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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/phipack">Debian Med / phipack</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/phipack/-/commit/92c7e22b94873f3cb4a1cdff83b5ebb1e277bd35">92c7e22b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-09-09T08:14:52+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Force signed char on every architecture
</pre>
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<h4>3 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#f999d70e966885dbdb06aed02884b3b4ae62f09e">
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+
debian/patches/phipack.unsigned.char.fixes.patch
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</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/phipack/-/commit/92c7e22b94873f3cb4a1cdff83b5ebb1e277bd35#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</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">@@ -3,6 +3,9 @@ phipack (0.0.20160614-5) UNRELEASED; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * Add salsa-ci file (routine-update)</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Fix compiler variable to enable cross building</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> Closes: #968242</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Force signed char on every architecture (Thanks a lot to</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> Lennart Sorensen)</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> Closes: #969552</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"> -- Andreas Tille <tille@debian.org> Tue, 08 Sep 2020 22:29:16 +0200</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<li id="f999d70e966885dbdb06aed02884b3b4ae62f09e">
<a href="https://salsa.debian.org/med-team/phipack/-/commit/92c7e22b94873f3cb4a1cdff83b5ebb1e277bd35#f999d70e966885dbdb06aed02884b3b4ae62f09e"><strong>debian/patches/phipack.unsigned.char.fixes.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Date: Tue, 8 Sep 2020 19:23:15 -0400</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">From: Lennart Sorensen <lsorense@csclub.uwaterloo.ca></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Force signed char on every architecture</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/969552</span></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">diff -ruN phipack-0.0.20160614/src/fasta.c phipack-0.0.20160614.arm64/src/fasta.c</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- phipack-0.0.20160614/src/fasta.c 2016-06-14 00:18:29.000000000 -0400</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ phipack-0.0.20160614.arm64/src/fasta.c 2020-09-08 19:08:06.672390326 -0400</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -36,7 +36,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> void read_sequence_name(FILE *in_file,char *name, int capacity)</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"> int i=0;</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char ch='\0';</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ signed char ch='\0';</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> </span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> ch=fgetc(in_file);</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> if(ch != '>')</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="p">@@ -97,7 +97,7 @@</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> {</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> int bases_read=0;</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> int new_limit;</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char ch;</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;">+ signed char ch;</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> char s[250];</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> </span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> ch=fgetc(in_file);</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="p">@@ -175,7 +175,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> int *seq_counter;</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> int i;</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"><span class="gd" style="color: #000; background-color: #fdd;">- char ch;</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ signed char ch;</span></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"> int cur_seqs;</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> int num_seqs=1,new_num;</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gh" style="color: #999;">diff -ruN phipack-0.0.20160614/src/global.c phipack-0.0.20160614.arm64/src/global.c</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- phipack-0.0.20160614/src/global.c 2016-06-13 22:33:15.000000000 -0400</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ phipack-0.0.20160614.arm64/src/global.c 2020-09-08 18:04:48.956444973 -0400</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="p">@@ -34,7 +34,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> const int AA_AMBIG_SIZE =2;</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"> const char GAP[] = {'-'};</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;">-const int GAP_SIZE=2;</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;">+const int GAP_SIZE=1;</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> cbool memberOf(const char *set, const int num, char ch)</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="p">@@ -79,10 +79,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> switch(alignKind)</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> case DNA:</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return (memberOf(DNA_MISSING,DNA_MISSING_SIZE,ch) || memberOf(DNA_AMBIG,DNA_AMBIG_SIZE,ch));</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return (memberOf(DNA_MISSING,DNA_MISSING_SIZE,ch) || memberOf(DNA_AMBIG,DNA_AMBIG_SIZE,ch)) ? TRUE : FALSE;</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> break;</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> case AA:</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return (memberOf(AA_MISSING,AA_MISSING_SIZE,ch) || memberOf(AA_AMBIG,AA_AMBIG_SIZE,ch));</span></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;">+ return (memberOf(AA_MISSING,AA_MISSING_SIZE,ch) || memberOf(AA_AMBIG,AA_AMBIG_SIZE,ch)) ? TRUE : FALSE;</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> break;</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> case OTHER:</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> if(ch == GLOBAL_MISSING)</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gh" style="color: #999;">diff -ruN phipack-0.0.20160614/src/main.c phipack-0.0.20160614.arm64/src/main.c</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;">--- phipack-0.0.20160614/src/main.c 2016-06-14 00:18:17.000000000 -0400</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ phipack-0.0.20160614.arm64/src/main.c 2020-09-08 19:17:18.230153542 -0400</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="p">@@ -71,7 +71,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> void get_params(int argc, char**argv, options *opt) </span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> { </span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char *cur,ch,nextch;</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ char *cur;</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ signed char ch,nextch;</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> char temp[MAX_SIZE+1];</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> int i;</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> cbool inFileFound=FALSE;</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gh" style="color: #999;">diff -ruN phipack-0.0.20160614/src/mem.c phipack-0.0.20160614.arm64/src/mem.c</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- phipack-0.0.20160614/src/mem.c 2016-06-13 22:33:15.000000000 -0400</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ phipack-0.0.20160614.arm64/src/mem.c 2020-09-08 19:12:52.415278666 -0400</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="p">@@ -96,7 +96,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> char ffclose(FILE *handle)</span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char f;</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ signed char f;</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> char s[MAX_SIZE+1];</span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> f=fclose(handle);</span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gh" style="color: #999;">diff -ruN phipack-0.0.20160614/src/misc.c phipack-0.0.20160614.arm64/src/misc.c</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- phipack-0.0.20160614/src/misc.c 2016-06-13 22:33:15.000000000 -0400</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ phipack-0.0.20160614.arm64/src/misc.c 2020-09-08 19:08:28.352322441 -0400</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="p">@@ -46,7 +46,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> char skip_all_space(FILE *in_file)</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> {</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char ch;</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ signed char ch;</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> ch=fgetc(in_file);</span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> while((ch != EOF) && isspace(ch))</span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="p">@@ -61,7 +61,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> char skip_newlines(FILE *in_file)</span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char ch;</span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ signed char ch;</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> ch=fgetc(in_file);</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> while((ch != EOF) && (ch == '\n'))</span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="p">@@ -76,7 +76,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> char skip_non_newline(FILE *in_file)</span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char ch;</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ signed char ch;</span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"> ch=fgetc(in_file);</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"> while((ch != EOF) && (ch != '\n'))</span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="p">@@ -90,7 +90,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> char skip_non_newline_space(FILE *in_file)</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> {</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char ch;</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ signed char ch;</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"> </span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"> ch=fgetc(in_file);</span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"> while((ch != EOF) && (ch != '\n') && isspace(ch))</span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gh" style="color: #999;">diff -ruN phipack-0.0.20160614/src/phylip.c phipack-0.0.20160614.arm64/src/phylip.c</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;">--- phipack-0.0.20160614/src/phylip.c 2016-06-14 00:18:17.000000000 -0400</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;">+++ phipack-0.0.20160614.arm64/src/phylip.c 2020-09-08 19:10:06.483985652 -0400</span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"><span class="p">@@ -30,7 +30,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"> void read_strict_name(FILE *in_file,char *name, int capacity)</span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"> int i;</span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char ch='\0';</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ signed char ch='\0';</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"> for(i=0;(i<PHYLIP_SIZE) && (ch!=EOF);i++)</span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"> ch=fgetc(in_file);</span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"><span class="p">@@ -51,7 +51,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> void read_relaxed_name(FILE *in_file,char *name, int capacity)</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"> {</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"> int i=0;</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char ch='\0',next_ch;</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ signed char ch='\0',next_ch;</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"> cbool double_space=FALSE;</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"> </span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"> while((i<capacity) && (ch!=EOF) && (double_space == FALSE))</span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="p">@@ -129,7 +129,7 @@</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"> int read_seq_bit(FILE *in_file, int base_limit, align_type* states, int index, int *num_bases)</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"> {</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"> int bases_read=num_bases[index];</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;">- char ch;</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;">+ signed char ch;</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"> char s[250];</span>
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153
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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"> ch=fgetc(in_file);</span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"><span class="p">@@ -213,7 +213,7 @@</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"> int *seq_counter;</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"> int i;</span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"> int cur_seq=0;</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char ch;</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ signed char ch;</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"> </span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"> in_file=fopen(file_name,"r");</span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"> if(in_file == NULL)</span>
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"><span class="gh" style="color: #999;">diff -ruN phipack-0.0.20160614/src/profile.c phipack-0.0.20160614.arm64/src/profile.c</span></span>
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<td class="diff-line-num new new_line" data-linenumber="165" 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">
165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- phipack-0.0.20160614/src/profile.c 2016-06-14 00:18:17.000000000 -0400</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ phipack-0.0.20160614.arm64/src/profile.c 2020-09-08 19:16:45.274292568 -0400</span></span>
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"><span class="p">@@ -71,7 +71,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"> void get_params(int argc, char**argv, options *opt) </span>
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"> { </span>
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char *cur,ch,nextch;</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;">+ char *cur;</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ signed char ch,nextch;</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"> char temp[MAX_SIZE+1];</span>
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"> int i;</span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"> cbool inFileFound=FALSE;</span>
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"><span class="gh" style="color: #999;">diff -ruN phipack-0.0.20160614/src/seqManip.c phipack-0.0.20160614.arm64/src/seqManip.c</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- phipack-0.0.20160614/src/seqManip.c 2016-06-14 00:18:17.000000000 -0400</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ phipack-0.0.20160614.arm64/src/seqManip.c 2020-09-08 19:14:37.974830794 -0400</span></span>
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"><span class="p">@@ -190,7 +190,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"> cbool validate_alignment(align_type **alignment, alignmentClass alignKind,int num_taxa, int num_sites)</span>
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"> int i,j;</span>
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char ch;</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ signed char ch;</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"> char s[MAX_SIZE+1];</span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"> </span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"> for(i=0;i<num_taxa;i++)</span></pre>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">hardening.patch</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">cross.patch</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">phipack.unsigned.char.fixes.patch</span></pre>
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