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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/freebayes">Debian Med / freebayes</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/freebayes/commit/3de08fb5519f42ba1043ee0afc8ebc400eca31ba">3de08fb5</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-23T11:33:45+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix patch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/freebayes/commit/a8cea70bc635d3b9c6b07ebbc7fdc13f294f15ef">a8cea70b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-23T11:34:38+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bump versioned Build-Depends: libseqlib-dev (>= 1.1.2+dfsg)
</pre>
</li>
</ul>
<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#e27a600b059fb5ae2fdea2749758a974686fd4a1">
debian/patches/use_debian_libs.patch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/freebayes/compare/cee63932c6c22923e54fddf2ed96c1e12a9cc1c6...a8cea70bc635d3b9c6b07ebbc7fdc13f294f15ef#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,6 +3,7 @@ freebayes (1.2.0-1) UNRELEASED; urgency=medium</td>
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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="LC3" class="line" lang="plaintext"> * New upstream version</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="LC4" class="line" lang="plaintext"> * Point Vcs fields to salsa.debian.org</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="LC5" class="line" lang="plaintext"> * Standards-Version: 4.1.4</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Bump versioned Build-Depends: libseqlib-dev (>= 1.1.2+dfsg)</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></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="LC8" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Thu, 26 Apr 2018 15:30:48 +0200</span>
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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="plaintext"></span>
</pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/freebayes/compare/cee63932c6c22923e54fddf2ed96c1e12a9cc1c6...a8cea70bc635d3b9c6b07ebbc7fdc13f294f15ef#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="12" style="width: 35px; color: rgba(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="12" style="width: 35px; color: rgba(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">@@ -12,7 +12,7 @@ Build-Depends: debhelper (>= 11~),</td>
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<td class="diff-line-num old_line" data-linenumber="12" style="width: 35px; color: rgba(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="LC12" class="line" lang="plaintext"> libbamtools-dev,</span>
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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(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="LC13" class="line" lang="plaintext"> libvcflib-dev (>= 1.0.0~rc1+dfsg1-4),</span>
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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(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="LC14" class="line" lang="plaintext"> libtabixpp-dev,</span>
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<td class="diff-line-num old old_line" data-linenumber="15" 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="LC15" class="line" lang="plaintext"> libseqlib-dev (>= 1.1.<span class="idiff left right">1+dfsg-4</span>),</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> libseqlib-dev (>= 1.1.<span class="idiff left right">2+dfsg</span>),</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> bc,</span>
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<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(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="LC17" class="line" lang="plaintext"> samtools,</span>
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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(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="LC18" class="line" lang="plaintext"> parallel,</span>
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<li id="e27a600b059fb5ae2fdea2749758a974686fd4a1">
<a href="https://salsa.debian.org/med-team/freebayes/compare/cee63932c6c22923e54fddf2ed96c1e12a9cc1c6...a8cea70bc635d3b9c6b07ebbc7fdc13f294f15ef#e27a600b059fb5ae2fdea2749758a974686fd4a1"><strong>debian/patches/use_debian_libs.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -34,10 +34,11 @@ Description: Use Debian packaged bamtools</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="diff"> OBJECTS=BedReader.o \</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="diff"> CNV.o \</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="diff"> fastlz.o \</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -75,17 +63,7 @@ OBJECTS=BedReader.o \</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -74,18 +62,7 @@ OBJECTS=BedReader.o \</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> Bias.o \</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="diff"> Contamination.o \</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="diff"> NonCall.o \</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"><span class="idiff left right"> </span> SegfaultHandler.o \</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;"><span class="idiff left right">-</span> SegfaultHandler.o \</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ../vcflib/tabixpp/tabix.o \</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ../vcflib/smithwaterman/SmithWatermanGotoh.o \</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ../vcflib/smithwaterman/disorder.cpp \</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -49,11 +50,11 @@ Description: Use Debian packaged bamtools</td>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(SEQLIB_ROOT)/bwa/libbwa.a \</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(SEQLIB_ROOT)/fermi-lite/libfml.a \</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(SEQLIB_ROOT)/htslib/libhts.a</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <span class="idiff left right">Variant</span>.o</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <span class="idiff left right">SegfaultHandler</span>.o</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="diff"> HEADERS=multichoose.h version_git.h</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -100,10 +7<span class="idiff left right">8</span>,10 @@ alleles ../bin/alleles: alleles.o $(OBJE</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -100,10 +7<span class="idiff left right">7</span>,10 @@ alleles ../bin/alleles: alleles.o $(OBJE</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="diff"> dummy ../bin/dummy: dummy.o $(OBJECTS) $(HEADERS) $(seqlib)</span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="diff"> $(CXX) $(CXXFLAGS) $(INCLUDE) dummy.o $(OBJECTS) -o ../bin/dummy $(LIBS)</span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="diff"> </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -66,7 +67,7 @@ Description: Use Debian packaged bamtools</td>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="diff"> $(CXX) $(CXXFLAGS) $(INCLUDE) bamfiltertech.o $(OBJECTS) -o ../bin/bamfiltertech $(LIBS)</span>
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67
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="diff"> </span>
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68
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="diff"> </span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -118,7 +9<span class="idiff left right">6</span>,7 @@ alleles.o: alleles.cpp AlleleParser.o Al</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -118,7 +9<span class="idiff left right">5</span>,7 @@ alleles.o: alleles.cpp AlleleParser.o Al</span></span>
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70
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="diff"> dummy.o: dummy.cpp AlleleParser.o Allele.o</span>
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71
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="diff"> $(CXX) $(CXXFLAGS) $(INCLUDE) -c dummy.cpp</span>
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72
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="76" style="width: 35px; color: rgba(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">@@ -75,7 +76,7 @@ Description: Use Debian packaged bamtools</td>
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75
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="diff"> $(CXX) $(CXXFLAGS) $(INCLUDE) -c freebayes.cpp</span>
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76
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="diff"> fastlz.o: fastlz.c fastlz.h</span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -139,7 +11<span class="idiff left right">7</span>,7 @@ Genotype.o: Genotype.cpp Genotype.h Alle</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -139,7 +11<span class="idiff left right">6</span>,7 @@ Genotype.o: Genotype.cpp Genotype.h Alle</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="diff"> Ewens.o: Ewens.cpp Ewens.h</span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="diff"> $(CXX) $(CXXFLAGS) $(INCLUDE) -c Ewens.cpp</span>
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81
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="diff"> </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -84,7 +85,7 @@ Description: Use Debian packaged bamtools</td>
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84
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="diff"> $(CXX) $(CXXFLAGS) $(INCLUDE) -c AlleleParser.cpp</span>
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85
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="diff"> Utility.o: Utility.cpp Utility.h Sum.h Product.h</span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -187,22 +16<span class="idiff left right">5</span>,12 @@ bamleftalign.o: bamleftalign.cpp LeftAli</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -187,22 +16<span class="idiff left right">4</span>,12 @@ bamleftalign.o: bamleftalign.cpp LeftAli</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="diff"> bamfiltertech.o: bamfiltertech.cpp</span>
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89
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="diff"> $(CXX) $(CXXFLAGS) $(INCLUDE) -c bamfiltertech.cpp</span>
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90
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="diff"> </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -108,7 +109,7 @@ Description: Use Debian packaged bamtools</td>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="diff"> VERSION_FILE=./version_git.h</span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="diff"> RELEASED_VERSION_FILE=./version_release.txt</span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -277,5 +24<span class="idiff left right">5</span>,3 @@ autoversion:</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -277,5 +24<span class="idiff left right">4</span>,3 @@ autoversion:</span></span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="diff"> clean:</span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="diff"> rm -rf *.o *.cgh *~ freebayes alleles ../bin/freebayes ../bin/alleles ../vcflib/*.o ../vcflib/tabixpp/*.{o,a} tabix.hpp</span>
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