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<h3>
Sascha Steinbiss pushed to branch master
at <a href="https://salsa.debian.org/med-team/genomethreader">Debian Med / genomethreader</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/genomethreader/commit/cb8612e35a7605a701ac0350717cdb79394b1686">cb8612e3</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2020-01-06T23:45:52+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">update patches
</pre>
</li>
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<h4>2 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f19f900306f42aafd11c9c6fd4e4e288988b9c4a">
debian/patches/debian-gt-libs.patch
</a>
</li>
<li class="file-stats">
<a href="#411b0a9c431115faa7f24dda94d08f1855b28c1b">
debian/patches/gt-path-fix.patch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="f19f900306f42aafd11c9c6fd4e4e288988b9c4a">
<a href="https://salsa.debian.org/med-team/genomethreader/commit/cb8612e35a7605a701ac0350717cdb79394b1686#f19f900306f42aafd11c9c6fd4e4e288988b9c4a"><strong>debian/patches/debian-gt-libs.patch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/Makefile</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">@@ -15,19 +15,1<span class="idiff left right">6</span> @@</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">@@ -15,19 +15,1<span class="idiff left right">7</span> @@</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"> # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"> #</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,6 +11,7 @@</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- -I$(CURDIR)/../genometools/src/external/lua-5.1.5/src \</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+INCLUDEOPT:=-I/usr/include/genometools \</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ -I/usr/include/vmatch \</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ -I/usr/include/lua5.1 \</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> -I$(CURDIR)/src -I$(CURDIR)/obj \</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"> # these variables are exported by the configuration script</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CC:=gcc</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -24,7 +25,7 @@</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"> ifneq ($(fpic),no)</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"> FPIC:=-fPIC</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="p">@@ -130,11 +12<span class="idiff left right">7</span>,11 @@</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="p">@@ -130,11 +12<span class="idiff left right">8</span>,11 @@</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="diff"> GTMAIN_DEP:=$(GTMAIN_SRC:%.c=obj/%.d)</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"> VSTREEDIR:=../vstree/src</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -41,7 +42,7 @@</td>
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41
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42
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="diff"> GTH_CPPFLAGS+=-I$(CURDIR)/$(VSTREEDIR)/include \</span>
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42
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43
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="diff"> -I$(CURDIR)/$(VSTREEDIR)/Vmatch \</span>
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43
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44
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="diff"> </span>
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44
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff"><span class="p">@@ -209,7 +20<span class="idiff left right">6</span>,7 @@</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="p">@@ -209,7 +20<span class="idiff left right">7</span>,7 @@</span></span>
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45
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46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="diff"> all: lib/libgenomethreader.a bin/gth bin/gthconsensus bin/gthbssmfileinfo \</span>
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46
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="diff"> bin/gthbssmbuild bin/gthbssmprint bin/gthbssmrmsd bin/gthbssmtrain \</span>
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47
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48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="diff"> bin/gthfilestat bin/gthmkbssmfiles bin/gthsplit bin/gthunit \</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="50" style="width: 35px; color: rgba(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="51" style="width: 35px; color: rgba(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">@@ -50,7 +51,7 @@</td>
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50
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51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="diff"> </span>
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51
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="diff"> lib/libgenomethreader.a: obj/gth_config.h $(LIBGENOMETHREADER_OBJ)</span>
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52
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53
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="diff"> @echo "[link $(@F)]"</span>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="diff"><span class="p">@@ -231,67 +22<span class="idiff left right">8</span>,67 @@</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="p">@@ -231,67 +22<span class="idiff left right">9</span>,67 @@</span></span>
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55
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="diff"> $(1): $(2)</span>
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55
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56
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="diff"> @echo "[link $$(@F)]"</span>
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56
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="diff"> @test -d $$(@D) || mkdir -p $$(@D)</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="136" style="width: 35px; color: rgba(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="137" style="width: 35px; color: rgba(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">@@ -136,7 +137,7 @@</td>
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136
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137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="diff"> </span>
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137
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="diff"> obj/gth_config.h: VERSION</span>
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="diff"> @echo '[create $@]'</span>
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139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="diff"><span class="p">@@ -321,9 +31<span class="idiff left right">8</span>,9 @@</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"><span class="p">@@ -321,9 +31<span class="idiff left right">9</span>,9 @@</span></span>
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140
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="diff"> $(1): $(2)</span>
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141
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="diff"> @echo "[compile $$(@F)]"</span>
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="diff"> @test -d $$(@D) || mkdir -p $$(@D)</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="149" style="width: 35px; color: rgba(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">@@ -148,7 +149,7 @@</td>
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148
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="diff"> $(3) -MM -MP -MT $$@</span>
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149
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="diff"> endef</span>
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150
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="diff"> </span>
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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="diff"><span class="p">@@ -332,17 +3<span class="idiff left right">29</span>,17 @@</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"><span class="p">@@ -332,17 +3<span class="idiff left right">30</span>,17 @@</span></span>
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152
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="diff"> obj/%.o: %.cxx</span>
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153
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="diff"> @echo "[compile $(@F)]"</span>
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154
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<td class="diff-line-num new_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="diff"> @test -d $(@D) || mkdir -p $(@D)</span>
</pre>
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<li id="411b0a9c431115faa7f24dda94d08f1855b28c1b">
<a href="https://salsa.debian.org/med-team/genomethreader/commit/cb8612e35a7605a701ac0350717cdb79394b1686#411b0a9c431115faa7f24dda94d08f1855b28c1b"><strong>debian/patches/gt-path-fix.patch</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -307,3 +307,14 @@</td>
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307
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307
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="diff"> "#{$gthtestdata}ngasp/test_ref2.gff3 " +</span>
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308
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308
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="diff"> "#{$gthtestdata}ngasp/ngasp.gff3", :maxtime => 300</span>
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<td class="diff-line-num old_line" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
309
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<td class="diff-line-num new_line" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
309
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="diff"> run "diff --strip-trailing-cr #{$last_stdout} #{$gthtestdata}ngasp/ngasp.specificity"</span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/Makefile</span></span>
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<td class="diff-line-num new new_line" data-linenumber="311" 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">
311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/Makefile</span></span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="diff"><span class="p">@@ -517,7 +517,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="diff"> -gtdonor -agacceptor -gzip</span>
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="diff"> @touch $@</span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="diff"> </span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-obj/old_train: ../genometools/bin/gt</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+obj/old_train: bin/gthmkbssmfiles</span></span>
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<td class="diff-line-num new new_line" data-linenumber="318" 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">
318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="diff"> @echo "[write old BSSMs]"</span>
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<td class="diff-line-num new new_line" data-linenumber="319" 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">
319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="diff"> @bin/gthmkbssmfiles bin/bssm</span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="diff"> @touch $@</span></pre>
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