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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/trinityrnaseq">Debian Med / trinityrnaseq</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/trinityrnaseq/commit/19afd712ef22113f45d60a5b728ae26b28587613">19afd712</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-01-02T07:34:27Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Default to Python 3, as needed.
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/trinityrnaseq/commit/4bc652fefe72ceb19a88dc7e7f5a5f52e4eb7734">4bc652fe</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-01-02T08:49:03Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use better Java version check from upstream
</pre>
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<h4>5 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="#00a08151b0460fba7ef3bd7696467e984099c63e">
<span class="new-file">
+
debian/patches/better_java_version_check
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<li class="file-stats">
<a href="#0a4e986b60a9240ca7d53abf5e2ed246987e8ffc">
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+
debian/patches/python3
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/trinityrnaseq/compare/9b4be3dade72675dc28a0a78b30e4e802faf313e...4bc652fefe72ceb19a88dc7e7f5a5f52e4eb7734#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">trinityrnaseq (2.6.6+dfsg-4) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Default to Python 3, as needed.</span>
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<td class="diff-line-num new new_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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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Use better Java version check from upstream</span>
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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="LC5" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="6" 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="LC6" class="line" lang="plaintext"> -- Michael R. Crusoe <michael.crusoe@gmail.com> Wed, 02 Jan 2019 00:48:52 -0800</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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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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<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">trinityrnaseq (2.6.6+dfsg-3) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * debian/control: add numpy dependency, required for</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/trinityrnaseq/compare/9b4be3dade72675dc28a0a78b30e4e802faf313e...4bc652fefe72ceb19a88dc7e7f5a5f52e4eb7734#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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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 +30,6 @@ Depends: ${shlibs:Depends},</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> ${java:Depends},</span>
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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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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> bowtie,</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> bowtie2,</span>
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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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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext"> python,</span>
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<td class="diff-line-num new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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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="LC33" class="line" lang="plaintext"> libwww-perl,</span>
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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="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="plaintext"> default-jre-headless,</span>
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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="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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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"> samtools,</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="45" 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="44" 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">@@ -45,7 +44,7 @@ Depends: ${shlibs:Depends},</td>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"> parafly,</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"> curl,</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext"> salmon,</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext"> python3-numpy<span class="idiff left right"> | python-numpy</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> python3-numpy</span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext">Recommends: ${java:Recommends},</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"> trinityrnaseq-examples</span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext">Suggests: collectl</span>
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<li id="00a08151b0460fba7ef3bd7696467e984099c63e">
<a href="https://salsa.debian.org/med-team/trinityrnaseq/compare/9b4be3dade72675dc28a0a78b30e4e802faf313e...4bc652fefe72ceb19a88dc7e7f5a5f52e4eb7734#00a08151b0460fba7ef3bd7696467e984099c63e"><strong>debian/patches/better_java_version_check</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Author: Michael R. Crusoe <michael.crusoe@gmail.com></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Description: Use updated Java version check from upstream</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/Trinity</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/Trinity</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -561,7 +561,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> my $CHRYSALIS_DEBUG_WELD_ALL = 0;</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> my $iworm_opts = "";</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-my $bypass_java_version_check = 0;</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+my $bypass_java_version_check = 1;</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> my $VERBOSE = 0;</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1028,24 +1028,33 @@</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> die "Error, must specify max memory for jellyfish to use, eg. --max_memory 10G \n";</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> ## Check Java version:</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> unless ($NO_RUN_INCHWORM_FLAG || $NO_RUN_CHRYSALIS_FLAG || $bypass_java_version_check || $TRINITY_COMPLETE_FLAG) {</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> my $java_version = `java -Xmx64m -version 2>&1 `;</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ unless ($java_version) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="24" 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">
24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ die "Error, cannot detect java via. 'java -Xmx64m -version'";</span></span>
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<td class="diff-line-num new new_line" data-linenumber="25" 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">
25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ </span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ my $version_id;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> if ($java_version =~ /(java|openjdk) version \"1\.(\d)\./) {</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">
29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- my $version_id = $2;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if ($version_id < $JAVA_VERSION_REQUIRED) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- die "Error, Trinity requires access to Java version 1.$JAVA_VERSION_REQUIRED or higher. Currently installed version is: $java_version";</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- else {</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print STDERR "\n\n\n********************************************************************\n"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- . "** Warning, Trinity cannot determine which version of Java is being used. Version 1.$JAVA_VERSION_REQUIRED is required. \n\nAttempting to continue in 30 seconds\n"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="37" 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">
37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- . "********************************************************************\n\n\n";</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sleep(30);</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-}</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $version_id = $2;</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ elsif ($java_version =~ /java version \"(\d+)(\.)?([._\d])+?\" ?/) {</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $version_id = $1;</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ elsif ($java_version =~ /java (\d+) /) {</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $version_id = $1;</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else {</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ die "Error, cannot extract java version info from: ($java_version) ... run with --bypass_java_version_check if you're sure that you have at least java version: $JAVA_VERSION_REQUIRED installed ";</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ </span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ($version_id < $JAVA_VERSION_REQUIRED) {</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ die "Error, Trinity requires access to Java version 1.$JAVA_VERSION_REQUIRED or higher. Currently installed version is: $java_version";</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+}</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> </span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> unless ($NO_VERSION_CHECK || $TRINITY_COMPLETE_FLAG) {</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> &version_check();</span></pre>
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<li id="0a4e986b60a9240ca7d53abf5e2ed246987e8ffc">
<a href="https://salsa.debian.org/med-team/trinityrnaseq/compare/9b4be3dade72675dc28a0a78b30e4e802faf313e...4bc652fefe72ceb19a88dc7e7f5a5f52e4eb7734#0a4e986b60a9240ca7d53abf5e2ed246987e8ffc"><strong>debian/patches/python3</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Author: Michael R. Crusoe <michael.crusoe@gmail.com></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Description: Default to running Python 3</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/Analysis/SuperTranscripts/AllelicVariants/run_variant_calling.py</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/Analysis/SuperTranscripts/AllelicVariants/run_variant_calling.py</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> # encoding: utf-8</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> from __future__ import (absolute_import, division,</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/Analysis/SuperTranscripts/Trinity_gene_splice_modeler.py</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;">+++ trinityrnaseq/Analysis/SuperTranscripts/Trinity_gene_splice_modeler.py</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> # encoding: utf-8</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> from __future__ import (absolute_import, division,</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/Analysis/SuperTranscripts/extract_supertranscript_from_reference.py</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/Analysis/SuperTranscripts/extract_supertranscript_from_reference.py</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> # encoding: utf-8</span>
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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"> from __future__ import (absolute_import, division, print_function, unicode_literals)</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/Analysis/SuperTranscripts/pylib/Compact_graph_partial.py</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/Analysis/SuperTranscripts/pylib/Compact_graph_partial.py</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> # encoding: utf-8</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> from __future__ import (absolute_import, division,</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/Analysis/SuperTranscripts/pylib/Compact_graph_whole.py</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/Analysis/SuperTranscripts/pylib/Compact_graph_whole.py</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;">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> # encoding: utf-8</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> from __future__ import (absolute_import, division,</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;">--- trinityrnaseq.orig/Analysis/SuperTranscripts/pylib/DP_matrix.py</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/Analysis/SuperTranscripts/pylib/DP_matrix.py</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> # encoding: utf-8</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> from __future__ import (absolute_import, division,</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;">--- trinityrnaseq.orig/Analysis/SuperTranscripts/pylib/Gene_splice_modeler.py</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;">+++ trinityrnaseq/Analysis/SuperTranscripts/pylib/Gene_splice_modeler.py</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> # encoding: utf-8</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> from __future__ import (absolute_import, division,</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/Analysis/SuperTranscripts/pylib/GraphCycleException.py</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/Analysis/SuperTranscripts/pylib/GraphCycleException.py</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> # encoding: utf-8</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> </span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> from __future__ import (absolute_import, division,</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/Analysis/SuperTranscripts/pylib/Node_alignment.py</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/Analysis/SuperTranscripts/pylib/Node_alignment.py</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> # encoding: utf-8</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> from __future__ import (absolute_import, division,</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/Analysis/SuperTranscripts/pylib/Node_path.py</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/Analysis/SuperTranscripts/pylib/Node_path.py</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> # encoding: utf-8</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> </span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> from __future__ import (absolute_import, division,</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/Analysis/SuperTranscripts/pylib/Splice_model_refiner.py</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/Analysis/SuperTranscripts/pylib/Splice_model_refiner.py</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> # encoding: utf-8</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> </span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> from __future__ import (absolute_import, division,</span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/Analysis/SuperTranscripts/pylib/TGLOBALS.py</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/Analysis/SuperTranscripts/pylib/TGLOBALS.py</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> DEBUG = False</span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/Analysis/SuperTranscripts/pylib/TGraph.py</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/Analysis/SuperTranscripts/pylib/TGraph.py</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> # encoding: utf-8</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> </span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> from __future__ import (absolute_import, division,</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/Analysis/SuperTranscripts/pylib/TNode.py</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/Analysis/SuperTranscripts/pylib/TNode.py</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> # encoding: utf-8</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> </span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"> from __future__ import (absolute_import, division,</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/Analysis/SuperTranscripts/pylib/Topological_sort.py</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/Analysis/SuperTranscripts/pylib/Topological_sort.py</span></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> # encoding: utf-8</span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"> from __future__ import (absolute_import, division,</span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/Analysis/SuperTranscripts/pylib/Trinity_fasta_parser.py</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/Analysis/SuperTranscripts/pylib/Trinity_fasta_parser.py</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"> # encoding: utf-8</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"> </span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"> from __future__ import (absolute_import, division,</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/Analysis/SuperTranscripts/pylib/Trinity_util.py</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/Analysis/SuperTranscripts/pylib/Trinity_util.py</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"> # encoding: utf-8</span>
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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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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> from __future__ import (absolute_import, division,</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/PyLib/Pipeliner.py</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/PyLib/Pipeliner.py</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"> # encoding: utf-8</span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"> </span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"> from __future__ import (absolute_import, division,</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/trinity-plugins/COLLECTL/util/collectl_dat_to_time_matrix.py</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/trinity-plugins/COLLECTL/util/collectl_dat_to_time_matrix.py</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"> # encoding: utf-8</span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"> </span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"> from __future__ import (absolute_import, division,</span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/trinity-plugins/DEXseq_util/dexseq_prepare_annotation.py</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/trinity-plugins/DEXseq_util/dexseq_prepare_annotation.py</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"> </span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"> import sys, collections, itertools, os.path, optparse</span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/util/misc/TPM_weighted_gene_length.py</span></span>
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/util/misc/TPM_weighted_gene_length.py</span></span>
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"> # encoding: utf-8</span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"> from __future__ import (absolute_import, division,</span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/util/support_scripts/trinity_installer.py</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/util/support_scripts/trinity_installer.py</span></span>
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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176
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"> import os, re, sys, subprocess</span>
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"> </span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/trinityrnaseq/compare/9b4be3dade72675dc28a0a78b30e4e802faf313e...4bc652fefe72ceb19a88dc7e7f5a5f52e4eb7734#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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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>
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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">@@ -11,3 +11,5 @@ build_with_gcc6.patch</td>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">NeedlemanWunschGotohBanded.patch</span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">disable-libieee</span>
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"># assume_modern_g++.patch</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">python3</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">better_java_version_check</span></pre>
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