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<h3>
Étienne Mollier pushed to branch upstream
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/b36bccd15b79ea86c241f0014673225bb1d34854">b36bccd1</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-11-12T16:17:53+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.0.177+ds</pre>
</li>
</ul>
<h4>15 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">
.gitignore
</a>
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<li class="file-stats">
<a href="#00fe7828d56d7a3ee4030d6cea057cf13f50e70c">
ChangeLog
</a>
</li>
<li class="file-stats">
<a href="#87db583be5c13c1f7b3c958b10e03d67b6a2ca06">
configure.ac
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<li class="file-stats">
<a href="#dee5c4430f3aa3a43132ee80817c8d207bada8d9">
release.sh
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</li>
<li class="file-stats">
<a href="#0cf1a4ac4c7f40ab2de2b4d5c207bafc2ad847a6">
<span class="new-file">
+
removespace.sh
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</li>
<li class="file-stats">
<a href="#67e794015a01b8816bd16290e5f8538236da8245">
src/Makefile.am
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<li class="file-stats">
<a href="#40ae775c772d41bff8f58cc32f7693b77a9497ac">
src/biobambam2/BamBamConfig.hpp.in
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</li>
<li class="file-stats">
<a href="#9c542eb79cd228f3e3385d418f89d6b514f558e0">
src/biobambam2/UpdateNumericalIndex.cpp
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<li class="file-stats">
<a href="#5393ade310e7cd11929979d7b18ab8cc6860e027">
src/programs/bamcollate2.cpp
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<li class="file-stats">
<a href="#731c8a82cbe64a38ffc549ef39ae18a3c5470e9a">
src/programs/bamconsensus.cpp
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<li class="file-stats">
<a href="#b8a20a8a09b5dbd365fb76fb83e47d3490234a84">
<span class="new-file">
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src/programs/bamdifference.cpp
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<li class="file-stats">
<a href="#f003bbc90ca3edf349c1e28704952dda9ef29682">
src/programs/bammerge.cpp
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<li class="file-stats">
<a href="#be752f41aab032268ccb172abc929cf063a40400">
src/programs/bamtofastq.cpp
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<li class="file-stats">
<a href="#5996963c0b0cac34c60d4ecc66918c31b32d6518">
src/programs/blastnxmltobam.cpp
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<li class="file-stats">
<a href="#ab5115e6c5d8836f3f68486cbaf80c86d2df924f">
<span class="new-file">
+
src/programs/fastaselectreg.cpp
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</li>
</ul>
<h4>Changes:</h4>
<li id="a5cc2925ca8258af241be7e5b0381edf30266302">
<a href="https://salsa.debian.org/med-team/biobambam2/-/commit/b36bccd15b79ea86c241f0014673225bb1d34854#a5cc2925ca8258af241be7e5b0381edf30266302"><strong>.gitignore</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="70" style="width: 35px; color: rgba(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">@@ -70,3 +70,5 @@ src/vcffiltersamples</td>
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<td class="diff-line-num new_line" data-linenumber="70" style="width: 35px; color: rgba(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="LC70" class="line" lang="plaintext">src/vcfdiff</span>
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<td class="diff-line-num new_line" data-linenumber="71" style="width: 35px; color: rgba(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="LC71" class="line" lang="plaintext">src/vcffilterfilterflags</span>
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<td class="diff-line-num old_line" data-linenumber="72" style="width: 35px; color: rgba(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="72" style="width: 35px; color: rgba(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="LC72" class="line" lang="plaintext">src/vcfreplacecontigsmap</span>
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<td class="diff-line-num new new_line" data-linenumber="73" style="width: 35px; color: rgba(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="LC73" class="line" lang="plaintext">src/fastaselectreg</span>
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<td class="diff-line-num new old_line" data-linenumber="73" style="width: 35px; color: rgba(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="74" style="width: 35px; color: rgba(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="LC74" class="line" lang="plaintext">src/bamdifference</span></pre>
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</li>
<li id="00fe7828d56d7a3ee4030d6cea057cf13f50e70c">
<a href="https://salsa.debian.org/med-team/biobambam2/-/commit/b36bccd15b79ea86c241f0014673225bb1d34854#00fe7828d56d7a3ee4030d6cea057cf13f50e70c"><strong>ChangeLog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">biobambam2 (2.0.177-1) unstable; urgency=medium</span>
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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Versioning cleanup</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- German Tischler-Höhle <germant@miltenyibiotec.de> Thu, 12 Nov 2020 10:39:59 +0100</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">biobambam2 (2.0.176-1) unstable; urgency=medium</span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(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="LC8" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(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="LC9" class="line" lang="plaintext"> * Adapt UpdateNumericalIndex to new libmaus2 api</span>
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(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="LC10" class="line" lang="plaintext"> * Fix output of orphaned read 2 instances in bamtofastq when splitting by readgroup</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * Remove references to non functional IRODS interface in libmaus2</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> * Add bamdifference program</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> -- German Tischler-Höhle <germant@miltenyibiotec.de> Thu, 12 Nov 2020 09:43:13 +0100</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">biobambam2 (2.0.175-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> * Add fastaselectreg</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> -- German Tischler-Höhle <germant@miltenyibiotec.de> Thu, 27 Aug 2020 10:08:12 +0200</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">biobambam2 (2.0.174-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> * Fix wrong operator for deallocating memory in bamconsensus</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> -- German Tischler-Höhle <germant@miltenyibiotec.de> Mon, 10 Aug 2020 11:26:08 +0200</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">biobambam2 (2.0.173-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> * Fix for libmaus2 update</span>
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<li id="87db583be5c13c1f7b3c958b10e03d67b6a2ca06">
<a href="https://salsa.debian.org/med-team/biobambam2/-/commit/b36bccd15b79ea86c241f0014673225bb1d34854#87db583be5c13c1f7b3c958b10e03d67b6a2ca06"><strong>configure.ac</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">AC_INIT(biobambam2,2.0.17<span class="idiff left right">3</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(biobambam2,2.0.17<span class="idiff left right">7</span>,[germant@miltenyibiotec.de],[biobambam2],[https://gitlab.com/german.tischler/biobambam2])</span>
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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 "${with_libmaus2}" ; then</td>
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="plaintext"> fi</span>
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="plaintext">fi</span>
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="plaintext">PKG_CHECK_MODULES([libmaus2],[libmaus2 >= 2.0.74<span class="idiff left right">0</span>])</span>
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext">PKG_CHECK_MODULES([libmaus2],[libmaus2 >= 2.0.74<span class="idiff left right">9</span>])</span>
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169
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="plaintext"></span>
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="plaintext">if test ! -z "${with_libmaus2}" ; then</span>
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171
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="plaintext"> if test ! -z "${PKGCONFIGPATHSAVE}" ; then</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -300,7 +300,7 @@ if test "${have_libmaus2_irods}" = "yes" ; then</td>
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="plaintext"> fi</span>
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="plaintext"> fi</span>
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC303" class="line" lang="plaintext"> PKG_CHECK_MODULES([libmaus2irods],[libmaus2irods >= 2.0.74<span class="idiff left right">0</span>])</span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="plaintext"> PKG_CHECK_MODULES([libmaus2irods],[libmaus2irods >= 2.0.74<span class="idiff left right">9</span>])</span>
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="plaintext"> LIBMAUS2IRODSCPPFLAGS="${libmaus2irods_CFLAGS}"</span>
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<pre style="margin: 0;"> <span id="LC306" class="line" lang="plaintext"> LIBMAUS2IRODSLIBS="${libmaus2irods_LIBS}"</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">@@ -463,7 +463,7 @@ AC_ARG_ENABLE(install_uncommon,</td>
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<pre style="margin: 0;"> <span id="LC463" class="line" lang="plaintext"> AS_HELP_STRING([--enable-install-uncommon],[enable installation of some uncommon programs (default no)]),</span>
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<pre style="margin: 0;"> <span id="LC464" class="line" lang="plaintext"> [install_uncommon=${enableval}],[install_uncommon=no])</span>
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465
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<pre style="margin: 0;"> <span id="LC465" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC466" class="line" lang="plaintext">UNCOMMON="bamfilter bamfilterbyname bamfixmatecoordinates bamfixmatecoordinatesnamesorted bamtoname bamdisthist fastabgzfextract bamheap bamfrontback bamrandomtag bamheap2 bamheap3 bamtagconversion fastqtobampar bambisect vcffilterinfo vcfpatchcontigprepend vcfconcat vcfsort filtergtf bamconsensus vcfreplacecontigs vcffiltersamples bamexploderg bamexondepth bamheadercat bammarkduplicatesoptdist vcfdiff bamsimpledepth bamdepthmerge bamcountflags vcffilterfilterflags vcfreplacecontigsmap"</span>
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466
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="plaintext">UNCOMMON="bamfilter bamfilterbyname bamfixmatecoordinates bamfixmatecoordinatesnamesorted bamtoname bamdisthist fastabgzfextract bamheap bamfrontback bamrandomtag bamheap2 bamheap3 bamtagconversion fastqtobampar bambisect vcffilterinfo vcfpatchcontigprepend vcfconcat vcfsort filtergtf bamconsensus vcfreplacecontigs vcffiltersamples bamexploderg bamexondepth bamheadercat bammarkduplicatesoptdist vcfdiff bamsimpledepth bamdepthmerge bamcountflags vcffilterfilterflags vcfreplacecontigsmap<span class="idiff left right"> fastaselectreg</span>"</span>
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467
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<pre style="margin: 0;"> <span id="LC467" class="line" lang="plaintext">UNCOMMONINSTALLED=</span>
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<pre style="margin: 0;"> <span id="LC468" class="line" lang="plaintext">UNCOMMONUNINSTALLED=</span>
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469
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<pre style="margin: 0;"> <span id="LC469" class="line" lang="plaintext">if test "${install_uncommon}" = "yes" ; then</span>
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<a href="https://salsa.debian.org/med-team/biobambam2/-/commit/b36bccd15b79ea86c241f0014673225bb1d34854#dee5c4430f3aa3a43132ee80817c8d207bada8d9"><strong>release.sh</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/bash</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-euxo</span> pipefail</span>
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2
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="shell"></span>
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3
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># update branches</span></span>
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4
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell">git checkout experimental</span>
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<a href="https://salsa.debian.org/med-team/biobambam2/-/commit/b36bccd15b79ea86c241f0014673225bb1d34854#0cf1a4ac4c7f40ab2de2b4d5c207bafc2ad847a6"><strong>removespace.sh</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/bash</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>i <span class="k" style="font-weight: 600;">in</span> <span class="sb" style="color: #d14;">`</span>find src <span class="nt" style="color: #000080;">-regex</span> .<span class="k" style="font-weight: 600;">*</span><span class="se" style="color: #d14;">\\\.</span><span class="o" style="font-weight: 600;">[</span>ch]pp<span class="sb" style="color: #d14;">`</span> <span class="sb" style="color: #d14;">`</span>find src <span class="nt" style="color: #000080;">-regex</span> .<span class="k" style="font-weight: 600;">*</span><span class="se" style="color: #d14;">\\\.</span><span class="o" style="font-weight: 600;">[</span>ch]<span class="sb" style="color: #d14;">`</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">ORIG</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">cat</span> <span class="nv" style="color: #008080;">$i</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"> <span class="nv" style="color: #008080;">PATCHED</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>perl <span class="nt" style="color: #000080;">-p</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"s/(</span><span class="se" style="color: #d14;">\s</span><span class="s2" style="color: #d14;">*)(</span><span class="nv" style="color: #008080;">$)</span><span class="s2" style="color: #d14;">/</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">/"</span> < <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">i</span><span class="k" style="font-weight: 600;">}</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"> </span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$ORIG</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$PATCHED</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">PATCHED</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">i</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># git add ${i}</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">i</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span></pre>
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<a href="https://salsa.debian.org/med-team/biobambam2/-/commit/b36bccd15b79ea86c241f0014673225bb1d34854#67e794015a01b8816bd16290e5f8538236da8245"><strong>src/Makefile.am</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">@@ -152,7 +152,8 @@ EXTRA_PROGRAMS = blastnxmltobam \</td>
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152
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="make"> vcfdiff <span class="se" style="color: #d14;">\</span></span>
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="make"> bamsimpledepth <span class="se" style="color: #d14;">\</span></span>
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="make"> bamdepthmerge <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="make"> bamcountflags</span>
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="make"> bamcountflags <span class="se" style="color: #d14;">\</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="make"> fastaselectreg</span>
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="make"></span>
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="make"><span class="nv" style="color: #008080;">populaterefcache_SOURCES</span> <span class="o" style="font-weight: 600;">=</span> programs/populaterefcache.cpp biobambam2/Licensing.cpp</span>
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158
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="make"><span class="nv" style="color: #008080;">populaterefcache_LDADD</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">${LIBMAUS2LIBS}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -703,3 +704,8 @@ bamcountflags_SOURCES = programs/bamcountflags.cpp biobambam2/Licensing.cpp</td>
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703
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704
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<pre style="margin: 0;"> <span id="LC704" class="line" lang="make"><span class="nv" style="color: #008080;">bamcountflags_LDADD</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">${LIBMAUS2LIBS}</span></span>
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704
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705
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<pre style="margin: 0;"> <span id="LC705" class="line" lang="make"><span class="nv" style="color: #008080;">bamcountflags_LDFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">${AM_CPPFLAGS}</span> <span class="nv" style="color: #008080;">${LIBMAUS2CPPFLAGS}</span> <span class="nv" style="color: #008080;">${LIBMAUS2LDFLAGS}</span> <span class="nv" style="color: #008080;">${AM_LDFLAGS}</span></span>
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705
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706
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<pre style="margin: 0;"> <span id="LC706" class="line" lang="make"><span class="nv" style="color: #008080;">bamcountflags_CPPFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">${AM_CPPFLAGS}</span> <span class="nv" style="color: #008080;">${LIBMAUS2CPPFLAGS}</span></span>
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707
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="make"></span>
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708
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="make"><span class="nv" style="color: #008080;">fastaselectreg_SOURCES</span> <span class="o" style="font-weight: 600;">=</span> programs/fastaselectreg.cpp biobambam2/Licensing.cpp</span>
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709
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="make"><span class="nv" style="color: #008080;">fastaselectreg_LDADD</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">${LIBMAUS2LIBS}</span></span>
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710
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="make"><span class="nv" style="color: #008080;">fastaselectreg_LDFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">${AM_CPPFLAGS}</span> <span class="nv" style="color: #008080;">${LIBMAUS2CPPFLAGS}</span> <span class="nv" style="color: #008080;">${LIBMAUS2LDFLAGS}</span> <span class="nv" style="color: #008080;">${AM_LDFLAGS}</span></span>
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711
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<pre style="margin: 0;">+<span id="LC711" class="line" lang="make"><span class="nv" style="color: #008080;">fastaselectreg_CPPFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">${AM_CPPFLAGS}</span> <span class="nv" style="color: #008080;">${LIBMAUS2CPPFLAGS}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/biobambam2/-/commit/b36bccd15b79ea86c241f0014673225bb1d34854#40ae775c772d41bff8f58cc32f7693b77a9497ac"><strong>src/biobambam2/BamBamConfig.hpp.in</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">@@ -22,7 +22,6 @@</td>
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22
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">@LIBMAUS2IOLIBDEFINE@</span>
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">@BIOBAMBAM_HAVE_XERCES_C@</span>
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24
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">@BIOBAMBAM_HAVE_GMP@</span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">@LIBMAUS2IRODSDEFINE@</span>
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26
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">@HAVE_PTHREAD_MUTEX_RECURSIVE_NP@</span>
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27
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">@HAVE_PTHREAD_MUTEX_RECURSIVE@</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"></span>
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<li id="9c542eb79cd228f3e3385d418f89d6b514f558e0">
<a href="https://salsa.debian.org/med-team/biobambam2/-/commit/b36bccd15b79ea86c241f0014673225bb1d34854#9c542eb79cd228f3e3385d418f89d6b514f558e0"><strong>src/biobambam2/UpdateNumericalIndex.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">@@ -28,6 +28,13 @@ namespace biobambam2</td>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</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;">GetFileSize</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">fileExists</span><span class="p">(</span><span class="n" style="color: #333;">indexfn</span><span class="p">)</span> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC31" 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;">string</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">replfn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indexfn</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".repl"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC32" 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;">aio</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">OutputStreamInstance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr_type</span> <span class="n" style="color: #333;">prepl</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">aio</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">OutputStreamInstance</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp"> <span class="n" style="color: #333;">replfn</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cpp"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cpp"> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// get index stats</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">alcnt</span><span class="p">,</span> <span class="n" style="color: #333;">mod</span><span class="p">,</span> <span class="n" style="color: #333;">numblocks</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC40" 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">@@ -59,20 +66,33 @@ namespace biobambam2</td>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// std::cerr << "replacing index position for " << i << " by " << start.first << "," << start.second << std::endl;</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC69" 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;">BamNumericalIndexGenerator</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ReplaceObject</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp"> <span class="n" style="color: #333;">blockid</span><span class="p">,</span><span class="n" style="color: #333;">start</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">,</span><span class="n" style="color: #333;">start</span><span class="p">.</span><span class="n" style="color: #333;">second</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp"> <span class="p">).</span><span class="n" style="color: #333;">serialise</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">prepl</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"> <span class="c" style="color: #998; font-style: italic;">#if 0</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> libmaus2::bambam::BamNumericalIndexGenerator::replaceValue(</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> indexfn,</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> blockid,</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> start.first,</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> start.second</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> );</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp"><span class="c" style="color: #998; font-style: italic;"> #endif</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp"> <span class="n" style="color: #333;">highestSet</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">blockid</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cpp"> <span class="n" style="color: #333;">prepl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">flush</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp"> <span class="n" style="color: #333;">prepl</span><span class="p">.</span><span class="n" style="color: #333;">reset</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC88" 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;">BamNumericalIndexGenerator</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">replaceValues</span><span class="p">(</span><span class="n" style="color: #333;">indexfn</span><span class="p">,</span><span class="n" style="color: #333;">replfn</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC90" 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;">aio</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">FileRemoval</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">removeFile</span><span class="p">(</span><span class="n" style="color: #333;">replfn</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// std::cerr << "shifting index positions for [" << highestSet+1 << "," << numblocks << ")" << " by " << static_cast<int64_t>(compdata.second.size()) - static_cast<int64_t>(compdata.first) << std::endl;</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// shift values in part we moved as is</span></span>
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<pre style="margin: 0;">-<span id="LC75" 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;">BamNumericalIndexGenerator</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">shiftValues</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC95" 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;">BamNumericalIndexGenerator</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">shiftValues<span class="idiff left right">Streaming</span></span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp"> <span class="n" style="color: #333;">indexfn</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp"> <span class="n" style="color: #333;">highestSet</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;">numblocks</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</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;">compdata</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">())</span> <span class="o" style="font-weight: 600;">-</span> <span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</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;">compdata</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/biobambam2/-/commit/b36bccd15b79ea86c241f0014673225bb1d34854#5393ade310e7cd11929979d7b18ab8cc6860e027"><strong>src/programs/bamcollate2.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">@@ -1403,29 +1403,14 @@ void bamcollate2(libmaus2::util::ArgInfo const & arginfo)</td>
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<pre style="margin: 0;"> <span id="LC1403" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1404" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1405" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC1406" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if defined(LIBMAUS2_HAVE_IRODS)</span></span>
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<pre style="margin: 0;">-<span id="LC1407" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/irods/IRodsInputStreamFactory.hpp></span></span>
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<pre style="margin: 0;">-<span id="LC1408" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">-<span id="LC1409" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1406" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">argv</span><span class="p">[])</span></span>
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<pre style="margin: 0;"> <span id="LC1407" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1408" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</span></span>
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<pre style="margin: 0;"> <span id="LC1409" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1414" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#if defined(LIBMAUS2_HAVE_IRODS)</span></span>
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<pre style="margin: 0;">-<span id="LC1415" 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;">irods</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">IRodsInputStreamFactory</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">registerHandler</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC1416" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">-<span id="LC1417" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1410" 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;">timing</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">RealTimeClock</span> <span class="n" style="color: #333;">rtc</span><span class="p">;</span> <span class="n" style="color: #333;">rtc</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC1411" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1412" 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;">ArgInfo</span> <span class="n" style="color: #333;">arginfo</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span><span class="n" style="color: #333;">argv</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC1413" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC1422" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#if defined(LIBMAUS2_HAVE_IRODS)</span></span>
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<pre style="margin: 0;">-<span id="LC1423" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// set program name for iRODS identification</span></span>
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1424
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<pre style="margin: 0;">-<span id="LC1424" 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;">stringstream</span> <span class="n" style="color: #333;">irods_id</span><span class="p">;</span></span>
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1425
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<pre style="margin: 0;">-<span id="LC1425" class="line" lang="cpp"> <span class="n" style="color: #333;">irods_id</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">PACKAGE_NAME</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">":"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">arginfo</span><span class="p">.</span><span class="n" style="color: #333;">getProgFileName</span><span class="p">(</span><span class="n" style="color: #333;">arginfo</span><span class="p">.</span><span class="n" style="color: #333;">progname</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">":"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">PACKAGE_VERSION</span><span class="p">;</span></span>
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1426
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<pre style="margin: 0;">-<span id="LC1426" class="line" lang="cpp"> <span class="n" style="color: #333;">setenv</span><span class="p">(</span><span class="n" style="color: #333;">SP_OPTION</span><span class="p">,</span> <span class="n" style="color: #333;">irods_id</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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1427
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<td class="diff-line-num new_line old" data-linenumber="1414" 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="LC1427" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1428
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<pre style="margin: 0;">-<span id="LC1428" class="line" lang="cpp"></span>
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1429
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1414
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<pre style="margin: 0;"> <span id="LC1414" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">arginfo</span><span class="p">.</span><span class="n" style="color: #333;">restargs</span><span class="p">.</span><span class="n" style="color: #333;">size</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>
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1430
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<td class="diff-line-num new_line" data-linenumber="1415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1415
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<pre style="margin: 0;"> <span id="LC1415" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span></span>
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1431
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1416
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<pre style="margin: 0;"> <span id="LC1416" class="line" lang="cpp"> <span class="n" style="color: #333;">arginfo</span><span class="p">.</span><span class="n" style="color: #333;">restargs</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="s" style="color: #d14;">"-v"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1526" style="width: 35px; color: rgba(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="1511" style="width: 35px; color: rgba(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">@@ -1526,14 +1511,6 @@ int main(int argc, char * argv[])</td>
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1526
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1511
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<pre style="margin: 0;"> <span id="LC1511" class="line" lang="cpp"></span>
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1527
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1512
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<pre style="margin: 0;"> <span id="LC1512" class="line" lang="cpp"> <span class="n" style="color: #333;">bamcollate2</span><span class="p">(</span><span class="n" style="color: #333;">arginfo</span><span class="p">);</span></span>
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1528
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1513
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<pre style="margin: 0;"> <span id="LC1513" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC1529" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#if defined(LIBMAUS2_HAVE_IRODS)</span></span>
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1530
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<pre style="margin: 0;">-<span id="LC1530" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// need a explicit call to disconnect to avoid atexit deallocation problems in iRODS 4.19+</span></span>
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1531
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<pre style="margin: 0;">-<span id="LC1531" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">irods</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">IRodsSystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">defaultIrodsSystem</span><span class="p">)</span></span>
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1532
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<pre style="margin: 0;">-<span id="LC1532" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1533" 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="LC1533" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">irods</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">IRodsSystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getDefaultIRodsSystem</span><span class="p">())</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">disconnect</span><span class="p">();</span></span>
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1534
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<pre style="margin: 0;">-<span id="LC1534" class="line" lang="cpp"> <span class="p">}</span></span>
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1535
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<pre style="margin: 0;">-<span id="LC1535" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">-<span id="LC1536" class="line" lang="cpp"></span>
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1537
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1514
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<pre style="margin: 0;"> <span id="LC1514" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">arginfo</span><span class="p">.</span><span class="n" style="color: #333;">getValue</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;">int</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="s" style="color: #d14;">"verbose"</span><span class="p">,</span><span class="n" style="color: #333;">getDefaultVerbose</span><span class="p">())</span> <span class="p">)</span></span>
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1515
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<pre style="margin: 0;"> <span id="LC1515" 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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[V] "</span> <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;">MemUsage</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" wall clock time "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">rtc</span><span class="p">.</span><span class="n" style="color: #333;">formatTime</span><span class="p">(</span><span class="n" style="color: #333;">rtc</span><span class="p">.</span><span class="n" style="color: #333;">getElapsedSeconds</span><span class="p">())</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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1539
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1516
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<pre style="margin: 0;"> <span id="LC1516" class="line" lang="cpp"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/biobambam2/-/commit/b36bccd15b79ea86c241f0014673225bb1d34854#731c8a82cbe64a38ffc549ef39ae18a3c5470e9a"><strong>src/programs/bamconsensus.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">@@ -3307,7 +3307,7 @@ struct ReferenceCache</td>
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3307
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3307
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<pre style="margin: 0;"> <span id="LC3307" class="line" lang="cpp"></span>
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3308
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3308
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<pre style="margin: 0;"> <span id="LC3308" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="o" style="font-weight: 600;">!</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">VuseCnt</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">id</span><span class="p">)</span> <span class="p">)</span></span>
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3309
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3309
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<pre style="margin: 0;"> <span id="LC3309" class="line" lang="cpp"> <span class="p">{</span></span>
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3310
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<pre style="margin: 0;">-<span id="LC3310" class="line" lang="cpp"> <span class="n" style="color: #333;">Vref</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">id</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=<span class="idiff left right">=</span></span> <span class="n" style="color: #333;">RefEntry</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">shared_ptr_type</span><span class="p">();</span></span>
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3310
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<pre style="margin: 0;">+<span id="LC3310" class="line" lang="cpp"> <span class="n" style="color: #333;">Vref</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="n" style="color: #333;">id</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RefEntry</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">shared_ptr_type</span><span class="p">();</span></span>
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3311
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<pre style="margin: 0;"> <span id="LC3311" 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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[V] reference cache deallocating "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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3312
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<pre style="margin: 0;"> <span id="LC3312" class="line" lang="cpp"> <span class="p">}</span></span>
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3313
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<pre style="margin: 0;"> <span id="LC3313" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/biobambam2/-/commit/b36bccd15b79ea86c241f0014673225bb1d34854#b8a20a8a09b5dbd365fb76fb83e47d3490234a84"><strong>src/programs/bamdifference.cpp</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> bambam</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> Copyright (C) 2009-2020 German Tischler-Höhle</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> Copyright (C) 2011-2013 Genome Research Limited</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> This program is free software: you can redistribute it and/or modify</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> it under the terms of the GNU General Public License as published by</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> the Free Software Foundation, either version 3 of the License, or</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> (at your option) any later version.</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> This program is distributed in the hope that it will be useful,</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> GNU General Public License for more details.</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> You should have received a copy of the GNU General Public License</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> along with this program. If not, see <http://www.gnu.org/licenses/>.</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">**/</span></span>
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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 <config.h></span></span>
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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/BamBlockWriterBaseFactory.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/BamWriter.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/bambam/BamHeaderUpdate.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/ArgInfo.hpp></span></span>
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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 <biobambam2/Licensing.hpp></span></span>
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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/BamMultiAlignmentDecoderFactory.hpp></span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/bambam/BamPeeker.hpp></span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/lz/BgzfDeflateOutputCallbackMD5.hpp></span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/bambam/BgzfDeflateOutputCallbackBamIndex.hpp></span></span>
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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="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;">getDefaultMD5</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 class="p">}</span></span>
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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="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">printVerbose</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;">ostream</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">errstr</span><span class="p">,</span> <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;">c0</span><span class="p">,</span> <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;">c1</span><span class="p">,</span> <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;">k</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;">verbose</span><span class="p">,</span> <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;">mod</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">((</span><span class="n" style="color: #333;">c0</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">c1</span><span class="p">)</span><span class="o" style="font-weight: 600;">%</span><span class="n" style="color: #333;">mod</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="LC35" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cpp"> <span class="n" style="color: #333;">errstr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[V] "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">c0</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"/"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">c1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"/"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">c0</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">c1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"/"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp"><span class="p">}</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="cm" style="color: #998; font-style: italic;">/*</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * compute difference of two name sorted alignments files (SAM/BAM/CRAM)</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">bamintersect</span><span class="p">(</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;">ArgParser</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">arg</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC45" 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;">ostream</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">verbstr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <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;">mod</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1024</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">1024</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cpp"></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;">ArgParser</span> <span class="n" style="color: #333;">arg0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arg</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"> <span class="n" style="color: #333;">arg0</span><span class="p">.</span><span class="n" style="color: #333;">replaceArg</span><span class="p">(</span><span class="s" style="color: #d14;">"I"</span><span class="p">,</span><span class="n" style="color: #333;">arg0</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="LC50" 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;">ArgParser</span> <span class="n" style="color: #333;">arg1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arg</span><span class="p">;</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp"> <span class="n" style="color: #333;">arg1</span><span class="p">.</span><span class="n" style="color: #333;">replaceArg</span><span class="p">(</span><span class="s" style="color: #d14;">"I"</span><span class="p">,</span><span class="n" style="color: #333;">arg0</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cpp"> <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;">verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">argPresent</span><span class="p">(</span><span class="s" style="color: #d14;">"verbose"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC55" 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;">BamAlignmentDecoderWrapper</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr_type</span> <span class="n" style="color: #333;">decwrapper0</span><span class="p">(</span><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;">BamMultiAlignmentDecoderFactory</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">construct</span><span class="p">(</span><span class="n" style="color: #333;">arg0</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC56" 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;">BamAlignmentDecoder</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">BD0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">decwrapper0</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getDecoder</span><span class="p">();</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" 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;">BamPeeker</span> <span class="n" style="color: #333;">BP0</span><span class="p">(</span><span class="n" style="color: #333;">BD0</span><span class="p">);</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" 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;">BamAlignment</span> <span class="n" style="color: #333;">algn0</span><span class="p">;</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC60" 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;">BamAlignmentDecoderWrapper</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr_type</span> <span class="n" style="color: #333;">decwrapper1</span><span class="p">(</span><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;">BamMultiAlignmentDecoderFactory</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">construct</span><span class="p">(</span><span class="n" style="color: #333;">arg1</span><span class="p">));</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" 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;">BamAlignmentDecoder</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">BD1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">decwrapper1</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getDecoder</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC62" 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;">BamPeeker</span> <span class="n" style="color: #333;">BP1</span><span class="p">(</span><span class="n" style="color: #333;">BD1</span><span class="p">);</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" 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;">BamAlignment</span> <span class="n" style="color: #333;">algn1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC65" 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;">string</span> <span class="n" style="color: #333;">md5filename</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp"></span>
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67
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<pre style="margin: 0;">+<span id="LC67" 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;">vector</span><span class="o" style="font-weight: 600;"><</span> <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;">lz</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BgzfDeflateOutputCallback</span> <span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">cbs</span><span class="p">;</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" 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;">lz</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BgzfDeflateOutputCallbackMD5</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr_type</span> <span class="n" style="color: #333;">Pmd5cb</span><span class="p">;</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">getParsedArgOrDefault</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="s" style="color: #d14;">"md5"</span><span class="p">,</span><span class="n" style="color: #333;">getDefaultMD5</span><span class="p">())</span> <span class="p">)</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp"> <span class="p">{</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <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;">BamBlockWriterBaseFactory</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getMD5FileName</span><span class="p">(</span><span class="n" style="color: #333;">arg</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</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="p">()</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"> <span class="n" style="color: #333;">md5filename</span> <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;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamBlockWriterBaseFactory</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getMD5FileName</span><span class="p">(</span><span class="n" style="color: #333;">arg</span><span class="p">);</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" 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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[V] no filename for md5 given, not creating hash"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">md5filename</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="p">)</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp"> <span class="p">{</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" 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;">lz</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BgzfDeflateOutputCallbackMD5</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr_type</span> <span class="n" style="color: #333;">Tmd5cb</span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <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;">lz</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BgzfDeflateOutputCallbackMD5</span><span class="p">);</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp"> <span class="n" style="color: #333;">Pmd5cb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">Tmd5cb</span><span class="p">);</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp"> <span class="n" style="color: #333;">cbs</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">Pmd5cb</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">());</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp"> <span class="p">}</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp"> <span class="p">}</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" 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;">vector</span><span class="o" style="font-weight: 600;"><</span> <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;">lz</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BgzfDeflateOutputCallback</span> <span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">Pcbs</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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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">cbs</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="p">)</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cpp"> <span class="n" style="color: #333;">Pcbs</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cbs</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp"></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// construct writer</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" 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;">BamBlockWriterBase</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr_type</span> <span class="n" style="color: #333;">Pwriter</span><span class="p">(</span><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;">BamBlockWriterBaseFactory</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">construct</span><span class="p">(</span><span class="n" style="color: #333;">BD0</span><span class="p">.</span><span class="n" style="color: #333;">getHeader</span><span class="p">(),</span><span class="n" style="color: #333;">arg</span><span class="p">,</span><span class="n" style="color: #333;">Pcbs</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC89" 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;">BamBlockWriterBase</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">wr</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Pwriter</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">c0</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;">c1</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;">k</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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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp"></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span> <span class="n" style="color: #333;">BP0</span><span class="p">.</span><span class="n" style="color: #333;">peekNext</span><span class="p">(</span><span class="n" style="color: #333;">algn0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">BP1</span><span class="p">.</span><span class="n" style="color: #333;">peekNext</span><span class="p">(</span><span class="n" style="color: #333;">algn1</span><span class="p">)</span> <span class="p">)</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp"> <span class="p">{</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp"> <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;">name0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">algn0</span><span class="p">.</span><span class="n" style="color: #333;">getName</span><span class="p">();</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cpp"> <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;">name1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">algn1</span><span class="p">.</span><span class="n" style="color: #333;">getName</span><span class="p">();</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cpp"> <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;">r</span> <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;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">StrCmpNum</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">strcmpnum</span><span class="p">(</span><span class="n" style="color: #333;">name0</span><span class="p">,</span><span class="n" style="color: #333;">name1</span><span class="p">);</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp"></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// name is in file0 but no in file1</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">r</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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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp"> <span class="p">{</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" 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;">string</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">name0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">algn0</span><span class="p">.</span><span class="n" style="color: #333;">getName</span><span class="p">();</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp"></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span> <span class="n" style="color: #333;">BP0</span><span class="p">.</span><span class="n" style="color: #333;">peekNext</span><span class="p">(</span><span class="n" style="color: #333;">algn0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">algn0</span><span class="p">.</span><span class="n" style="color: #333;">getName</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">name0</span> <span class="p">)</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"> <span class="p">{</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp"> <span class="n" style="color: #333;">BP0</span><span class="p">.</span><span class="n" style="color: #333;">getNext</span><span class="p">(</span><span class="n" style="color: #333;">algn0</span><span class="p">);</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp"> <span class="n" style="color: #333;">wr</span><span class="p">.</span><span class="n" style="color: #333;">writeAlignment</span><span class="p">(</span><span class="n" style="color: #333;">algn0</span><span class="p">);</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">c0</span><span class="p">;</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">k</span><span class="p">;</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp"></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp"> <span class="n" style="color: #333;">printVerbose</span><span class="p">(</span><span class="n" style="color: #333;">verbstr</span><span class="p">,</span> <span class="n" style="color: #333;">c0</span><span class="p">,</span> <span class="n" style="color: #333;">c1</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">,</span> <span class="n" style="color: #333;">mod</span><span class="p">);</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp"> <span class="p">}</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="cpp"> <span class="p">}</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// name is in both files, drop data</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp"> <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;">r</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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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cpp"> <span class="p">{</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" 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;">string</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">algn0</span><span class="p">.</span><span class="n" style="color: #333;">getName</span><span class="p">();</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cpp"></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span> <span class="n" style="color: #333;">BP0</span><span class="p">.</span><span class="n" style="color: #333;">peekNext</span><span class="p">(</span><span class="n" style="color: #333;">algn0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">algn0</span><span class="p">.</span><span class="n" style="color: #333;">getName</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">name</span> <span class="p">)</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp"> <span class="p">{</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp"> <span class="n" style="color: #333;">BP0</span><span class="p">.</span><span class="n" style="color: #333;">getNext</span><span class="p">(</span><span class="n" style="color: #333;">algn0</span><span class="p">);</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp"></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">c0</span><span class="p">;</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="cpp"> <span class="n" style="color: #333;">printVerbose</span><span class="p">(</span><span class="n" style="color: #333;">verbstr</span><span class="p">,</span> <span class="n" style="color: #333;">c0</span><span class="p">,</span> <span class="n" style="color: #333;">c1</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">,</span> <span class="n" style="color: #333;">mod</span><span class="p">);</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span> <span class="n" style="color: #333;">BP1</span><span class="p">.</span><span class="n" style="color: #333;">peekNext</span><span class="p">(</span><span class="n" style="color: #333;">algn1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">algn1</span><span class="p">.</span><span class="n" style="color: #333;">getName</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">name</span> <span class="p">)</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp"> <span class="p">{</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp"> <span class="n" style="color: #333;">BP1</span><span class="p">.</span><span class="n" style="color: #333;">getNext</span><span class="p">(</span><span class="n" style="color: #333;">algn1</span><span class="p">);</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cpp"></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">c1</span><span class="p">;</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp"> <span class="n" style="color: #333;">printVerbose</span><span class="p">(</span><span class="n" style="color: #333;">verbstr</span><span class="p">,</span> <span class="n" style="color: #333;">c0</span><span class="p">,</span> <span class="n" style="color: #333;">c1</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">,</span> <span class="n" style="color: #333;">mod</span><span class="p">);</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cpp"> <span class="p">}</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cpp"> <span class="p">}</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// name is only in file1, drop data</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cpp"> <span class="p">{</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" 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;">string</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">name1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">algn1</span><span class="p">.</span><span class="n" style="color: #333;">getName</span><span class="p">();</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="cpp"></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span> <span class="n" style="color: #333;">BP1</span><span class="p">.</span><span class="n" style="color: #333;">peekNext</span><span class="p">(</span><span class="n" style="color: #333;">algn1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">algn1</span><span class="p">.</span><span class="n" style="color: #333;">getName</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">name1</span> <span class="p">)</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="cpp"> <span class="p">{</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="cpp"> <span class="n" style="color: #333;">BP1</span><span class="p">.</span><span class="n" style="color: #333;">getNext</span><span class="p">(</span><span class="n" style="color: #333;">algn1</span><span class="p">);</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="cpp"> <span class="n" style="color: #333;">wr</span><span class="p">.</span><span class="n" style="color: #333;">writeAlignment</span><span class="p">(</span><span class="n" style="color: #333;">algn1</span><span class="p">);</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="cpp"></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">c1</span><span class="p">;</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="cpp"> <span class="n" style="color: #333;">printVerbose</span><span class="p">(</span><span class="n" style="color: #333;">verbstr</span><span class="p">,</span> <span class="n" style="color: #333;">c0</span><span class="p">,</span> <span class="n" style="color: #333;">c1</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">,</span><span class="n" style="color: #333;">mod</span><span class="p">);</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cpp"> <span class="p">}</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="cpp"> <span class="p">}</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="cpp"> <span class="p">}</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="cpp"></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// names only in file0 at end</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span> <span class="n" style="color: #333;">BP0</span><span class="p">.</span><span class="n" style="color: #333;">getNext</span><span class="p">(</span><span class="n" style="color: #333;">algn0</span><span class="p">)</span> <span class="p">)</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="cpp"> <span class="p">{</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="cpp"> <span class="n" style="color: #333;">wr</span><span class="p">.</span><span class="n" style="color: #333;">writeAlignment</span><span class="p">(</span><span class="n" style="color: #333;">algn0</span><span class="p">);</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="cpp"></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">c0</span><span class="p">;</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">k</span><span class="p">;</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="cpp"></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="cpp"> <span class="n" style="color: #333;">printVerbose</span><span class="p">(</span><span class="n" style="color: #333;">verbstr</span><span class="p">,</span> <span class="n" style="color: #333;">c0</span><span class="p">,</span> <span class="n" style="color: #333;">c1</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">,</span><span class="n" style="color: #333;">mod</span><span class="p">);</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="cpp"> <span class="p">}</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="cpp"></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="cpp"> <span class="n" style="color: #333;">Pwriter</span><span class="p">.</span><span class="n" style="color: #333;">reset</span><span class="p">();</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="cpp"></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">Pmd5cb</span> <span class="p">)</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="cpp"> <span class="n" style="color: #333;">Pmd5cb</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">saveDigestAsFile</span><span class="p">(</span><span class="n" style="color: #333;">md5filename</span><span class="p">);</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="cpp"></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">EXIT_SUCCESS</span><span class="p">;</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="cpp"><span class="p">}</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="cpp"></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">argv</span><span class="p">[])</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="cpp"><span class="p">{</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
174
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<pre style="margin: 0;">+<span id="LC174" 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;">vector</span><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;">ArgParser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ArgumentDefinition</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">Vformatcons</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="cpp"> <span class="n" style="color: #333;">Vformatcons</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</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;">ArgParser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ArgumentDefinition</span><span class="p">(</span><span class="s" style="color: #d14;">"h"</span><span class="p">,</span><span class="s" style="color: #d14;">"help"</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="cpp"> <span class="n" style="color: #333;">Vformatcons</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</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;">ArgParser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ArgumentDefinition</span><span class="p">(</span><span class="s" style="color: #d14;">"v"</span><span class="p">,</span><span class="s" style="color: #d14;">"version"</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="cpp"> <span class="n" style="color: #333;">Vformatcons</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</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;">ArgParser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ArgumentDefinition</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">"verbose"</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">));</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="cpp"></span>
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179
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<pre style="margin: 0;">+<span id="LC179" 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;">vector</span><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;">ArgParser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ArgumentDefinition</span><span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Vformatin</span> <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;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamAlignmentDecoderInfo</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getArgumentDefinitions</span><span class="p">();</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" 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;">vector</span><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;">ArgParser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ArgumentDefinition</span><span class="o" style="font-weight: 600;">></span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Vformatout</span> <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;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamBlockWriterBaseFactory</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getArgumentDefinitions</span><span class="p">();</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="cpp"></span>
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182
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<pre style="margin: 0;">+<span id="LC182" 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;">vector</span><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;">ArgParser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ArgumentDefinition</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">Vformat</span> <span class="o" style="font-weight: 600;">=</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" 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;">ArgParser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">mergeFormat</span><span class="p">(</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;">ArgParser</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">mergeFormat</span><span class="p">(</span><span class="n" style="color: #333;">Vformatin</span><span class="p">,</span><span class="n" style="color: #333;">Vformatout</span><span class="p">),</span><span class="n" style="color: #333;">Vformatcons</span><span class="p">);</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="cpp"></span>
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185
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<pre style="margin: 0;">+<span id="LC185" 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;">ArgParser</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">arg</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span><span class="n" style="color: #333;">argv</span><span class="p">,</span><span class="n" style="color: #333;">Vformat</span><span class="p">);</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="cpp"></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">argPresent</span><span class="p">(</span><span class="s" style="color: #d14;">"version"</span><span class="p">)</span> <span class="p">)</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="cpp"> <span class="p">{</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" 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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">biobambam2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Licensing</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">license</span><span class="p">();</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">EXIT_SUCCESS</span><span class="p">;</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="cpp"> <span class="p">}</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="cpp"> <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;">arg</span><span class="p">.</span><span class="n" style="color: #333;">argPresent</span><span class="p">(</span><span class="s" style="color: #d14;">"help"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span> <span class="p">)</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="cpp"> <span class="p">{</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" 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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">biobambam2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Licensing</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">license</span><span class="p">();</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" 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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" 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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"usage: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">progname</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" full.bam partial.bam"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" 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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" 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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Argument:"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" 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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="cpp"></span>
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201
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<pre style="margin: 0;">+<span id="LC201" 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;">vector</span><span class="o" style="font-weight: 600;"><</span> <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="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</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="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">V</span><span class="p">;</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="cpp"></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="cpp"> <span class="n" style="color: #333;">V</span><span class="p">.</span><span class="n" style="color: #333;">push_back</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;">pair</span><span class="o" style="font-weight: 600;"><</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="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="p">(</span> <span class="s" style="color: #d14;">"-v/--verbose"</span><span class="p">,</span> <span class="s" style="color: #d14;">"print progress report"</span> <span class="p">)</span> <span class="p">);</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="cpp"> <span class="n" style="color: #333;">V</span><span class="p">.</span><span class="n" style="color: #333;">push_back</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;">pair</span><span class="o" style="font-weight: 600;"><</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="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="p">(</span> <span class="s" style="color: #d14;">"--md5 <["</span><span class="o" style="font-weight: 600;">+::</span><span class="n" style="color: #333;">biobambam2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Licensing</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">formatNumber</span><span class="p">(</span><span class="n" style="color: #333;">getDefaultMD5</span><span class="p">())</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"]>"</span><span class="p">,</span> <span class="s" style="color: #d14;">"create md5 check sum (default: 0)"</span> <span class="p">)</span> <span class="p">);</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="cpp"> <span class="n" style="color: #333;">V</span><span class="p">.</span><span class="n" style="color: #333;">push_back</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;">pair</span><span class="o" style="font-weight: 600;"><</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="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="p">(</span> <span class="s" style="color: #d14;">"--md5filename <filename>"</span><span class="p">,</span> <span class="s" style="color: #d14;">"file name for md5 check sum (default: extend output file name)"</span> <span class="p">)</span> <span class="p">);</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="cpp"></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">biobambam2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Licensing</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">printMap</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;">cerr</span><span class="p">,</span><span class="n" style="color: #333;">V</span><span class="p">);</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="cpp"></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">argPresent</span><span class="p">(</span><span class="s" style="color: #d14;">"help"</span><span class="p">)</span> <span class="p">)</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">EXIT_SUCCESS</span><span class="p">;</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">EXIT_FAILURE</span><span class="p">;</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="cpp"> <span class="p">}</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">bamintersect</span><span class="p">(</span><span class="n" style="color: #333;">arg</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">catch</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;">exception</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ex</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC219" 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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">ex</span><span class="p">.</span><span class="n" style="color: #333;">what</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">EXIT_FAILURE</span><span class="p">;</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="cpp"> <span class="p">}</span></span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="cpp"><span class="p">}</span></span></pre>
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<li id="f003bbc90ca3edf349c1e28704952dda9ef29682">
<a href="https://salsa.debian.org/med-team/biobambam2/-/commit/b36bccd15b79ea86c241f0014673225bb1d34854#f003bbc90ca3edf349c1e28704952dda9ef29682"><strong>src/programs/bammerge.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">@@ -38,10 +38,6 @@ static std::string getDefaultSortOrder() { return "coordinate"; }</td>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"><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;">getDefaultMD5</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 class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cpp"><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;">getDefaultIndex</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 class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"></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;">#if defined(LIBMAUS2_HAVE_IRODS)</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/irods/IRodsInputStreamFactory.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;">#endif</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC41" 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;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamHeader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr_type</span> <span class="nf" style="color: #900; font-weight: 600;">updateHeader</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC42" 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;">ArgInfo</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">arginfo</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC43" 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;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">BamHeader</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">header</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="239" style="width: 35px; color: rgba(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">@@ -239,14 +235,6 @@ int bammerge(libmaus2::util::ArgInfo const & arginfo)</td>
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="cpp"> <span class="n" style="color: #333;">Pindex</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">flush</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="p">(</span><span class="n" style="color: #333;">indexfilename</span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#if defined(LIBMAUS2_HAVE_IRODS)</span></span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// need a explicit call to disconnect to avoid atexit deallocation problems in iRODS 4.19+</span></span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">irods</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">IRodsSystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">defaultIrodsSystem</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">irods</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">IRodsSystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getDefaultIRodsSystem</span><span class="p">())</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">disconnect</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">EXIT_SUCCESS</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="cpp"></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">@@ -254,19 +242,8 @@ int main(int argc, char * argv[])</td>
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</span></span>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#if defined(LIBMAUS2_HAVE_IRODS)</span></span>
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<pre style="margin: 0;">-<span id="LC258" 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;">irods</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">IRodsInputStreamFactory</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">registerHandler</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC245" 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;">ArgInfo</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">arginfo</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span><span class="n" style="color: #333;">argv</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#if defined(LIBMAUS2_HAVE_IRODS)</span></span>
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// set program name for iRODS identification</span></span>
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<pre style="margin: 0;">-<span id="LC265" 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;">stringstream</span> <span class="n" style="color: #333;">irods_id</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="cpp"> <span class="n" style="color: #333;">irods_id</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">PACKAGE_NAME</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">":"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">arginfo</span><span class="p">.</span><span class="n" style="color: #333;">getProgFileName</span><span class="p">(</span><span class="n" style="color: #333;">arginfo</span><span class="p">.</span><span class="n" style="color: #333;">progname</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">":"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">PACKAGE_VERSION</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="cpp"> <span class="n" style="color: #333;">setenv</span><span class="p">(</span><span class="n" style="color: #333;">SP_OPTION</span><span class="p">,</span> <span class="n" style="color: #333;">irods_id</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">arginfo</span><span class="p">.</span><span class="n" style="color: #333;">restargs</span><span class="p">.</span><span class="n" style="color: #333;">size</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>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span></span>
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249
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="cpp"> <span class="n" style="color: #333;">arginfo</span><span class="p">.</span><span class="n" style="color: #333;">restargs</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="s" style="color: #d14;">"-v"</span></span>
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<a href="https://salsa.debian.org/med-team/biobambam2/-/commit/b36bccd15b79ea86c241f0014673225bb1d34854#be752f41aab032268ccb172abc929cf063a40400"><strong>src/programs/bamtofastq.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">@@ -761,7 +761,7 @@ void bamtofastqCollating(</td>
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761
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761
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<pre style="margin: 0;"> <span id="LC761" class="line" lang="cpp"> <span class="p">}</span></span>
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762
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762
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<pre style="margin: 0;"> <span id="LC762" class="line" lang="cpp"></span>
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763
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<pre style="margin: 0;"> <span id="LC763" class="line" lang="cpp"> <span class="n" style="color: #333;">AOS</span><span class="p">[</span><span class="n" style="color: #333;">rgfshift</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">O2map</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">write</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;">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;">T</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()),</span><span class="n" style="color: #333;">la</span><span class="p">);</span></span>
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764
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<pre style="margin: 0;">-<span id="LC764" class="line" lang="cpp"> <span class="n" style="color: #333;">filefrags</span><span class="p">[</span><span class="n" style="color: #333;">rgfshift</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">Omap</span><span class="p">]</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC764" class="line" lang="cpp"> <span class="n" style="color: #333;">filefrags</span><span class="p">[</span><span class="n" style="color: #333;">rgfshift</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">O<span class="idiff left right">2</span>map</span><span class="p">]</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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765
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<pre style="margin: 0;"> <span id="LC765" class="line" lang="cpp"></span>
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766
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766
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<pre style="margin: 0;"> <span id="LC766" class="line" lang="cpp"> <span class="n" style="color: #333;">combs</span><span class="p">.</span><span class="n" style="color: #333;">orphans2</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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767
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<pre style="margin: 0;"> <span id="LC767" class="line" lang="cpp"> <span class="n" style="color: #333;">cnt</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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1240,29 +1240,14 @@ void bamtofastq(libmaus2::util::ArgInfo const & arginfo)</td>
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1240
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1240
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<pre style="margin: 0;"> <span id="LC1240" class="line" lang="cpp"> <span class="p">}</span></span>
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1241
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<pre style="margin: 0;"> <span id="LC1241" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1242" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC1243" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if defined(LIBMAUS2_HAVE_IRODS)</span></span>
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<pre style="margin: 0;">-<span id="LC1244" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/irods/IRodsInputStreamFactory.hpp></span></span>
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<pre style="margin: 0;">-<span id="LC1245" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">-<span id="LC1246" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1243" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">argv</span><span class="p">[])</span></span>
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<pre style="margin: 0;"> <span id="LC1244" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1245" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</span></span>
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<pre style="margin: 0;"> <span id="LC1246" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1251" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#if defined(LIBMAUS2_HAVE_IRODS)</span></span>
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<pre style="margin: 0;">-<span id="LC1252" 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;">irods</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">IRodsInputStreamFactory</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">registerHandler</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC1253" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">-<span id="LC1254" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1247" 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;">timing</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">RealTimeClock</span> <span class="n" style="color: #333;">rtc</span><span class="p">;</span> <span class="n" style="color: #333;">rtc</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC1248" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1249" 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;">ArgInfo</span> <span class="n" style="color: #333;">arginfo</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span><span class="n" style="color: #333;">argv</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC1250" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC1259" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#if defined(LIBMAUS2_HAVE_IRODS)</span></span>
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<pre style="margin: 0;">-<span id="LC1260" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// set program name for iRODS identification</span></span>
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<pre style="margin: 0;">-<span id="LC1261" 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;">stringstream</span> <span class="n" style="color: #333;">irods_id</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC1262" class="line" lang="cpp"> <span class="n" style="color: #333;">irods_id</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">PACKAGE_NAME</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">":"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">arginfo</span><span class="p">.</span><span class="n" style="color: #333;">getProgFileName</span><span class="p">(</span><span class="n" style="color: #333;">arginfo</span><span class="p">.</span><span class="n" style="color: #333;">progname</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">":"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">PACKAGE_VERSION</span><span class="p">;</span></span>
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1263
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<pre style="margin: 0;">-<span id="LC1263" class="line" lang="cpp"> <span class="n" style="color: #333;">setenv</span><span class="p">(</span><span class="n" style="color: #333;">SP_OPTION</span><span class="p">,</span> <span class="n" style="color: #333;">irods_id</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC1264" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">-<span id="LC1265" class="line" lang="cpp"></span>
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1251
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<pre style="margin: 0;"> <span id="LC1251" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">arginfo</span><span class="p">.</span><span class="n" style="color: #333;">restargs</span><span class="p">.</span><span class="n" style="color: #333;">size</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>
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<pre style="margin: 0;"> <span id="LC1252" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span></span>
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1253
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<pre style="margin: 0;"> <span id="LC1253" class="line" lang="cpp"> <span class="n" style="color: #333;">arginfo</span><span class="p">.</span><span class="n" style="color: #333;">restargs</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="s" style="color: #d14;">"-v"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1369" style="width: 35px; color: rgba(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">@@ -1369,14 +1354,6 @@ int main(int argc, char * argv[])</td>
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1369
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1354
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<pre style="margin: 0;"> <span id="LC1354" class="line" lang="cpp"></span>
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1370
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1355
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<pre style="margin: 0;"> <span id="LC1355" class="line" lang="cpp"> <span class="n" style="color: #333;">bamtofastq</span><span class="p">(</span><span class="n" style="color: #333;">arginfo</span><span class="p">);</span></span>
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1371
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1356
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<pre style="margin: 0;"> <span id="LC1356" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC1372" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#if defined(LIBMAUS2_HAVE_IRODS)</span></span>
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<pre style="margin: 0;">-<span id="LC1373" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// need a explicit call to disconnect to avoid atexit deallocation problems in iRODS 4.19+</span></span>
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<pre style="margin: 0;">-<span id="LC1374" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">irods</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">IRodsSystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">defaultIrodsSystem</span><span class="p">)</span></span>
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1375
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<pre style="margin: 0;">-<span id="LC1375" class="line" lang="cpp"> <span class="p">{</span></span>
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1376
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<pre style="margin: 0;">-<span id="LC1376" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">libmaus2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">irods</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">IRodsSystem</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getDefaultIRodsSystem</span><span class="p">())</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">disconnect</span><span class="p">();</span></span>
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1377
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<pre style="margin: 0;">-<span id="LC1377" class="line" lang="cpp"> <span class="p">}</span></span>
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1378
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<pre style="margin: 0;">-<span id="LC1378" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1379
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<pre style="margin: 0;">-<span id="LC1379" class="line" lang="cpp"></span>
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1380
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1357
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<pre style="margin: 0;"> <span id="LC1357" 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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[V] "</span> <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;">MemUsage</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" wall clock time "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">rtc</span><span class="p">.</span><span class="n" style="color: #333;">formatTime</span><span class="p">(</span><span class="n" style="color: #333;">rtc</span><span class="p">.</span><span class="n" style="color: #333;">getElapsedSeconds</span><span class="p">())</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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1381
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1358
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<pre style="margin: 0;"> <span id="LC1358" class="line" lang="cpp"> <span class="p">}</span></span>
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1382
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1359
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<pre style="margin: 0;"> <span id="LC1359" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">catch</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;">exception</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ex</span><span class="p">)</span></span>
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<li id="5996963c0b0cac34c60d4ecc66918c31b32d6518">
<a href="https://salsa.debian.org/med-team/biobambam2/-/commit/b36bccd15b79ea86c241f0014673225bb1d34854#5996963c0b0cac34c60d4ecc66918c31b32d6518"><strong>src/programs/blastnxmltobam.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">@@ -54,7 +54,7 @@ static std::string stripAfterSpace(std::string const & s)</td>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp"><span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">XercesUtf8Transcoder</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">XercesUtf8Transcoder</span> <span class="n" style="color: #333;">this_type</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;"><span class="idiff left">libmaus2</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">util</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">unique_ptr</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">this_type</span></span><span class="o" style="font-weight: 600;"><span class="idiff">>::</span></span><span class="n" style="color: #333;"><span class="idiff right">type</span></span> <span class="n" style="color: #333;">unique_ptr_type</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">unique_ptr</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">this_type</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">></span></span> <span class="n" style="color: #333;">unique_ptr_type</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp"> <span class="n" style="color: #333;">xercesc</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">XMLTransService</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ts</span><span class="p">;</span></span>
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60
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp"> <span class="n" style="color: #333;">xercesc</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">XMLTranscoder</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">utf8transcoder</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">@@ -1136,12 +1136,12 @@ int main(int argc, char * argv[])</td>
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1136
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1136
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<pre style="margin: 0;"> <span id="LC1136" 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;">string</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">reffn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arginfo</span><span class="p">.</span><span class="n" style="color: #333;">restargs</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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1137
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1137
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<pre style="margin: 0;"> <span id="LC1137" 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;">string</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">queriesfn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arginfo</span><span class="p">.</span><span class="n" style="color: #333;">restargs</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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1138
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1138
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<pre style="margin: 0;"> <span id="LC1138" class="line" lang="cpp"></span>
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1139
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<pre style="margin: 0;">-<span id="LC1139" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">libmaus2</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">util</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">unique_ptr</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">vector</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">libmaus2</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">bambam</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">CramRange</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">>::</span></span><span class="n" style="color: #333;"><span class="idiff right">type</span></span> <span class="n" style="color: #333;">Pranges</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1139" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">unique_ptr</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">vector</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">libmaus2</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">bambam</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">CramRange</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">></span></span> <span class="n" style="color: #333;">Pranges</span><span class="p">;</span></span>
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1140
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1140
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<pre style="margin: 0;"> <span id="LC1140" 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;">vector</span><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;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CramRange</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ranges</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1141" class="line" lang="cpp"></span>
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1142
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<pre style="margin: 0;"> <span id="LC1142" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">arginfo</span><span class="p">.</span><span class="n" style="color: #333;">hasArg</span><span class="p">(</span><span class="s" style="color: #d14;">"range"</span><span class="p">)</span> <span class="p">)</span></span>
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1143
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<pre style="margin: 0;"> <span id="LC1143" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1144" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">libmaus2</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">util</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">unique_ptr</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">vector</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">libmaus2</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">bambam</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">CramRange</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">>::</span></span><span class="n" style="color: #333;"><span class="idiff right">type</span></span> <span class="n" style="color: #333;">Tranges</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC1144" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">unique_ptr</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">vector</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">libmaus2</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">bambam</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">CramRange</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">></span></span> <span class="n" style="color: #333;">Tranges</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC1145" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><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;">bambam</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CramRange</span><span class="o" style="font-weight: 600;">></span></span>
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<pre style="margin: 0;"> <span id="LC1146" class="line" lang="cpp"> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC1147" class="line" lang="cpp"> <span class="n" style="color: #333;">Pranges</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">Tranges</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/biobambam2/-/commit/b36bccd15b79ea86c241f0014673225bb1d34854#ab5115e6c5d8836f3f68486cbaf80c86d2df924f"><strong>src/programs/fastaselectreg.cpp</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> biobambam2</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> Copyright (C) 2020 German Tischler</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> This program is free software: you can redistribute it and/or modify</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> it under the terms of the GNU General Public License as published by</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> the Free Software Foundation, either version 3 of the License, or</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> (at your option) any later version.</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> This program is distributed in the hope that it will be useful,</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> GNU General Public License for more details.</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> You should have received a copy of the GNU General Public License</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> along with this program. If not, see <http://www.gnu.org/licenses/>.</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cpp"></span>
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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 <iostream></span></span>
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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/util/ArgParser.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/fastx/StreamFastAReader.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/lz/PlainOrGzipStream.hpp></span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp"></span>
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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 <biobambam2/BamBamConfig.hpp></span></span>
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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 <biobambam2/Licensing.hpp></span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp"></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <regex></span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp"></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <libmaus2/lz/GzipOutputStream.hpp></span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp"></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="nf" style="color: #900; font-weight: 600;">getDefaultLineLength</span><span class="p">()</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cpp"><span class="p">{</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">80</span><span class="p">;</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp"><span class="p">}</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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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * read a FastA file (possibly gziped) from stdin, select sequences with (short)</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * names matching a given regular expression (argument, Posix extended regex)</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * and output selected sequences on stdout (gziped if -g or --gzip is set).</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Options:</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * - singleline: output a single line of sequence data per record (i.e. do not wrap)</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * - longname: do not shorten the sequence name line</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * - dataonly: output data only, drop FastA headers (lines starting with >)</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * - up: transform all sequence symbols to upper case</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * - gzip: compress output using gzip</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * - verbose: print which sequences are kept and which are discarded</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * - l<len>: wrap sequence lines after this number of symbols (default 80)</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> **/</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">fastaselectreg</span><span class="p">(</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;">ArgParser</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">arg</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC52" 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;">PlainOrGzipStream</span> <span class="n" style="color: #333;">POS</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;">cin</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC53" 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;">fastx</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">StreamFastAReaderWrapper</span> <span class="n" style="color: #333;">SFA</span><span class="p">(</span><span class="n" style="color: #333;">POS</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC54" 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;">fastx</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">StreamFastAReaderWrapper</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pattern_type</span> <span class="n" style="color: #333;">pattern</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC55" 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;">linelength</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">uniqueArgPresent</span><span class="p">(</span><span class="s" style="color: #d14;">"l"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">getUnsignedNumericArg</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="s" style="color: #d14;">"l"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">getDefaultLineLength</span><span class="p">();</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" 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;">regex</span> <span class="n" style="color: #333;">reg</span><span class="p">(</span><span class="n" style="color: #333;">arg</span><span class="p">[</span><span class="mi" style="color: #099;">0</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;">regex_constants</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">extended</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp"> <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;">singleline</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">argPresent</span><span class="p">(</span><span class="s" style="color: #d14;">"s"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">argPresent</span><span class="p">(</span><span class="s" style="color: #d14;">"singleline"</span><span class="p">);</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp"> <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;">longname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">argPresent</span><span class="p">(</span><span class="s" style="color: #d14;">"L"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">argPresent</span><span class="p">(</span><span class="s" style="color: #d14;">"longname"</span><span class="p">);</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="cpp"> <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;">dataonly</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">argPresent</span><span class="p">(</span><span class="s" style="color: #d14;">"d"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">argPresent</span><span class="p">(</span><span class="s" style="color: #d14;">"dataonly"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cpp"> <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;">up</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">argPresent</span><span class="p">(</span><span class="s" style="color: #d14;">"u"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">argPresent</span><span class="p">(</span><span class="s" style="color: #d14;">"toupper"</span><span class="p">);</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp"> <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;">gzip</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">argPresent</span><span class="p">(</span><span class="s" style="color: #d14;">"g"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">argPresent</span><span class="p">(</span><span class="s" style="color: #d14;">"gzip"</span><span class="p">);</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp"> <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;">verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">argPresent</span><span class="p">(</span><span class="s" style="color: #d14;">"verbose"</span><span class="p">);</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp"></span>
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65
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<pre style="margin: 0;">+<span id="LC65" 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;">GzipOutputStream</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr_type</span> <span class="n" style="color: #333;">gzptr</span><span class="p">;</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" 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;">ostream</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ostr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span><span class="p">;</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">gzip</span> <span class="p">)</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp"> <span class="p">{</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" 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;">GzipOutputStream</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr_type</span> <span class="n" style="color: #333;">tgzptr</span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <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;">GzipOutputStream</span><span class="p">(</span><span class="n" style="color: #333;">ostr</span><span class="p">));</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp"> <span class="n" style="color: #333;">gzptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">tgzptr</span><span class="p">);</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp"> <span class="p">}</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" 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;">ostream</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">OSI</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gzptr</span> <span class="o" style="font-weight: 600;">?</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">gzptr</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">ostr</span><span class="p">;</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span> <span class="n" style="color: #333;">SFA</span><span class="p">.</span><span class="n" style="color: #333;">getNextPatternUnlocked</span><span class="p">(</span><span class="n" style="color: #333;">pattern</span><span class="p">)</span> <span class="p">)</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp"> <span class="p">{</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" 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;">string</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">spat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern</span><span class="p">.</span><span class="n" style="color: #333;">spattern</span><span class="p">;</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp"></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">up</span> <span class="p">)</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">spat</span><span class="p">.</span><span class="n" style="color: #333;">size</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>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp"> <span class="n" style="color: #333;">spat</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;">toupper</span><span class="p">(</span><span class="n" style="color: #333;">spat</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC81" 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;">string</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">shortname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pattern</span><span class="p">.</span><span class="n" style="color: #333;">getShortStringId</span><span class="p">();</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp"></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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;">regex_match</span><span class="p">(</span><span class="n" style="color: #333;">shortname</span><span class="p">,</span><span class="n" style="color: #333;">reg</span><span class="p">)</span> <span class="p">)</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp"> <span class="p">{</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">verbose</span> <span class="p">)</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" 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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[K] keeping "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">shortname</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp"></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp"> <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;">longname</span> <span class="p">)</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern</span><span class="p">.</span><span class="n" style="color: #333;">sid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">shortname</span><span class="p">;</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cpp"></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">dataonly</span> <span class="p">)</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp"> <span class="n" style="color: #333;">OSI</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">pattern</span><span class="p">.</span><span class="n" style="color: #333;">spattern</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span><span class="n" style="color: #333;">pattern</span><span class="p">.</span><span class="n" style="color: #333;">spattern</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp"> <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;">singleline</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp"> <span class="n" style="color: #333;">OSI</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">pattern</span><span class="p">;</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cpp"> <span class="n" style="color: #333;">pattern</span><span class="p">.</span><span class="n" style="color: #333;">printMultiLine</span><span class="p">(</span><span class="n" style="color: #333;">OSI</span><span class="p">,</span><span class="n" style="color: #333;">linelength</span><span class="p">);</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cpp"> <span class="p">}</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp"> <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;">verbose</span> <span class="p">)</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp"> <span class="p">{</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" 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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[K] discarding "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">shortname</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp"> <span class="p">}</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp"> <span class="p">}</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp"></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">EXIT_SUCCESS</span><span class="p">;</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"><span class="p">}</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp"></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">argv</span><span class="p">[])</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"><span class="p">{</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cpp"> <span class="p">{</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" 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;">ArgParser</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">arg</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span><span class="n" style="color: #333;">argv</span><span class="p">);</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp"></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="cpp"> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">uniqueArgPresent</span><span class="p">(</span><span class="s" style="color: #d14;">"v"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">uniqueArgPresent</span><span class="p">(</span><span class="s" style="color: #d14;">"version"</span><span class="p">)</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="cpp"> <span class="p">)</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp"> <span class="p">{</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" 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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">biobambam2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Licensing</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">license</span><span class="p">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">EXIT_SUCCESS</span><span class="p">;</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cpp"> <span class="p">}</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp"> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">uniqueArgPresent</span><span class="p">(</span><span class="s" style="color: #d14;">"h"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">uniqueArgPresent</span><span class="p">(</span><span class="s" style="color: #d14;">"help"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp"> <span class="p">)</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC124" 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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">biobambam2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Licensing</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">license</span><span class="p">();</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" 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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" 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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"usage: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">progname</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" <regex> <in.fasta > out.fasta"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" 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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" 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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"options:"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" 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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cpp"></span>
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131
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<pre style="margin: 0;">+<span id="LC131" 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;">vector</span><span class="o" style="font-weight: 600;"><</span> <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="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</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="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">V</span><span class="p">;</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp"></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cpp"> <span class="n" style="color: #333;">V</span><span class="p">.</span><span class="n" style="color: #333;">push_back</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;">pair</span><span class="o" style="font-weight: 600;"><</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="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="p">(</span> <span class="s" style="color: #d14;">"-v/--version"</span><span class="p">,</span> <span class="s" style="color: #d14;">"print version number and quit"</span> <span class="p">)</span> <span class="p">);</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cpp"> <span class="n" style="color: #333;">V</span><span class="p">.</span><span class="n" style="color: #333;">push_back</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;">pair</span><span class="o" style="font-weight: 600;"><</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="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="p">(</span> <span class="s" style="color: #d14;">"-h/--help"</span><span class="p">,</span> <span class="s" style="color: #d14;">"print help message and quit"</span> <span class="p">)</span> <span class="p">);</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="cpp"> <span class="n" style="color: #333;">V</span><span class="p">.</span><span class="n" style="color: #333;">push_back</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;">pair</span><span class="o" style="font-weight: 600;"><</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="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="p">(</span> <span class="s" style="color: #d14;">"-l<cols>"</span><span class="p">,</span> <span class="s" style="color: #d14;">"line length (default: "</span><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;">NumberSerialisation</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">formatNumber</span><span class="p">(</span><span class="n" style="color: #333;">getDefaultLineLength</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="s" style="color: #d14;">")"</span> <span class="p">)</span> <span class="p">);</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="cpp"> <span class="n" style="color: #333;">V</span><span class="p">.</span><span class="n" style="color: #333;">push_back</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;">pair</span><span class="o" style="font-weight: 600;"><</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="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="p">(</span> <span class="s" style="color: #d14;">"-s/--singleline"</span><span class="p">,</span> <span class="s" style="color: #d14;">"do not wrap sequence data lines"</span> <span class="p">)</span> <span class="p">);</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cpp"> <span class="n" style="color: #333;">V</span><span class="p">.</span><span class="n" style="color: #333;">push_back</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;">pair</span><span class="o" style="font-weight: 600;"><</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="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="p">(</span> <span class="s" style="color: #d14;">"-L/--longname"</span><span class="p">,</span> <span class="s" style="color: #d14;">"do not shorten name"</span> <span class="p">)</span> <span class="p">);</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="cpp"> <span class="n" style="color: #333;">V</span><span class="p">.</span><span class="n" style="color: #333;">push_back</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;">pair</span><span class="o" style="font-weight: 600;"><</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="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="p">(</span> <span class="s" style="color: #d14;">"-d/--dataonly"</span><span class="p">,</span> <span class="s" style="color: #d14;">"do not print FastA header (data only)"</span> <span class="p">)</span> <span class="p">);</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="cpp"> <span class="n" style="color: #333;">V</span><span class="p">.</span><span class="n" style="color: #333;">push_back</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;">pair</span><span class="o" style="font-weight: 600;"><</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="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="p">(</span> <span class="s" style="color: #d14;">"-u/--toupper"</span><span class="p">,</span> <span class="s" style="color: #d14;">"convert sequence symbols to upper case"</span> <span class="p">)</span> <span class="p">);</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cpp"> <span class="n" style="color: #333;">V</span><span class="p">.</span><span class="n" style="color: #333;">push_back</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;">pair</span><span class="o" style="font-weight: 600;"><</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="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="p">(</span> <span class="s" style="color: #d14;">"-g/--gzip"</span><span class="p">,</span> <span class="s" style="color: #d14;">"compress output"</span> <span class="p">)</span> <span class="p">);</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">biobambam2</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Licensing</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">printMap</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;">cerr</span><span class="p">,</span><span class="n" style="color: #333;">V</span><span class="p">);</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="cpp"></span>
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144
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<pre style="margin: 0;">+<span id="LC144" 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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">EXIT_SUCCESS</span><span class="p">;</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="cpp"></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cpp"> <span class="p">}</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="cpp"></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">fastaselectreg</span><span class="p">(</span><span class="n" style="color: #333;">arg</span><span class="p">);</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="cpp"> <span class="p">}</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">catch</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;">exception</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ex</span><span class="p">)</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="cpp"> <span class="p">{</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" 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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">ex</span><span class="p">.</span><span class="n" style="color: #333;">what</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">EXIT_FAILURE</span><span class="p">;</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="cpp"> <span class="p">}</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="cpp"><span class="p">}</span></span></pre>
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