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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/subread">Debian Med / subread</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/subread/-/commit/80c6355b322521e4765d1668bf2b32ec4fbec1b3">80c6355b</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-05-19T22:22:51+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refresh patches
</pre>
</li>
</ul>
<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">
debian/patches/2to3.patch
</a>
</li>
<li class="file-stats">
<a href="#e5dd98c113be2752e1d0ece7dd39cb253d83216c">
debian/patches/arch_specific_flags.patch
</a>
</li>
<li class="file-stats">
<a href="#fb9e8d937d72f3a26397728040ed9ba05f3aea89">
debian/patches/fix_ftbfs_kfreebsd.patch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="555c85016bd79aa8bbb523506af81b69d9c69534">
<a href="https://salsa.debian.org/med-team/subread/-/commit/80c6355b322521e4765d1668bf2b32ec4fbec1b3#555c85016bd79aa8bbb523506af81b69d9c69534"><strong>debian/patches/2to3.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,7 +5,7 @@ Last-Update: Thu, 05 Sep 2019 09:01:45 +0200</td>
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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">--- a/test/subread-align/readname_cigar_match.py</span>
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<td class="old_line diff-line-num" data-linenumber="7" 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="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/test/subread-align/readname_cigar_match.py</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="p">@@ -68,10 +68,10 @@</span><span class="idiff left right"> while True:</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -68,10 +68,10 @@</span></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"> if not is_correct:</span>
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<td class="old_line diff-line-num" 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">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> if is_cigar_problem:</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="21" 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="21" 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">@@ -21,7 +21,7 @@ Last-Update: Thu, 05 Sep 2019 09:01:45 +0200</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+print("RES: %d reads\t%d unmapped\t%d error_pos\t%d error_cigar\t%d correct_indel"%(all_r,unmapped, error_pos, error_cig, correct_indel))</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;">--- a/test/subread-align/readname_ora_match.py</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;">+++ b/test/subread-align/readname_ora_match.py</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"><span class="p">@@ -29,7 +29,7 @@</span><span class="idiff left right"> def main():</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="p">@@ -29,7 +29,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="diff"> line +=1</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"> </span>
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<td class="old_line diff-line-num" data-linenumber="27" 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="LC27" class="line" lang="diff"> if line % 100000 == 0:</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -30,7 +30,7 @@ Last-Update: Thu, 05 Sep 2019 09:01:45 +0200</td>
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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"> if fl.find("NNNNNNNN")>0:</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="diff"> NN+=1</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"><span class="p">@@ -76,8 +76,8 @@</span><span class="idiff left right"> def main():</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="p">@@ -76,8 +76,8 @@</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="diff"> old_read_name = t_name</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="diff"> </span>
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<a href="https://salsa.debian.org/med-team/subread/-/commit/80c6355b322521e4765d1668bf2b32ec4fbec1b3#e5dd98c113be2752e1d0ece7dd39cb253d83216c"><strong>debian/patches/arch_specific_flags.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,7 +9,7 @@ Description: Inject architecture specific flags:</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"><span class="p">Author: Alex Mestiashvili <alex@biotec.tu-dresden.de></span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/Makefile.Linux</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/Makefile.Linux</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="p">@@ -7,9 +7,9 @@</span><span class="idiff left right"> OPT_LEVEL = 3</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="p">@@ -7,9 +7,9 @@</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> include makefile.version</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> -include ~/.R/DBPZ_debug_makefile</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -24,7 +24,7 @@ Author: Alex Mestiashvili <alex@biotec.tu-dresden.de></td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="diff"> ALL_LIBS= core core-junction core-indel sambam-file sublog gene-algorithms hashtable input-files sorted-hashtable gene-value-index exon-algorithms HelperFunctions interval_merge long-hashtable core-bigtable seek-zlib input-blc</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/longread-one/Makefile</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/longread-one/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="p">@@ -4,9 +4,9 @@</span><span class="idiff left right"> OPT_LEVEL = 3</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="p">@@ -4,9 +4,9 @@</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="diff"> include ../makefile.version</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="diff"> include make.version</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="diff"> </span>
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<a href="https://salsa.debian.org/med-team/subread/-/commit/80c6355b322521e4765d1668bf2b32ec4fbec1b3#fb9e8d937d72f3a26397728040ed9ba05f3aea89"><strong>debian/patches/fix_ftbfs_kfreebsd.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,7 +2,7 @@ Subject: Fix ftbfs on kfreebsd</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">From: Alex Mestiashvili <alex@biotec.tu-dresden.de></span></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;">--- a/src/HelperFunctions.c</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;">+++ b/src/HelperFunctions.c</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="p">@@ -84<span class="idiff left">8</span>,6 +84<span class="idiff">8</span>,9 @@</span><span class="idiff right"> int mac_str(char * str_buff)</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -84<span class="idiff left">9</span>,6 +84<span class="idiff right">9</span>,9 @@</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"> #if defined(FREEBSD) || defined(__MINGW32__)</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"> return 1;</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> #else</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,7 +12,7 @@ From: Alex Mestiashvili <alex@biotec.tu-dresden.de></td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"> #ifdef MACOS</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> int mib[6], x1, ret = 1;</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> size_t len;</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="p">@@ -94<span class="idiff left">0</span>,6 +94<span class="idiff">3</span>,7 @@</span><span class="idiff right"> int mac_str(char * str_buff)</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="p">@@ -94<span class="idiff left">1</span>,6 +94<span class="idiff right">4</span>,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"> return 1;</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"> #endif</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> #endif</span>
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