d4c9132f5653efa0c6bda8746270a3f">
src/programs/bam12split.cpp
</a>
</li>
<li class="file-stats">
<a href="#3357db5c537ef273c0208887b5f0500fde233036">
src/programs/bam12strip.cpp
</a>
</li>
<li class="file-stats">
<a href="#3b06d7c0df977f4386ad9e6694957bfbc058149f">
src/programs/bamauxmerge2.cpp
</a>
</li>
<li class="file-stats">
<a href="#e5cb3e3a7ae5d93708da3cbc60a7378a64d1183f">
src/programs/bamauxsort.cpp
</a>
</li>
<li class="file-stats">
<a href="#69564be010fba721dc185239c85c9d18ebefad83">
src/programs/bamfastcat.cpp
</a>
</li>
<li class="file-stats">
<a href="#0b20c6e030426637a6eb018a0148e5caa5d1c4c8">
src/programs/bamfilteraux.cpp
</a>
</li>
<li class="file-stats">
<a href="#2bcca0119361ca8be7efd810c71e6bb649b2407e">
src/programs/bamfilterk.cpp
</a>
</li>
<li class="file-stats">
<a href="#0ca2108c540bc79ea6ba65027104f39309c8c2da">
src/programs/bamfilternames.cpp
</a>
</li>
<li class="file-stats">
<a href="#91b677d9fdeb03bd528f14f043e3c34241608a85">
src/programs/bamfilterrefid.cpp
</a>
</li>
<li class="file-stats">
<a href="#ea3b93ee0fc6ecc88a4c308d9e775460cc069a19">
src/programs/bamfilterrg.cpp
</a>
</li>
<li class="file-stats">
<a href="#f6b22330facbdb99232cfb2d0e56bb7d6838207d">
src/programs/bamfixmatecoordinates.cpp
</a>
</li>
<li class="file-stats">
<a href="#271e49033ee905cf5f07b443a94aa2397f1dcfa6">
src/programs/bamfixmateinformation.cpp
</a>
</li>
<li class="file-stats">
<a href="#825c9dbbfa9b91c5079dfc612fedaf896fe6bfef">
src/programs/bamflagsplit.cpp
</a>
</li>
<li class="file-stats">
<a href="#adda26115eb904dfde73f9af842d611a484dd96d">
src/programs/bammdnm.cpp
</a>
</li>
<li class="file-stats">
<a href="#8e8a31c2e2de658322e9a5f09d7a0aa8ad3d34e7">
src/programs/bamrandomtag.cpp
</a>
</li>
<li class="file-stats">
<a href="#75cd4b6fcab80d710439480f5f6e632072e8e49c">
src/programs/bamreheader.cpp
</a>
</li>
<li class="file-stats">
<a href="#32099417d6349eb66fc916c178067874542cb535">
src/programs/bamreplacechecksums.cpp
</a>
</li>
<li class="file-stats">
<a href="#de57bf5a34898545f171f24670439327f7d0fd92">
src/programs/bamsort.cpp
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="00fe7828d56d7a3ee4030d6cea057cf13f50e70c">
<a href="https://salsa.debian.org/med-team/biobambam2/-/compare/c0a239ed3bf7d15be3a43f49803351a6a5498895...81dd7b7e23e1dcc763939c7b75df933c6bd84638#00fe7828d56d7a3ee4030d6cea057cf13f50e70c"><strong>ChangeLog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">biobambam2 (2.0.183-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Adapt to change in libmaus2 (rename GetObject to GetCObject)</span>
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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
</pre>
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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="LC5" class="line" lang="plaintext"> -- German Tischler-Höhle <germant@miltenyibiotec.de> Mon, 02 Aug 2021 17:54:00 +0200</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
</pre>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">biobambam2 (2.0.182-1) unstable; urgency=medium</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * Add O (output file) option for bamfastcat</span>
</pre>
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<li id="87db583be5c13c1f7b3c958b10e03d67b6a2ca06">
<a href="https://salsa.debian.org/med-team/biobambam2/-/compare/c0a239ed3bf7d15be3a43f49803351a6a5498895...81dd7b7e23e1dcc763939c7b75df933c6bd84638#87db583be5c13c1f7b3c958b10e03d67b6a2ca06"><strong>configure.ac</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">AC_INIT(biobambam2,2.0.18<span class="idiff left right">2</span>,[germant@miltenyibiotec.de],[biobambam2],[https://gitlab.com/german.tischler/biobambam2])</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">AC_INIT(biobambam2,2.0.18<span class="idiff left right">3</span>,[germant@miltenyibiotec.de],[biobambam2],[https://gitlab.com/german.tischler/biobambam2])</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="plaintext">AC_CANONICAL_SYSTEM</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">AC_PROG_LIBTOOL</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -165,7 +165,7 @@ if test ! -z "${with_libmaus2}" ; then</td>
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="plaintext"> fi</span>
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="plaintext">fi</span>
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="plaintext">PKG_CHECK_MODULES([libmaus2],[libmaus2 >= 2.0.<span class="idiff left right">774</span>])</span>
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext">PKG_CHECK_MODULES([libmaus2],[libmaus2 >= 2.0.<span class="idiff left right">800</span>])</span>
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="plaintext">if test ! -z "${with_libmaus2}" ; then</span>
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="plaintext"> if test ! -z "${PKGCONFIGPATHSAVE}" ; then</span>
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<a href="https://salsa.debian.org/med-team/biobambam2/-/compare/c0a239ed3bf7d15be3a43f49803351a6a5498895...81dd7b7e23e1dcc763939c7b75df933c6bd84638#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">biobambam2 (2.0.18<span class="idiff left">2</span>+ds-1<span class="idiff right">~0exp0) UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">biobambam2 (2.0.18<span class="idiff left">3</span>+ds-1<span class="idiff right">) unstable</span>; urgency=medium</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"> * New upstream version</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * all patches removed after application upstream</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * d/control: updated my uploader address</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Standards-Version: 4.6.0 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * d/control: build depends on libmaus2-dev (>= 2.0.800); fixes configure</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> error at build time.</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> -- Étienne Mollier <emollier@debian.org> Tue, 2<span class="idiff left">9 Jun</span> 2021 <span class="idiff right">23:14:44</span> +0200</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> -- Étienne Mollier <emollier@debian.org> Tue, 2<span class="idiff left">4 Aug</span> 2021 <span class="idiff right">16:37:12</span> +0200</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">biobambam2 (2.0.179+ds-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/biobambam2/-/compare/c0a239ed3bf7d15be3a43f49803351a6a5498895...81dd7b7e23e1dcc763939c7b75df933c6bd84638#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -6,8 +6,8 @@ Section: science</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> pkg-config,</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> libmaus2-dev</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">5.1</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> libmaus2-dev<span class="idiff left right"> (>= 2.0.800)</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">6.0</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/biobambam2</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/biobambam2.git</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Homepage: https://gitlab.com/german.tischler/biobambam2</span>
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<li id="0815eab16a52d3bd513af16e288f25eb877061dd">
<a href="https://salsa.debian.org/med-team/biobambam2/-/compare/c0a239ed3bf7d15be3a43f49803351a6a5498895...81dd7b7e23e1dcc763939c7b75df933c6bd84638#0815eab16a52d3bd513af16e288f25eb877061dd"><strong>src/biobambam2/ReadHeader.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -20,8 +20,8 @@</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/lz/BgzfInflate.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/bambam/BamHeader.hpp></span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/GetObject.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/lz/BgzfDeflate.hpp></span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/GetCObject.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="p">,</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">readHeader</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">istream</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">in</span><span class="p">,</span> <span class="n" style="color: #333;">biobambam2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">HeaderUpdate</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">HU</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">level</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">dropheader</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"><span class="p">{</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -45,7 +45,7 @@ std::pair<uint64_t,std::string> readHeader(std::istream & in, biobambam2::Header</td>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cpp"> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">lz</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BgzfInflateBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BaseBlockInfo</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">BBI</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">base</span><span class="p">.</span><span class="n" style="color: #333;">readBlock</span><span class="p">(</span><span class="n" style="color: #333;">in</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">decompsize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">base</span><span class="p">.</span><span class="n" style="color: #333;">decompressBlock</span><span class="p">(</span><span class="n" style="color: #333;">decompBuffer</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span><span class="n" style="color: #333;">BBI</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">udecomp</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">reinterpret_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*></span><span class="p">(</span><span class="n" style="color: #333;">decompBuffer</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">());</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="cpp"> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetObject</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*></span> <span class="n" style="color: #333;">GO</span><span class="p">(</span><span class="n" style="color: #333;">udecomp</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp"> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Get<span class="idiff left right">C</span>Object</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*></span> <span class="n" style="color: #333;">GO</span><span class="p">(</span><span class="n" style="color: #333;">udecomp</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">P</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BHPS</span><span class="p">.</span><span class="n" style="color: #333;">parseHeader</span><span class="p">(</span><span class="n" style="color: #333;">GO</span><span class="p">,</span><span class="n" style="color: #333;">decompsize</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/biobambam2/-/compare/c0a239ed3bf7d15be3a43f49803351a6a5498895...81dd7b7e23e1dcc763939c7b75df933c6bd84638#f6d6a44a2d4c9132f5653efa0c6bda8746270a3f"><strong>src/programs/bam12split.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -33,7 +33,6 @@</td>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/bambam/ProgramHeaderLineSet.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/ArgInfo.hpp></span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/GetObject.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/PutObject.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/TempFileRemovalContainer.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/biobambam2/-/compare/c0a239ed3bf7d15be3a43f49803351a6a5498895...81dd7b7e23e1dcc763939c7b75df933c6bd84638#3357db5c537ef273c0208887b5f0500fde233036"><strong>src/programs/bam12strip.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -33,7 +33,6 @@</td>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/bambam/ProgramHeaderLineSet.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/ArgInfo.hpp></span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/GetObject.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/PutObject.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/TempFileRemovalContainer.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"></span>
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<li id="3b06d7c0df977f4386ad9e6694957bfbc058149f">
<a href="https://salsa.debian.org/med-team/biobambam2/-/compare/c0a239ed3bf7d15be3a43f49803351a6a5498895...81dd7b7e23e1dcc763939c7b75df933c6bd84638#3b06d7c0df977f4386ad9e6694957bfbc058149f"><strong>src/programs/bamauxmerge2.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -43,7 +43,7 @@</td>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/Histogram.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <biobambam2/KmerPoisson.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/bambam/BamHeaderParserState.hpp></span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/GetObject.hpp></span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/Get<span class="idiff left right">C</span>Object.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/LELoad.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/bambam/ProgramHeaderLineSet.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/fastx/FastAReader.hpp></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">@@ -1002,7 +1002,7 @@ struct BlockProcessDispatcher : public libmaus2::parallel::SimpleThreadWorkPacka</td>
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<pre style="margin: 0;"> <span id="LC1002" class="line" lang="cpp"> <span class="n" style="color: #333;">DataBlockTypeInfo</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pointer_type</span> <span class="n" style="color: #333;">tptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">deFSH</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC1003" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1004" class="line" lang="cpp"> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamHeaderParserState</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">BHPS</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">BHPS</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC1005" class="line" lang="cpp"> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetObject</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*></span> <span class="n" style="color: #333;">GO</span><span class="p">(</span><span class="k" style="font-weight: 600;">reinterpret_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*></span><span class="p">(</span><span class="n" style="color: #333;">tptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">c</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC1005" class="line" lang="cpp"> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Get<span class="idiff left right">C</span>Object</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*></span> <span class="n" style="color: #333;">GO</span><span class="p">(</span><span class="k" style="font-weight: 600;">reinterpret_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*></span><span class="p">(</span><span class="n" style="color: #333;">tptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">c</span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC1006" class="line" lang="cpp"></span>
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1007
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<pre style="margin: 0;"> <span id="LC1007" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">HPB</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BHPS</span><span class="p">.</span><span class="n" style="color: #333;">parseHeader</span><span class="p">(</span><span class="n" style="color: #333;">GO</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="LC1008" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">HP</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BHPS</span><span class="p">.</span><span class="n" style="color: #333;">parseHeader</span><span class="p">(</span><span class="n" style="color: #333;">GO</span><span class="p">,</span> <span class="n" style="color: #333;">tptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/biobambam2/-/compare/c0a239ed3bf7d15be3a43f49803351a6a5498895...81dd7b7e23e1dcc763939c7b75df933c6bd84638#e5cb3e3a7ae5d93708da3cbc60a7378a64d1183f"><strong>src/programs/bamauxsort.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -33,7 +33,6 @@</td>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/bambam/ProgramHeaderLineSet.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/ArgInfo.hpp></span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/GetObject.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/PutObject.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/TempFileRemovalContainer.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/biobambam2/-/compare/c0a239ed3bf7d15be3a43f49803351a6a5498895...81dd7b7e23e1dcc763939c7b75df933c6bd84638#69564be010fba721dc185239c85c9d18ebefad83"><strong>src/programs/bamfastcat.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,7 +19,6 @@</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/bambam/BamHeader.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/bambam/SamDecoder.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/ArgInfo.hpp></span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/GetObject.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/LineBuffer.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/Concat.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/bambam/BamBlockWriterBaseFactory.hpp></span></span>
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<a href="https://salsa.debian.org/med-team/biobambam2/-/compare/c0a239ed3bf7d15be3a43f49803351a6a5498895...81dd7b7e23e1dcc763939c7b75df933c6bd84638#0b20c6e030426637a6eb018a0148e5caa5d1c4c8"><strong>src/programs/bamfilteraux.cpp</strong></a>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/bambam/ProgramHeaderLineSet.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/ArgInfo.hpp></span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/GetObject.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/PutObject.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/TempFileRemovalContainer.hpp></span></span>
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38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/biobambam2/-/compare/c0a239ed3bf7d15be3a43f49803351a6a5498895...81dd7b7e23e1dcc763939c7b75df933c6bd84638#2bcca0119361ca8be7efd810c71e6bb649b2407e"><strong>src/programs/bamfilterk.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,7 +19,6 @@</td>
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/bambam/BamHeader.hpp></span></span>
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20
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/bambam/SamDecoder.hpp></span></span>
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/ArgInfo.hpp></span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/GetObject.hpp></span></span>
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23
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/LineBuffer.hpp></span></span>
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24
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/Concat.hpp></span></span>
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25
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/bambam/BamBlockWriterBaseFactory.hpp></span></span>
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<a href="https://salsa.debian.org/med-team/biobambam2/-/compare/c0a239ed3bf7d15be3a43f49803351a6a5498895...81dd7b7e23e1dcc763939c7b75df933c6bd84638#0ca2108c540bc79ea6ba65027104f39309c8c2da"><strong>src/programs/bamfilternames.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -30,7 +30,6 @@</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/bambam/ProgramHeaderLineSet.hpp></span></span>
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31
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/ArgInfo.hpp></span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/GetObject.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/PutObject.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/TempFileRemovalContainer.hpp></span></span>
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35
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/biobambam2/-/compare/c0a239ed3bf7d15be3a43f49803351a6a5498895...81dd7b7e23e1dcc763939c7b75df933c6bd84638#91b677d9fdeb03bd528f14f043e3c34241608a85"><strong>src/programs/bamfilterrefid.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -30,7 +30,6 @@</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/bambam/ProgramHeaderLineSet.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/ArgInfo.hpp></span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/GetObject.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/PutObject.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/TempFileRemovalContainer.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"></span>
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<li id="ea3b93ee0fc6ecc88a4c308d9e775460cc069a19">
<a href="https://salsa.debian.org/med-team/biobambam2/-/compare/c0a239ed3bf7d15be3a43f49803351a6a5498895...81dd7b7e23e1dcc763939c7b75df933c6bd84638#ea3b93ee0fc6ecc88a4c308d9e775460cc069a19"><strong>src/programs/bamfilterrg.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -30,7 +30,6 @@</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/bambam/ProgramHeaderLineSet.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/ArgInfo.hpp></span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/GetObject.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/PutObject.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/TempFileRemovalContainer.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/biobambam2/-/compare/c0a239ed3bf7d15be3a43f49803351a6a5498895...81dd7b7e23e1dcc763939c7b75df933c6bd84638#f6b22330facbdb99232cfb2d0e56bb7d6838207d"><strong>src/programs/bamfixmatecoordinates.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -29,7 +29,6 @@</td>
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/fastx/CompactFastEncoder.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/bambam/BamAlignmentEncoderBase.hpp></span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/GetObject.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/CountPutObject.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/ArgInfo.hpp></span></span>
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<a href="https://salsa.debian.org/med-team/biobambam2/-/compare/c0a239ed3bf7d15be3a43f49803351a6a5498895...81dd7b7e23e1dcc763939c7b75df933c6bd84638#271e49033ee905cf5f07b443a94aa2397f1dcfa6"><strong>src/programs/bamfixmateinformation.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -34,7 +34,6 @@</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/bambam/ProgramHeaderLineSet.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/ArgInfo.hpp></span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/GetObject.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/PutObject.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/TempFileRemovalContainer.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/biobambam2/-/compare/c0a239ed3bf7d15be3a43f49803351a6a5498895...81dd7b7e23e1dcc763939c7b75df933c6bd84638#825c9dbbfa9b91c5079dfc612fedaf896fe6bfef"><strong>src/programs/bamflagsplit.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -35,7 +35,6 @@</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/aio/OutputStreamInstance.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/ArgInfo.hpp></span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/GetObject.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/PutObject.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/TempFileRemovalContainer.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/biobambam2/-/compare/c0a239ed3bf7d15be3a43f49803351a6a5498895...81dd7b7e23e1dcc763939c7b75df933c6bd84638#adda26115eb904dfde73f9af842d611a484dd96d"><strong>src/programs/bammdnm.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -147,7 +147,7 @@ static int bammdnm(libmaus2::util::ArgInfo const & arginfo)</td>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span> <span class="n" style="color: #333;">haveheader</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">pa</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">pc</span><span class="p">)</span> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GetObject</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*></span> <span class="n" style="color: #333;">G</span><span class="p">(</span><span class="n" style="color: #333;">pa</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">util</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Get<span class="idiff left right">C</span>Object</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*></span> <span class="n" style="color: #333;">G</span><span class="p">(</span><span class="n" style="color: #333;">pa</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">P</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bamheaderparsestate</span><span class="p">.</span><span class="n" style="color: #333;">parseHeader</span><span class="p">(</span><span class="n" style="color: #333;">G</span><span class="p">,</span><span class="n" style="color: #333;">bgzfinfo</span><span class="p">.</span><span class="n" style="color: #333;">uncompressed</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// header complete?</span></span>
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<li id="8e8a31c2e2de658322e9a5f09d7a0aa8ad3d34e7">
<a href="https://salsa.debian.org/med-team/biobambam2/-/compare/c0a239ed3bf7d15be3a43f49803351a6a5498895...81dd7b7e23e1dcc763939c7b75df933c6bd84638#8e8a31c2e2de658322e9a5f09d7a0aa8ad3d34e7"><strong>src/programs/bamrandomtag.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -33,7 +33,6 @@</td>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/bambam/ProgramHeaderLineSet.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/ArgInfo.hpp></span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/GetObject.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/PutObject.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/TempFileRemovalContainer.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/biobambam2/-/compare/c0a239ed3bf7d15be3a43f49803351a6a5498895...81dd7b7e23e1dcc763939c7b75df933c6bd84638#75cd4b6fcab80d710439480f5f6e632072e8e49c"><strong>src/programs/bamreheader.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -20,7 +20,6 @@</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/bambam/BamHeader.hpp></span></span>
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21
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/bambam/SamDecoder.hpp></span></span>
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/ArgInfo.hpp></span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/GetObject.hpp></span></span>
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/LineBuffer.hpp></span></span>
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25
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/Concat.hpp></span></span>
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26
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/bambam/BamBlockWriterBaseFactory.hpp></span></span>
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<a href="https://salsa.debian.org/med-team/biobambam2/-/compare/c0a239ed3bf7d15be3a43f49803351a6a5498895...81dd7b7e23e1dcc763939c7b75df933c6bd84638#32099417d6349eb66fc916c178067874542cb535"><strong>src/programs/bamreplacechecksums.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -20,7 +20,6 @@</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/bambam/BamHeader.hpp></span></span>
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/bambam/SamDecoder.hpp></span></span>
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/ArgInfo.hpp></span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/GetObject.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/LineBuffer.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/Concat.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/bambam/BamBlockWriterBaseFactory.hpp></span></span>
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<a href="https://salsa.debian.org/med-team/biobambam2/-/compare/c0a239ed3bf7d15be3a43f49803351a6a5498895...81dd7b7e23e1dcc763939c7b75df933c6bd84638#de57bf5a34898545f171f24670439327f7d0fd92"><strong>src/programs/bamsort.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -38,7 +38,6 @@</td>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/bambam/ProgramHeaderLineSet.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/ArgInfo.hpp></span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/GetObject.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/PutObject.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/util/TempFileRemovalContainer.hpp></span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/bambam/ChecksumsFactory.hpp></span></span>
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