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<h3>

Andreas Tille pushed to branch upstream

at <a href="https://salsa.debian.org/med-team/segemehl">Debian Med / segemehl</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/segemehl/commit/c43e3da4a55a7830f3855647bcc93fc3ba7f8913">c43e3da4</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-12-04T09:13:56Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.3.2</pre>

</li>

</ul>

<h4>10 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">

Makefile

</a>

</li>

<li class="file-stats">

<a href="#73a7ba9107dd4cfcfe0535d89abcea2e22dccac2">

Makefile.bak

</a>

</li>

<li class="file-stats">

<a href="#c879736bc4600d92e5683925c65282a9ab8989b8">

include/version.h

</a>

</li>

<li class="file-stats">

<a href="#d15b4ce2ccb17c25c6ddda769fea509c9a860979">

include/version.h.bak

</a>

</li>

<li class="file-stats">

<a href="#49cfca3ba0c6de143651770e7b1ae8aae5c3a7ff">

libs/biofiles.c

</a>

</li>

<li class="file-stats">

<a href="#78b9626f18f502deb715aae39a74a38737e4bf3d">

libs/gzidx.c

</a>

</li>

<li class="file-stats">

<a href="#5bee75db0d128a8723dfa418084565536c5b1fcf">

libs/haarz.c

</a>

</li>

<li class="file-stats">

<a href="#3b57e51818aa12c0e7b2aa12afe948a3497dfc35">

libs/manopt.c

</a>

</li>

<li class="file-stats">

<a href="#e3898fa62334b4ca938ab0571797fab5e4704e7d">

libs/multicharseq.c

</a>

</li>

<li class="file-stats">

<a href="#ada2196463c4fc6111aca438facbe014f2a026b0">

libs/samio.c

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">

<a href="https://salsa.debian.org/med-team/segemehl/commit/c43e3da4a55a7830f3855647bcc93fc3ba7f8913#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c"><strong>Makefile</strong></a>

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1

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1" class="line" lang="make"><span class="nv" style="color: teal;">CC</span><span class="o" style="font-weight: 600;">?=</span>gcc</span>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="make"><span class="nv" style="color: teal;">LD</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">CC</span><span class="k" style="font-weight: 600;">}</span></span>

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3" class="line" lang="make"><span class="nv" style="color: teal;">CFLAGS</span><span class="o" style="font-weight: 600;">=</span>  <span class="nt" style="color: navy;">-Wall</span> <span class="nt" style="color: navy;">-pedantic</span> <span class="nt" style="color: navy;">-std</span><span class="o" style="font-weight: 600;">=</span>c99 <span class="nt" style="color: navy;">-g</span> <span class="nt" style="color: navy;">-O3</span> <span class="nt" style="color: navy;">-DSORTEDUNMAPPED</span> <span class="nt" style="color: navy;">-D_LARGEFILE_SOURCE</span> <span class="nt" style="color: navy;">-D_FILE_OFFSET_BITS</span><span class="o" style="font-weight: 600;">=</span>64 <span class="nt" style="color: navy;">-DDBGNFO</span> <span class="nt" style="color: navy;">-DSHOWALIGN</span> <span class="nt" style="color: navy;">-DDBGLEVEL</span><span class="o" style="font-weight: 600;">=</span>0 <span class="nt" style="color: navy;">-DPROGNFO</span> <span class="nt" style="color: navy;">-Ilibs</span> <span class="nt" style="color: navy;">-Ilibs</span>/sufarray <span class="nt" style="color: navy;">-Isamtools</span></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="make"><span class="nv" style="color: teal;">CFLAGS</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">+</span>=</span>  <span class="nt" style="color: navy;">-Wall</span> <span class="nt" style="color: navy;">-pedantic</span> <span class="nt" style="color: navy;">-std</span><span class="o" style="font-weight: 600;">=</span>c99 <span class="nt" style="color: navy;">-g</span> <span class="nt" style="color: navy;">-O3</span> <span class="nt" style="color: navy;">-DSORTEDUNMAPPED</span> <span class="nt" style="color: navy;">-D_LARGEFILE_SOURCE</span> <span class="nt" style="color: navy;">-D_FILE_OFFSET_BITS</span><span class="o" style="font-weight: 600;">=</span>64 <span class="nt" style="color: navy;">-DDBGNFO</span> <span class="nt" style="color: navy;">-DSHOWALIGN</span> <span class="nt" style="color: navy;">-DDBGLEVEL</span><span class="o" style="font-weight: 600;">=</span>0 <span class="nt" style="color: navy;">-DPROGNFO</span> <span class="nt" style="color: navy;">-Ilibs</span> <span class="nt" style="color: navy;">-Ilibs</span>/sufarray <span class="nt" style="color: navy;">-Isamtools</span></span>

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<td class="diff-line-num old_line" data-linenumber="4" 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="4" 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="LC4" class="line" lang="make"><span class="nv" style="color: teal;">CFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="sb" style="color: #d14;">`</span>pkg-config <span class="nt" style="color: navy;">--cflags</span> htslib<span class="sb" style="color: #d14;">`</span></span>

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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5" class="line" lang="make"><span class="nv" style="color: teal;">INC</span> <span class="o" style="font-weight: 600;">:=</span> <span class="nt" style="color: navy;">-I</span> include</span>

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC6" class="line" lang="make"><span class="nv" style="color: teal;">CTAGS</span> <span class="o" style="font-weight: 600;">=</span> ctags <span class="o" style="font-weight: 600;">></span> tags</span>

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<td class="diff-line-num new_line old" data-linenumber="7" 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="LC7" class="line" lang="make"><span class="nv" style="color: teal;">LIB</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: navy;">-lm</span> <span class="nt" style="color: navy;">-lpthread</span> <span class="nt" style="color: navy;">-lz</span> <span class="nt" style="color: navy;">-lncurses</span> <span class="nt" style="color: navy;">-L</span> libs <span class="nt" style="color: navy;">-lform</span> <span class="nt" style="color: navy;">-lmenu</span> <span class="nt" style="color: navy;">-L</span>/usr/local/lib/</span>

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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="7" 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="LC7" class="line" lang="make"><span class="nv" style="color: teal;">LIB</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">+</span>=</span> <span class="nt" style="color: navy;">-lm</span> <span class="nt" style="color: navy;">-lpthread</span> <span class="nt" style="color: navy;">-lz</span> <span class="nt" style="color: navy;">-lncurses</span> <span class="nt" style="color: navy;">-L</span> libs <span class="nt" style="color: navy;">-lform</span> <span class="nt" style="color: navy;">-lmenu</span> <span class="nt" style="color: navy;">-L</span>/usr/local/lib/</span>

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<td class="diff-line-num old_line" data-linenumber="8" 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="LC8" class="line" lang="make"><span class="nv" style="color: teal;">LIB</span> <span class="o" style="font-weight: 600;">+=</span> <span class="sb" style="color: #d14;">`</span>pkg-config <span class="nt" style="color: navy;">--libs</span> htslib<span class="sb" style="color: #d14;">`</span></span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="make"><span class="nv" style="color: teal;">LIB</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s2" style="color: #d14;">"-Wl,-rpath,</span><span class="sb" style="color: #d14;">`</span>pkg-config <span class="nt" style="color: navy;">--variable</span><span class="o" style="font-weight: 600;">=</span>libdir htslib<span class="sb" style="color: #d14;">`</span><span class="s2" style="color: #d14;">"</span></span>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="make"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -30,7 +30,7 @@ LIBOBJECTS :=  $(patsubst $(LIBDIR)/%,$(BUILDDIR)/%,$(LIBSOURCES:.$(SRCEXT)=.o))</td>

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30

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<td class="diff-line-num new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC30" class="line" lang="make"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

31

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<td class="diff-line-num new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="make"><span class="nl">$(PRGTARGETS)</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(OBJECTS)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

32

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<td class="diff-line-num new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="make">  <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Linking </span><span class="nv" style="color: teal;">$@</span><span class="s2" style="color: #d14;">"</span><span class="p">;</span>  </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="33" 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="LC33" class="line" lang="make">  <span class="nv" style="color: teal;">$(LD)</span> <span class="nv" style="color: teal;">$(LIBOBJECTS)</span> <span class="nv" style="color: teal;">$(BUILDDIR)</span>/<span class="nv" style="color: teal;">$@</span>.o <span class="nt" style="color: navy;">-o</span> <span class="nv" style="color: teal;">$(TARGETDIR)</span>/<span class="nv" style="color: teal;">$@$(TARGETEXT)</span> <span class="nv" style="color: teal;">$(LIB)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

33

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="make">  <span class="nv" style="color: teal;">$(LD)</span> <span class="nv" style="color: teal;">$(LIBOBJECTS)</span> <span class="nv" style="color: teal;">$(BUILDDIR)</span>/<span class="nv" style="color: teal;">$@</span>.o <span class="nt" style="color: navy;">-o</span> <span class="nv" style="color: teal;">$(TARGETDIR)</span>/<span class="nv" style="color: teal;">$@$(TARGETEXT)</span> <span class="nv" style="color: teal;">$(LIB)</span><span class="idiff left"> </span><span class="nv" style="color: teal;"><span class="idiff right">$(LDFLAGS)</span></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

34

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<td class="diff-line-num new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

34

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC34" class="line" lang="make"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

35

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<td class="diff-line-num new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC35" class="line" lang="make"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

36

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<td class="diff-line-num new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

36

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC36" class="line" lang="make"><span class="nl">$(BUILDDIR)/%.o</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(LIBDIR)/%.c</span></span>

</pre>

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</table>

<br>

</li>

<li id="73a7ba9107dd4cfcfe0535d89abcea2e22dccac2">

<a href="https://salsa.debian.org/med-team/segemehl/commit/c43e3da4a55a7830f3855647bcc93fc3ba7f8913#73a7ba9107dd4cfcfe0535d89abcea2e22dccac2"><strong>Makefile.bak</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num old_line" data-linenumber="1" 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">

1

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<td class="diff-line-num new_line" data-linenumber="1" 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">

1

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1" class="line" lang="make"><span class="nv" style="color: teal;">CC</span><span class="o" style="font-weight: 600;">?=</span>gcc</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2" class="line" lang="make"><span class="nv" style="color: teal;">LD</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">CC</span><span class="k" style="font-weight: 600;">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="3" 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">

3

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<td class="diff-line-num new_line old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3" class="line" lang="make"><span class="nv" style="color: teal;">CFLAGS</span><span class="o" style="font-weight: 600;">=</span>  <span class="nt" style="color: navy;">-Wall</span> <span class="nt" style="color: navy;">-pedantic</span> <span class="nt" style="color: navy;">-std</span><span class="o" style="font-weight: 600;">=</span>c99 <span class="nt" style="color: navy;">-g</span> <span class="nt" style="color: navy;">-O3</span> <span class="nt" style="color: navy;">-DSORTEDUNMAPPED</span> <span class="nt" style="color: navy;">-D_LARGEFILE_SOURCE</span> <span class="nt" style="color: navy;">-D_FILE_OFFSET_BITS</span><span class="o" style="font-weight: 600;">=</span>64 <span class="nt" style="color: navy;">-DDBGNFO</span> <span class="nt" style="color: navy;">-DSHOWALIGN</span> <span class="nt" style="color: navy;">-DDBGLEVEL</span><span class="o" style="font-weight: 600;">=</span>0 <span class="nt" style="color: navy;">-DPROGNFO</span> <span class="nt" style="color: navy;">-Ilibs</span> <span class="nt" style="color: navy;">-Ilibs</span>/sufarray <span class="nt" style="color: navy;">-Isamtools</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<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">

3

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="make"><span class="nv" style="color: teal;">CFLAGS</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">+</span>=</span>  <span class="nt" style="color: navy;">-Wall</span> <span class="nt" style="color: navy;">-pedantic</span> <span class="nt" style="color: navy;">-std</span><span class="o" style="font-weight: 600;">=</span>c99 <span class="nt" style="color: navy;">-g</span> <span class="nt" style="color: navy;">-O3</span> <span class="nt" style="color: navy;">-DSORTEDUNMAPPED</span> <span class="nt" style="color: navy;">-D_LARGEFILE_SOURCE</span> <span class="nt" style="color: navy;">-D_FILE_OFFSET_BITS</span><span class="o" style="font-weight: 600;">=</span>64 <span class="nt" style="color: navy;">-DDBGNFO</span> <span class="nt" style="color: navy;">-DSHOWALIGN</span> <span class="nt" style="color: navy;">-DDBGLEVEL</span><span class="o" style="font-weight: 600;">=</span>0 <span class="nt" style="color: navy;">-DPROGNFO</span> <span class="nt" style="color: navy;">-Ilibs</span> <span class="nt" style="color: navy;">-Ilibs</span>/sufarray <span class="nt" style="color: navy;">-Isamtools</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4" 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">

4

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<td class="diff-line-num new_line" data-linenumber="4" 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">

4

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4" class="line" lang="make"><span class="nv" style="color: teal;">CFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="sb" style="color: #d14;">`</span>pkg-config <span class="nt" style="color: navy;">--cflags</span> htslib<span class="sb" style="color: #d14;">`</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5" class="line" lang="make"><span class="nv" style="color: teal;">INC</span> <span class="o" style="font-weight: 600;">:=</span> <span class="nt" style="color: navy;">-I</span> include</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

</td>

<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC6" class="line" lang="make"><span class="nv" style="color: teal;">CTAGS</span> <span class="o" style="font-weight: 600;">=</span> ctags <span class="o" style="font-weight: 600;">></span> tags</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="7" 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">

7

</td>

<td class="diff-line-num new_line old" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC7" class="line" lang="make"><span class="nv" style="color: teal;">LIB</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: navy;">-lm</span> <span class="nt" style="color: navy;">-lpthread</span> <span class="nt" style="color: navy;">-lz</span> <span class="nt" style="color: navy;">-lncurses</span> <span class="nt" style="color: navy;">-L</span> libs <span class="nt" style="color: navy;">-lform</span> <span class="nt" style="color: navy;">-lmenu</span> <span class="nt" style="color: navy;">-L</span>/usr/local/lib/</span>

</pre>

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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="7" 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">

7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="make"><span class="nv" style="color: teal;">LIB</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">+</span>=</span> <span class="nt" style="color: navy;">-lm</span> <span class="nt" style="color: navy;">-lpthread</span> <span class="nt" style="color: navy;">-lz</span> <span class="nt" style="color: navy;">-lncurses</span> <span class="nt" style="color: navy;">-L</span> libs <span class="nt" style="color: navy;">-lform</span> <span class="nt" style="color: navy;">-lmenu</span> <span class="nt" style="color: navy;">-L</span>/usr/local/lib/</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="8" 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="8" 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="LC8" class="line" lang="make"><span class="nv" style="color: teal;">LIB</span> <span class="o" style="font-weight: 600;">+=</span> <span class="sb" style="color: #d14;">`</span>pkg-config <span class="nt" style="color: navy;">--libs</span> htslib<span class="sb" style="color: #d14;">`</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="9" 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="9" 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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC9" class="line" lang="make"><span class="nv" style="color: teal;">LIB</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s2" style="color: #d14;">"-Wl,-rpath,</span><span class="sb" style="color: #d14;">`</span>pkg-config <span class="nt" style="color: navy;">--variable</span><span class="o" style="font-weight: 600;">=</span>libdir htslib<span class="sb" style="color: #d14;">`</span><span class="s2" style="color: #d14;">"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="10" 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="10" 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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC10" class="line" lang="make"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -30,7 +30,7 @@ LIBOBJECTS :=  $(patsubst $(LIBDIR)/%,$(BUILDDIR)/%,$(LIBSOURCES:.$(SRCEXT)=.o))</td>

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<td class="diff-line-num new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC30" class="line" lang="make"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC31" class="line" lang="make"><span class="nl">$(PRGTARGETS)</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(OBJECTS)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC32" class="line" lang="make">  <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Linking </span><span class="nv" style="color: teal;">$@</span><span class="s2" style="color: #d14;">"</span><span class="p">;</span>  </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC33" class="line" lang="make">  <span class="nv" style="color: teal;">$(LD)</span> <span class="nv" style="color: teal;">$(LIBOBJECTS)</span> <span class="nv" style="color: teal;">$(BUILDDIR)</span>/<span class="nv" style="color: teal;">$@</span>.o <span class="nt" style="color: navy;">-o</span> <span class="nv" style="color: teal;">$(TARGETDIR)</span>/<span class="nv" style="color: teal;">$@$(TARGETEXT)</span> <span class="nv" style="color: teal;">$(LIB)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="make">  <span class="nv" style="color: teal;">$(LD)</span> <span class="nv" style="color: teal;">$(LIBOBJECTS)</span> <span class="nv" style="color: teal;">$(BUILDDIR)</span>/<span class="nv" style="color: teal;">$@</span>.o <span class="nt" style="color: navy;">-o</span> <span class="nv" style="color: teal;">$(TARGETDIR)</span>/<span class="nv" style="color: teal;">$@$(TARGETEXT)</span> <span class="nv" style="color: teal;">$(LIB)</span><span class="idiff left"> </span><span class="nv" style="color: teal;"><span class="idiff right">$(LDFLAGS)</span></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC34" class="line" lang="make"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC35" class="line" lang="make"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC36" class="line" lang="make"><span class="nl">$(BUILDDIR)/%.o</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(LIBDIR)/%.c</span></span>

</pre>

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<br>

</li>

<li id="c879736bc4600d92e5683925c65282a9ab8989b8">

<a href="https://salsa.debian.org/med-team/segemehl/commit/c43e3da4a55a7830f3855647bcc93fc3ba7f8913#c879736bc4600d92e5683925c65282a9ab8989b8"><strong>include/version.h</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="24" 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">@@ -24,11 +24,11 @@</td>

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<td class="diff-line-num old_line" data-linenumber="24" 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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC24" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="25" 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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC25" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="26" 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="26" 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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC26" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="27" 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="LC27" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define VERSION "<span class="idiff left right">v0.3.0</span>"</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="28" 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="27" 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="LC27" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define VERSION "<span class="idiff left right">0.3.2</span>"</span></span>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define REVISION "g<span class="idiff left right">0690723</span>"</span></span>

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<td class="diff-line-num new new_line" data-linenumber="29" 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="LC29" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define REVISION "g<span class="idiff left right">664b3dd</span>"</span></span>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define TIME "2018-1<span class="idiff left right">0-02 21:03:46 +02</span>00"</span></span>

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<td class="diff-line-num new new_line" data-linenumber="31" 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="LC31" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define TIME "2018-1<span class="idiff left right">1-11 17:18:49 +01</span>00"</span></span>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="c"></span></pre>

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</li>

<li id="d15b4ce2ccb17c25c6ddda769fea509c9a860979">

<a href="https://salsa.debian.org/med-team/segemehl/commit/c43e3da4a55a7830f3855647bcc93fc3ba7f8913#d15b4ce2ccb17c25c6ddda769fea509c9a860979"><strong>include/version.h.bak</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">@@ -12,6 +12,6 @@</td>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">#define VERSION "v0.3.0"</span>

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">#define REVISION "g<span class="idiff left right">0690723</span>"</span>

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">#define TIME "2018-1<span class="idiff left right">0-02 21:03:46 +02</span>00"</span>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">#define REVISION "g<span class="idiff left right">664b3dd</span>"</span>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">#define TIME "2018-1<span class="idiff left right">1-11 17:18:49 +01</span>00"</span>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span></pre>

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<li id="49cfca3ba0c6de143651770e7b1ae8aae5c3a7ff">

<a href="https://salsa.debian.org/med-team/segemehl/commit/c43e3da4a55a7830f3855647bcc93fc3ba7f8913#49cfca3ba0c6de143651770e7b1ae8aae5c3a7ff"><strong>libs/biofiles.c</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1586" 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">@@ -1586,7 +1586,7 @@ bl_fastxAddMate(void *space,</td>

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<pre style="margin: 0;"> <span id="LC1586" class="line" lang="c"></span>

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<td class="diff-line-num old_line" data-linenumber="1587" 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">

1587

</td>

<td class="diff-line-num new_line" data-linenumber="1587" 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">

1587

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<pre style="margin: 0;"> <span id="LC1587" class="line" lang="c">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bl_fastaCheckMateID</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">descr</span><span class="p">,</span> <span class="n" style="color: #333;">descrlen</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span>  </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1588" 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">

1588

</td>

<td class="diff-line-num new_line" data-linenumber="1588" 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">

1588

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1588" class="line" lang="c">    <span class="n" style="color: #333;">NFO</span><span class="p">(</span><span class="s" style="color: #d14;">"The fasta/fastq IDs in both mate files do not match.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">);</span> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1589" 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">

1589

</td>

<td class="diff-line-num new_line old" data-linenumber="1589" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1589" class="line" lang="c">    <span class="n" style="color: #333;">NFO</span><span class="p">(</span><span class="s" style="color: #d14;">"The first mismatch occured at fastq number %u</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1589" 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">

1589

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1589" class="line" lang="c">    <span class="n" style="color: #333;">NFO</span><span class="p">(</span><span class="s" style="color: #d14;">"The first mismatch occur<span class="idiff left right">r</span>ed at fastq number %u</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1590" 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">

1590

</td>

<td class="diff-line-num new_line" data-linenumber="1590" 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">

1590

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<pre style="margin: 0;"> <span id="LC1590" class="line" lang="c">    <span class="n" style="color: #333;">NFO</span><span class="p">(</span><span class="s" style="color: #d14;">"Exiting.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1591" 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">

1591

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<td class="diff-line-num new_line" data-linenumber="1591" 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">

1591

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1591" class="line" lang="c">    <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="n" style="color: #333;">EXIT_FAILURE</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1592" 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="1592" 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">

1592

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1592" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3448" 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="3448" 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">@@ -3448,7 +3448,7 @@ bl_annotationRead (void *space, char *fn) {</td>

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<td class="diff-line-num old_line" data-linenumber="3448" 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">

3448

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<td class="diff-line-num new_line" data-linenumber="3448" 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">

3448

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<pre style="margin: 0;"> <span id="LC3448" class="line" lang="c">  <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">suf</span><span class="p">,</span> <span class="s" style="color: #d14;">".gff"</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;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">suf</span><span class="p">,</span> <span class="s" style="color: #d14;">".gff3"</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3449" 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">

3449

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<td class="diff-line-num new_line" data-linenumber="3449" 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">

3449

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3449" class="line" lang="c">   <span class="n" style="color: #333;">annot</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bl_GFFread</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">fn</span><span class="p">);</span> </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3450" 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">

3450

</td>

<td class="diff-line-num new_line" data-linenumber="3450" 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">

3450

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<pre style="margin: 0;"> <span id="LC3450" class="line" lang="c">  <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="3451" 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">

3451

</td>

<td class="diff-line-num new_line old" data-linenumber="3451" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3451" class="line" lang="c">    <span class="n" style="color: #333;">NFO</span><span class="p">(</span><span class="s" style="color: #d14;">"please provide a bed or gff file with the approriate extension.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3452" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="3451" 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">

3451

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3451" class="line" lang="c">    <span class="n" style="color: #333;">NFO</span><span class="p">(</span><span class="s" style="color: #d14;">"please provide a bed or gff file with the appro<span class="idiff left right">p</span>riate extension.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="3452" 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">

3452

</td>

<td class="diff-line-num new_line" data-linenumber="3452" 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">

3452

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<pre style="margin: 0;"> <span id="LC3452" class="line" lang="c">    <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="n" style="color: #333;">EXIT_FAILURE</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="3453" 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">

3453

</td>

<td class="diff-line-num new_line" data-linenumber="3453" 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">

3453

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3453" class="line" lang="c">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3454" 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">

3454

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<td class="diff-line-num new_line" data-linenumber="3454" 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">

3454

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3454" class="line" lang="c">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">annot</span><span class="p">;</span></span>

</pre>

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</table>

<br>

</li>

<li id="78b9626f18f502deb715aae39a74a38737e4bf3d">

<a href="https://salsa.debian.org/med-team/segemehl/commit/c43e3da4a55a7830f3855647bcc93fc3ba7f8913#78b9626f18f502deb715aae39a74a38737e4bf3d"><strong>libs/gzidx.c</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="554" 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">@@ -554,7 +554,7 @@ int bl_bgzFillStream(FILE *fp, unsigned char *input, z_stream *strm) {</td>

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554

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<td class="diff-line-num new_line" data-linenumber="554" 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="LC554" class="line" lang="c">  <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fread</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">input</span><span class="p">[</span><span class="n" style="color: #333;">strm</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">avail_in</span><span class="p">],</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">CHUNK</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">strm</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">avail_in</span><span class="p">,</span> <span class="n" style="color: #333;">fp</span><span class="p">);</span></span>

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<td class="diff-line-num old_line" data-linenumber="555" 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">

555

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<td class="diff-line-num new_line" data-linenumber="555" 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="LC555" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ferror</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="556" 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">

556

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<td class="diff-line-num new_line" data-linenumber="556" 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="LC556" class="line" lang="c">    <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"error reading bgz file.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="557" 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">

557

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<td class="diff-line-num new_line old" data-linenumber="557" 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="LC557" class="line" lang="c">    <span class="n" style="color: #333;">perror</span><span class="p">(</span><span class="s" style="color: #d14;">"The following error occured:"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="558" 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="557" 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="LC557" class="line" lang="c">    <span class="n" style="color: #333;">perror</span><span class="p">(</span><span class="s" style="color: #d14;">"The following error occur<span class="idiff left right">r</span>ed:"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="558" 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">

558

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<td class="diff-line-num new_line" data-linenumber="558" 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="LC558" class="line" lang="c">    <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="n" style="color: #333;">EXIT_FAILURE</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="559" 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="559" 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="LC559" class="line" lang="c">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="560" 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="560" 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">

560

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<pre style="margin: 0;"> <span id="LC560" class="line" lang="c"></span>

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<br>

</li>

<li id="5bee75db0d128a8723dfa418084565536c5b1fcf">

<a href="https://salsa.debian.org/med-team/segemehl/commit/c43e3da4a55a7830f3855647bcc93fc3ba7f8913#5bee75db0d128a8723dfa418084565536c5b1fcf"><strong>libs/haarz.c</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -413,7 +413,7 @@ int main(int argc,char** argv) {</td>

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<pre style="margin: 0;"> <span id="LC413" class="line" lang="c">  <span class="n" style="color: #333;">prg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">manopt_getopts</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">prgset</span><span class="p">,</span> <span class="n" style="color: #333;">MIN</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span><span class="mi" style="color: #099;">2</span><span class="p">),</span> <span class="n" style="color: #333;">argv</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC414" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

415

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<pre style="margin: 0;"> <span id="LC415" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">prg</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">noofvalues</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span> </span>

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<td class="diff-line-num old old_line" data-linenumber="416" 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">

416

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<td class="diff-line-num new_line old" data-linenumber="416" 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="LC416" class="line" lang="c">    <span class="n" style="color: #333;">manopt_help</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">prgset</span><span class="p">,</span> <span class="s" style="color: #d14;">"program<span class="idiff left right">m</span> needs to be selected</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="416" 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="LC416" class="line" lang="c">    <span class="n" style="color: #333;">manopt_help</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">prgset</span><span class="p">,</span> <span class="s" style="color: #d14;">"program needs to be selected</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="417" 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="417" 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="LC417" class="line" lang="c">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="418" 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="418" 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="LC418" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="419" 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="419" 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">

419

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC419" class="line" lang="c">  <span class="n" style="color: #333;">manopt_initoptionset</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">optset</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> </span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="833" 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="833" 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">@@ -833,7 +833,7 @@ int main(int argc,char** argv) {</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="833" 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">

833

</td>

<td class="diff-line-num new_line" data-linenumber="833" 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">

833

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC833" class="line" lang="c">    <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="834" 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">

834

</td>

<td class="diff-line-num new_line" data-linenumber="834" 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">

834

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC834" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="835" 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">

835

</td>

<td class="diff-line-num new_line" data-linenumber="835" 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">

835

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC835" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="836" 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">

836

</td>

<td class="diff-line-num new_line old" data-linenumber="836" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC836" class="line" lang="c">    <span class="n" style="color: #333;">bl_BEDwrite</span><span class="p">(</span><span class="n" style="color: #333;">ptr</span><span class="p">,</span> <span class="n" style="color: #333;">mspl</span><span class="p">.</span><span class="n" style="color: #333;">noofitems</span><span class="p">,</span> <span class="n" style="color: #333;">stdout</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="836" 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">

836

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC836" class="line" lang="c">    <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>bl_BEDwrite(ptr, mspl.noofitems, stdout);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="837" 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">

837

</td>

<td class="diff-line-num new_line" data-linenumber="837" 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">

837

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC837" class="line" lang="c">    <span class="n" style="color: #333;">NFO</span><span class="p">(</span><span class="s" style="color: #d14;">"summarizing %d splits.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">mspl</span><span class="p">.</span><span class="n" style="color: #333;">noofitems</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="838" 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">

838

</td>

<td class="diff-line-num new_line" data-linenumber="838" 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">

838

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC838" class="line" lang="c">    <span class="n" style="color: #333;">bl_splitSummarize</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">mspl</span><span class="p">,</span> <span class="n" style="color: #333;">mintotalsplit</span><span class="p">,</span> <span class="n" style="color: #333;">minmedianqual</span><span class="p">,</span> <span class="n" style="color: #333;">nostrand</span><span class="p">);</span> </span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="839" 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">

839

</td>

<td class="diff-line-num new_line" data-linenumber="839" 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">

839

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC839" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="848" 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="848" 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">@@ -848,7 +848,7 @@ int main(int argc,char** argv) {</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="848" 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">

848

</td>

<td class="diff-line-num new_line" data-linenumber="848" 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">

848

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC848" class="line" lang="c">    <span class="n" style="color: #333;">FREEMEMORY</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">unflagged</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="849" 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">

849

</td>

<td class="diff-line-num new_line" data-linenumber="849" 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">

849

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC849" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="850" 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">

850

</td>

<td class="diff-line-num new_line" data-linenumber="850" 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">

850

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC850" class="line" lang="c">  <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="851" 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">

851

</td>

<td class="diff-line-num new_line old" data-linenumber="851" 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">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC851" class="line" lang="c">    <span class="n" style="color: #333;">manopt_help</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">prgset</span><span class="p">,</span> <span class="s" style="color: #d14;">"unkown program selected</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="851" 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">

851

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC851" class="line" lang="c">    <span class="n" style="color: #333;">manopt_help</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">prgset</span><span class="p">,</span> <span class="s" style="color: #d14;">"unk<span class="idiff left right">n</span>own program selected</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="852" 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">

852

</td>

<td class="diff-line-num new_line" data-linenumber="852" 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">

852

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC852" class="line" lang="c">  <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="853" 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">

853

</td>

<td class="diff-line-num new_line" data-linenumber="853" 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">

853

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC853" class="line" lang="c"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="854" 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">

854

</td>

<td class="diff-line-num new_line" data-linenumber="854" 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">

854

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC854" class="line" lang="c">  <span class="n" style="color: #333;">manopt_destructoptionset</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">optset</span><span class="p">);</span></span>

</pre>

</td>

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<br>

</li>

<li id="3b57e51818aa12c0e7b2aa12afe948a3497dfc35">

<a href="https://salsa.debian.org/med-team/segemehl/commit/c43e3da4a55a7830f3855647bcc93fc3ba7f8913#3b57e51818aa12c0e7b2aa12afe948a3497dfc35"><strong>libs/manopt.c</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1039" 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="1039" 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">@@ -1039,7 +1039,7 @@ manopt_checkconstraint(manopt_optionset* optset,</td>

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<pre style="margin: 0;"> <span id="LC1039" class="line" lang="c">    <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">MANOPT_BLOCKSEPARATOR</span><span class="p">:</span></span>

</pre>

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1040

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<pre style="margin: 0;"> <span id="LC1040" class="line" lang="c">      <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

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1041

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<pre style="margin: 0;"> <span id="LC1041" class="line" lang="c">    <span class="nl">default:</span></span>

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<td class="diff-line-num old old_line" data-linenumber="1042" 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="LC1042" class="line" lang="c">      <span class="n" style="color: #333;">manopt_help</span><span class="p">(</span><span class="n" style="color: #333;">optset</span><span class="p">,</span> <span class="s" style="color: #d14;">"unkown option %s type</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">argset</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">args</span><span class="p">[</span><span class="n" style="color: #333;">arg</span><span class="p">].</span><span class="n" style="color: #333;">flagname</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1043" 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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1042

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<pre style="margin: 0;">+<span id="LC1042" class="line" lang="c">      <span class="n" style="color: #333;">manopt_help</span><span class="p">(</span><span class="n" style="color: #333;">optset</span><span class="p">,</span> <span class="s" style="color: #d14;">"unk<span class="idiff left right">n</span>own option %s type</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">argset</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">args</span><span class="p">[</span><span class="n" style="color: #333;">arg</span><span class="p">].</span><span class="n" style="color: #333;">flagname</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="1043" 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">

1043

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<pre style="margin: 0;"> <span id="LC1043" class="line" lang="c">      <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1044" 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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1044

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<pre style="margin: 0;"> <span id="LC1044" class="line" lang="c">  <span class="p">}</span></span>

</pre>

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1045

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<pre style="margin: 0;"> <span id="LC1045" class="line" lang="c"></span>

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</li>

<li id="e3898fa62334b4ca938ab0571797fab5e4704e7d">

<a href="https://salsa.debian.org/med-team/segemehl/commit/c43e3da4a55a7830f3855647bcc93fc3ba7f8913#e3898fa62334b4ca938ab0571797fab5e4704e7d"><strong>libs/multicharseq.c</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="423" 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="423" 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">@@ -423,7 +423,7 @@ initMultiCharSeqAlignment(</td>

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<pre style="margin: 0;"> <span id="LC423" class="line" lang="c">  <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">refstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MAX</span><span class="p">(</span><span class="n" style="color: #333;">sub_start</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">Lint</span><span class="p">)</span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">loff</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC424" class="line" lang="c">  </span>

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<td class="diff-line-num old_line" data-linenumber="425" 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="425" 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="LC425" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">refstart</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">sub_end</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new_line old" data-linenumber="426" 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="LC426" class="line" lang="c">    <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"refstart > substart: skiping MultiCharSeqAlignment</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="427" 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="426" 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">

426

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<pre style="margin: 0;">+<span id="LC426" class="line" lang="c">    <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"refstart > substart: skip<span class="idiff left right">p</span>ing MultiCharSeqAlignment</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

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427

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<td class="diff-line-num new_line" data-linenumber="427" 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="LC427" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC428" class="line" lang="c">  <span class="p">}</span></span>

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429

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<pre style="margin: 0;"> <span id="LC429" class="line" lang="c"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="480" 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="480" 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">@@ -480,7 +480,7 @@ initMultiCharSeqAlignmentOpt(</td>

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480

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<pre style="margin: 0;"> <span id="LC480" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="481" 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="LC481" class="line" lang="c">  <span class="c1" style="color: #998; font-style: italic;">//this should not happen  </span></span>

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<td class="diff-line-num old_line" data-linenumber="482" 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">

482

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482

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<pre style="margin: 0;"> <span id="LC482" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">refstart</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">sub_end</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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483

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<td class="diff-line-num new_line old" data-linenumber="483" 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="LC483" class="line" lang="c">    <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"refstart > substart: skiping MultiCharSeqAlignment</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="484" 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="483" 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="LC483" class="line" lang="c">    <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"refstart > substart: skip<span class="idiff left right">p</span>ing MultiCharSeqAlignment</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

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484

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<td class="diff-line-num new_line" data-linenumber="484" 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="LC484" class="line" lang="c">    <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="485" 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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485

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<pre style="margin: 0;"> <span id="LC485" class="line" lang="c">  <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC486" class="line" lang="c"></span>

</pre>

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<br>

</li>

<li id="ada2196463c4fc6111aca438facbe014f2a026b0">

<a href="https://salsa.debian.org/med-team/segemehl/commit/c43e3da4a55a7830f3855647bcc93fc3ba7f8913#ada2196463c4fc6111aca438facbe014f2a026b0"><strong>libs/samio.c</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1292" 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="1292" 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">@@ -1292,7 +1292,7 @@ bl_samprintSamlist (samlist_t *l, mapping_t* m, segemehl_t *nfo)</td>

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<pre style="margin: 0;"> <span id="LC1292" class="line" lang="c">      <span class="n" style="color: #333;">bl_samcloseDevice</span><span class="p">(</span><span class="n" style="color: #333;">fx</span><span class="p">,</span> <span class="n" style="color: #333;">nfo</span><span class="p">);</span></span>

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<td class="diff-line-num new_line" data-linenumber="1293" 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="LC1293" class="line" lang="c">      <span class="n" style="color: #333;">fx</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1294" 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="1294" 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="LC1294" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="1295" 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="LC1295" class="line" lang="c">  <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1296" 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="1295" 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="LC1295" class="line" lang="c">  <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">nfo</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">bamdev</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1296" 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="1296" 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="LC1296" class="line" lang="c">    <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">noofrecs</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC1297" class="line" lang="c">      <span class="n" style="color: #333;">bl_bamPrintBamrec</span><span class="p">(</span><span class="n" style="color: #333;">nfo</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bamdev</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">recs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">nfo</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bamhdr</span><span class="p">,</span> <span class="n" style="color: #333;">nfo</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mtx3</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="1298" 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="LC1298" class="line" lang="c">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1378" 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="1378" 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">@@ -1378,10 +1378,14 @@ bl_samprintEmptyAlign (char *desc, char* seq, char* qual, char hasPaired,</td>

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<td class="diff-line-num new_line" data-linenumber="1378" 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="LC1378" class="line" lang="c">  <span class="n" style="color: #333;">bl_samsetMultipleHits</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">samlist</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">recs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1379" 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="1379" 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="LC1379" class="line" lang="c">  <span class="n" style="color: #333;">bl_samsetMatchId</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">samlist</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">recs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1380" 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="1380" 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="LC1380" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="1381" 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="LC1381" class="line" lang="c">  <span class="n" style="color: #333;">dev</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bl_samgetDevice</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fx</span><span class="p">,</span> <span class="n" style="color: #333;">nfo</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="1381" 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="LC1382" class="line" lang="c">  <span class="n" style="color: #333;">bl_samprintSamrec</span><span class="p">(</span><span class="n" style="color: #333;">dev</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">samlist</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">recs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">lf</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="1381" 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="LC1383" class="line" lang="c">  <span class="n" style="color: #333;">bl_samcloseDevice</span><span class="p">(</span><span class="n" style="color: #333;">fx</span><span class="p">,</span> <span class="n" style="color: #333;">nfo</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="1381" 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="LC1384" class="line" lang="c"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1385" 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="LC1381" class="line" lang="c">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">nfo</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bamdev</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1385" 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="LC1382" class="line" lang="c">    <span class="n" style="color: #333;">dev</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bl_samgetDevice</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fx</span><span class="p">,</span> <span class="n" style="color: #333;">nfo</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1385" 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="1383" 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="LC1383" class="line" lang="c">    <span class="n" style="color: #333;">bl_samprintSamrec</span><span class="p">(</span><span class="n" style="color: #333;">dev</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">samlist</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">recs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">lf</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1385" 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="1384" 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="LC1384" class="line" lang="c">    <span class="n" style="color: #333;">bl_samcloseDevice</span><span class="p">(</span><span class="n" style="color: #333;">fx</span><span class="p">,</span> <span class="n" style="color: #333;">nfo</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="1385" 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="LC1385" class="line" lang="c">  <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="1386" 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="LC1386" class="line" lang="c">    <span class="n" style="color: #333;">bl_bamPrintBamrec</span><span class="p">(</span><span class="n" style="color: #333;">nfo</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bamdev</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">samlist</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">recs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">nfo</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bamhdr</span><span class="p">,</span> <span class="n" style="color: #333;">nfo</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mtx3</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1387" 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">

1387

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1387" class="line" lang="c">  <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1388" 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">

1388

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1388" class="line" lang="c">  </span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1385" 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">

1385

</td>

<td class="diff-line-num new_line" data-linenumber="1389" 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">

1389

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1389" class="line" lang="c">  <span class="n" style="color: #333;">bl_samdestructSamList</span><span class="p">(</span><span class="n" style="color: #333;">samlist</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1386" 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">

1386

</td>

<td class="diff-line-num new_line" data-linenumber="1390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1390

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1390" class="line" lang="c">  <span class="n" style="color: #333;">FREEMEMORY</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">samlist</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1387" 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">

1387

</td>

<td class="diff-line-num new_line" data-linenumber="1391" 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">

1391

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1391" class="line" lang="c"></span>

</pre>

</td>

</tr>

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