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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/sift">Debian Med / sift</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/sift/commit/4a2c15772a02139e4e87f8c5aaf901d8ea9f4cad">4a2c1577</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2018-07-13T13:39:25+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Technically works as 6.2.1.
</pre>
</li>
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<h4>10 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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</li>
<li class="file-stats">
<a href="#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32">
debian/docs
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<li class="file-stats">
<a href="#9cfeae84830b4cee099267388e7b03eeb5c4ee24">
debian/patches/fix_gcc_warnings
</a>
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<li class="file-stats">
<a href="#8429ad65ebd2ab6adcb9ec42b408b0aa7d272279">
debian/patches/fix_perl_interpreter_and_lib_path
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<li class="file-stats">
<a href="#c53a6a0c5788a03f80ac1101bb0f08d31eb8249a">
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−
debian/patches/jarfile
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<li class="file-stats">
<a href="#5053077081e60564d2ba8d7dfed0c73e49a574a4">
debian/patches/ld-as-needed
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#85ccdeeb03055211183e48520592d9a93592b330">
<span class="new-file">
+
debian/source/lintian-overrides
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/sift/commit/4a2c15772a02139e4e87f8c5aaf901d8ea9f4cad#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">sift (6.2.1-1) 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"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * New upstream version.</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"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> Thu, 12 Jul 2018 12:54:01 +0200</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">sift (4.0.3b-7) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * d/u/metadata:</span>
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<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/sift/commit/4a2c15772a02139e4e87f8c5aaf901d8ea9f4cad#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,6 +7,16 @@ Disclaimer: This package is not part of Debian because of the non-free</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> FHCRC NONCOMMERCIAL LICENSE license. The license does not restrict</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> auto-building of the package. Distribution on a royalty-free basis</span>
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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> is allowed, therefore Debian is allowed to distribute the program.</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Files-Excluded: bin/choose_seqs_via_psiblastseedmedian</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> bin/clump_output_alignedseq</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> bin/consensus_to_seq</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> bin/fastaseqs</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> bin/info_on_seqs</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> bin/process_alignment</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> bin/psiblast_res_to_fasta_dbpairwise</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> bin/seqs_from_psiblast_res</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> blimps/obj/*.o</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Files: *</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Copyright: 1993-2008, Fred Hutchinson Cancer Research Center</span>
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<a href="https://salsa.debian.org/med-team/sift/commit/4a2c15772a02139e4e87f8c5aaf901d8ea9f4cad#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32"><strong>debian/docs</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">README</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">README_4.0.3</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">#README</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">#README_4.0.3</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">INSTALL</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">VERSION_UPDATE</span></pre>
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<a href="https://salsa.debian.org/med-team/sift/commit/4a2c15772a02139e4e87f8c5aaf901d8ea9f4cad#9cfeae84830b4cee099267388e7b03eeb5c4ee24"><strong>debian/patches/fix_gcc_warnings</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff">Description: Fix gcc warnings.</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff">Author: Michael Bienia <geser@ubuntu.com></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/Alignment.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/Alignment.c</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;">@@ -766,7 +766,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gh" style="color: #999;">Index: sift/src/Alignment.c</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- sift.orig/src/Alignment.c</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ sift/src/Alignment.c</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -766,7 +766,7 @@ read_psiblast_header_until_first (FILE*</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> void</span>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> read_psiblast_header_until_first_alignment (FILE* fp)</span>
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8
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> {</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,7 +13,7 @@ Author: Michael Bienia <geser@ubuntu.com></td>
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11
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> </span>
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12
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> read_psiblast_header_until_first (fp);</span>
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13
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<td class="diff-line-num new_line" data-linenumber="15" 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">
15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> </span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -783,7 +783,7 @@</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -783,7 +783,7 @@<span class="idiff left right"> read_psiblast_header_until_first_alignme</span></span></span>
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15
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"> int </span>
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16
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> read_psiblast_header_until_first_no_error (FILE* fp,int return_error )</span>
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17
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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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="20" 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="22" 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">@@ -20,18 +22,11 @@ Author: Michael Bienia <geser@ubuntu.com></td>
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20
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="diff"> </span>
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21
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="diff"> while (!feof (fp) && fgets (line, LINE_LEN, fp) != NULL &&</span>
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22
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="diff"> strstr (line, "Sequences producing significant alignments") == NULL)</span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1694,7 +1694,7 @@</span></span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"> assert (fp != NULL);</span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"> fgets (line, LARGE_BUFF_LENGTH, fp);</span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"> if (strstr (line, "Query") == NULL) {</span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fprintf (stderr,"%s line should have Query:\n");</span></span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf (stderr,"'%s' line should have 'Query'\n", line);</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"> exit (-1);</span>
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30
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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"> strptr = strtok (line, " \t\r\n"); /* this should be Query */</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/PN_convert.c</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/PN_convert.c</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2184,7 +2184,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gh" style="color: #999;">Index: sift/src/PN_convert.c</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></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;">--- sift.orig/src/PN_convert.c</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;">+++ sift/src/PN_convert.c</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;">@@ -2032,7 +2032,7 @@ void init_frq_qij()</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="diff"> else</span>
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"> {</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="diff"> fprintf (stderr, "Can't open file '%s': %s.\n", qijname, strerror(errno) );</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="40" 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">@@ -40,35 +35,11 @@ Author: Michael Bienia <geser@ubuntu.com></td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="diff"> system( "pwd" );</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="diff"> exit (-1);</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="diff"> }</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;">--- a/src/Psiblast.c</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;">+++ b/src/Psiblast.c</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;">@@ -77,14 +77,14 @@</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"> buff = strstr(Buffer, "Score=");</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff"> if (buff != NULL) {</span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sscanf (buff, "Score = %d", alignment->score);</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;">+ sscanf (buff, "Score = %d", &alignment->score);</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="diff"> } else {</span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="diff"> fprintf (errorfp, "Unable to read Score, parsing incorrect");</span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="diff"> exit (-1);</span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="diff"> buff = strstr (Buffer, "Expect = ");</span>
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56
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="diff"> if (buff != NULL) {</span>
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57
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sscanf (buff, "Expect = %lf", alignment->evalue);</span></span>
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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sscanf (buff, "Expect = %lf", &alignment->evalue);</span></span>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="diff"> } else {</span>
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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="diff"> fprintf (errorfp, "Unable to read e-value, parsing incorrect");</span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="diff"> exit (-1);</span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -95,7 +95,7 @@</span></span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="diff"> fgets (Buffer, LARGE_BUFF_LENGTH, fp); /* get blank line */</span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="diff"> fgets (Buffer, LARGE_BUFF_LENGTH, fp); /* get first line */;</span>
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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="diff"> get_start_pos = TRUE;</span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- while (Buffer != "\n") {</span></span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ while ( strcmp( Buffer, "\n" ) != 0 ) {</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="diff"> read_4_alignment_lines (Buffer, alignment, fp, get_start_pos);</span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="diff"> get_start_pos = FALSE; /* read 1rst 4 alignment lines*/</span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="diff"> /* already got the starting pos*/</span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -274,7 +274,7 @@</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gh" style="color: #999;">Index: sift/src/Psiblast.c</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</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;">--- sift.orig/src/Psiblast.c</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;">+++ sift/src/Psiblast.c</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -302,7 +302,7 @@ get_top_seq (char next_seq_to_add[], Has</span></span>
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72
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43
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="diff"> FILE* psiblastfp;</span>
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73
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44
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="diff"> char name[KEY_WIDTH];</span>
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74
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45
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="diff"> char *strptr;</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">@@ -77,25 +48,3 @@ Author: Michael Bienia <geser@ubuntu.com></td>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="diff"> </span>
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49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="diff"> </span>
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79
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="diff"> if ((psiblastfp = fopen (psiblastres_file, "r")) == NULL)</span></pre>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/clump_output_alignedseq.c</span></span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/clump_output_alignedseq.c</span></span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -137,7 +137,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="diff"> char queryfilename[LARGE_BUFF_LENGTH];</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"> if (argc < 4) {</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;">- printf ("clump.c : Clusters sequences into % clus");</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ printf ("clump.c : Clusters sequences into %% clus");</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="diff"> }</span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="diff"> if (argc > 1 ) strcpy (seqfilename, argv[1]);</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;">--- a/src/Matrix_Info.c</span></span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/Matrix_Info.c</span></span>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -467,7 +467,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="diff"> case 2: /* +- phenotype is - */</span>
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95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="diff"> if ( matrix->weights[aa_atob[c]][l] >= 0) {</span>
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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="diff"> pos_error_fp++; error_fp++; </span>
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97
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- printf ("incorrect less severe %d %d %c\n", l, matrix->weights[aa_atob[c]][l], c);</span></span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ printf ("incorrect less severe %d %g %c\n", l, matrix->weights[aa_atob[c]][l], c);</span></span>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="diff"> print_type = print_incorrect;</span>
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100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="diff"> } else if (matrix->weights[aa_atob[c]][l] < 0){</span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="diff"> pos_notobserved_intolerant++;</span></pre>
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<a href="https://salsa.debian.org/med-team/sift/commit/4a2c15772a02139e4e87f8c5aaf901d8ea9f4cad#8429ad65ebd2ab6adcb9ec42b408b0aa7d272279"><strong>debian/patches/fix_perl_interpreter_and_lib_path</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">@@ -3,74 +3,20 @@</td>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff">* Enhance verbosity in csh scripts for bug hunting.</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff">* Add blast processors argument SIFT_for_submitting_fasta_seq.csh .</span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff">* Trailing whitespace removed from lines.</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/bin/SIFT_exome_nssnvs.pl</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;">+++ b/bin/SIFT_exome_nssnvs.pl</span></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,8 @@</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/local/bin/perl</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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11
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<pre style="margin: 0;">-<span id="LC11" 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="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#Location of all the SIFT grot on Debian.</span></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+use lib '/usr/lib/sift/bin';</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;">+</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> use List::Util qw[min max];</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> use File::Copy;</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> use Getopt::Std;</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -12,7 +16,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"> $| = 1;</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"> system("umask 006");</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-$ENV{'SIFT_HOME'} = '/usr/local/projects/SIFT/sift4.0.2/';</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;">+$ENV{'SIFT_HOME'} = '/usr/lib/sift/';</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"> my $SIFT_HOME = $ENV{'SIFT_HOME'};</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"> use vars qw($opt_i $opt_d $opt_o $opt_A $opt_B $opt_C $opt_D $opt_E $opt_F $opt_G $opt_H $opt_I $opt_J $opt_K $opt_L);</span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"> getopts("i:d:o:A:B:C:D:E:F:G:H:I:J:K:L:");</span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -62,7 +66,7 @@</span></span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"> my $oo12 = defined($opt_L) ? 1:0;</span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"> my $pid = $$;</span>
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30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"> my $bin = "$SIFT_HOME/bin";</span>
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<td class="diff-line-num old old_line" data-linenumber="31" 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">
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;">-my $tmp = defined($opt_o) ? "$opt_o/$pid" : "$SIFT_HOME/tmp/$pid";</span></span>
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32
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+my $tmp = defined($opt_o) ? "$opt_o/$pid" : "/tmp/sift_$pid";</span></span>
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33
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"> my $Variation_db_dir = $opt_d;</span>
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34
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"> mkdir $tmp;</span>
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35
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"> my $num_coords_per_split = 1000;</span>
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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;">--- a/bin/SIFT_exome_indels.pl</span></span>
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37
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/bin/SIFT_exome_indels.pl</span></span>
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38
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,6 @@</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;">-#!/usr/local/bin/perl</span></span>
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40
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</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;">+</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;">+use lib '/usr/lib/sift/bin';</span></span>
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<td class="diff-line-num old old_line" data-linenumber="43" 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">
43
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff"> </span>
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44
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff"> # This program is licensed to you under the Fred</span>
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45
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"> # Hutchinos Cancer Research Center (FHCRC)</span>
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<td class="diff-line-num old old_line" data-linenumber="46" 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">
46
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -12,7 +14,7 @@</span></span>
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47
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"> use Tie::IxHash;</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff"> use File::Copy;</span>
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<td class="diff-line-num old old_line" data-linenumber="49" 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">
49
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"> use Getopt::Std;</span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-$ENV{'SIFT_HOME'} = '/usr/local/projects/SIFT/sift4.0.1';</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;">+$ENV{'SIFT_HOME'} = '/usr/lib/sift';</span></span>
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52
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="diff"> $SIFT_HOME = $ENV{'SIFT_HOME'};</span>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="diff"> use vars qw($opt_i $opt_c $opt_d $opt_o);</span>
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54
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="diff"> getopts("i:c:d:o:");</span>
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55
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -38,7 +40,7 @@</span></span>
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56
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="diff"> system("umask 006");</span>
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57
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="diff"> my $bin = "$SIFT_HOME/bin";</span>
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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="diff"> my $pid = $$;</span>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-my $tmp = defined($opt_o) ? "$opt_o/$pid" : "$SIFT_HOME/tmp/$pid";</span></span>
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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+my $tmp = defined($opt_o) ? "$opt_o/$pid" : "/tmp/sift_$pid";</span></span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="diff"> require "$bin/SIFT_subroutines.pm";</span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="diff"> mkdir $tmp;</span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="diff"> chmod 0777, $tmp;</span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/bin/perlscripts/get_BLINK_seq.pl</span></span>
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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/bin/perlscripts/get_BLINK_seq.pl</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gh" style="color: #999;">Index: sift/bin/perlscripts/get_BLINK_seq.pl</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- sift.orig/bin/perlscripts/get_BLINK_seq.pl</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ sift/bin/perlscripts/get_BLINK_seq.pl</span></span>
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66
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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67
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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;">-#!/usr/local/bin/perl </span></span>
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68
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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69
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> #use strict;</span>
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70
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> use LWP::Simple;</span>
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71
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> use LWP::UserAgent;</span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/bin/seqs_chosen_via_median_info.csh</span></span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/bin/seqs_chosen_via_median_info.csh</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gh" style="color: #999;">Index: sift/bin/seqs_chosen_via_median_info.csh</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- sift.orig/bin/seqs_chosen_via_median_info.csh</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ sift/bin/seqs_chosen_via_median_info.csh</span></span>
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74
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,7 +1,8 @@</span></span>
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75
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/bin/csh</span></span>
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76
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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;">+#!/bin/csh -e</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="81" 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="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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -81,298 +27,21 @@</td>
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"> </span>
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82
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="diff"> # This program is licensed to you under the Fred</span>
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83
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="diff"> # Hutchinos Cancer Research Center (FHCRC)</span>
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84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -9,14 +10,16 @@</span></span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="diff"> # http://blocks.fhcrc.org/sift/license.html and should be attached</span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="diff"> # to this software</span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="diff"> </span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-set tmpdir = $SIFT_DIR/tmp</span></span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-set bindir = $SIFT_DIR/bin</span></span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-unalias cp</span></span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-unalias rm</span></span>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+unalias cp || true</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;">+unalias rm || true</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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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="diff"> set seq_database = $2</span>
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97
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="diff"> set median_threshold = 2.75;</span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if ( $3 == "" ) then</span></span>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ set blastprocessors = 1</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;">+else</span></span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ set blastprocessors = $3</span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+endif</span></span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="diff"> </span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="diff"> # Cleanup query sequence. NCBI stuff is intolerant of format</span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="diff"> # deviations.</span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -24,22 +27,24 @@</span></span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="diff"> set tail = $1:t</span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="diff"> set pid = $tail:r</span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="diff"> echo tail is $tail</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;">-set query = $tmpdir/$tail.query</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;">+set query = $TMPDIR/$tail.query</span></span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="diff"> echo query is $query</span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="diff"> </span>
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114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-$bindir/fastaseqs $1 $query >& /dev/null</span></span>
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115
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+echo "fastaseqs $1 $query >& /dev/null"</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;">+fastaseqs $1 $query >& /dev/null</span></span>
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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="diff"> </span>
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118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="diff"> </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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<pre style="margin: 0;">-<span id="LC120" class="line" lang="diff"> # (1) PSIBLAST</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"><span class="gd" style="color: #000; background-color: #fdd;">- set iterations = 1 </span></span>
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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+set iterations = 2</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="diff"> # the query is called $$.fasta, get pid from that</span>
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125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="diff"> ####### FILTER ############################</span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="diff"> #$BLASTFILTER/seg $query -x > $query.imp</span>
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128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+echo "cp $query $query.unfiltered"</span></span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="diff"> cp $query $query.unfiltered</span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#mv -f $query.imp $query # this has the filtered query </span></span>
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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#mv -f $query.imp $query # this has the filtered query</span></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="diff"> </span>
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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="diff"> # b option, # of alignments to show (else it is 250)</span>
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="diff"> # m option, type of alignment 0-pairwise, 6-flat master slave w/out identites</span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -47,10 +52,18 @@</span></span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="diff"> # make error file & remove only if PSI-BLAST is finished within time allotted</span>
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137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="diff"> # not filtering query because Jorja says new statistics take care of that</span>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="diff"> </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;">-echo "PSI-BLAST time limit exceeded." > $tmpdir/$pid.time.error</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;">+echo "PSI-BLAST time limit exceeded." > $TMPDIR/$pid.time.error</span></span>
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141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="diff"> limit cputime 30m</span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="diff"> </span>
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143
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-$NCBI/blastpgp -d $seq_database -i $query -o $query.out -m 0 -j $iterations -e .0001 -h 0.002 -b 399</span></span>
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144
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if ( $?SIFT_DEBUG ) then</span></span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ echo "if ! ( -e "/tmp/savethis.out" ) blastpgp -a $blastprocessors -d $seq_database -i $query -o /tmp/savethis.out -m 0 -j $iterations -e .0001 -h 0.002 -b 399"</span></span>
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146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ! ( -e "/tmp/savethis.out" ) blastpgp -a $blastprocessors -d $seq_database -i $query -o /tmp/savethis.out -m 0 -j $iterations -e .0001 -h 0.002 -b 399;</span></span>
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147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ echo "cp -a /tmp/savethis.out $query.out"</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;">+ cp -a /tmp/savethis.out $query.out</span></span>
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149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+else</span></span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ echo "blastpgp -a $blastprocessors -d $seq_database -i $query -o $query.out -m 0 -j $iterations -e .0001 -h 0.002 -b 399"</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;">+ blastpgp -a $blastprocessors -d $seq_database -i $query -o $query.out -m 0 -j $iterations -e .0001 -h 0.002 -b 399</span></span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+endif</span></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"> if ($status != 0) then</span>
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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="diff"> echo "exiting because stauts not equal to 0"</span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -59,45 +72,50 @@</span></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="diff"> unlimit cputime</span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="diff"> </span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="diff"> # finished within 10 minutes, remove error file</span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-rm -f $tmpdir/$pid.time.error</span></span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+echo "rm -f $TMPDIR/$pid.time.error"</span></span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+rm -f $TMPDIR/$pid.time.error</span></span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="diff"> </span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="diff"> ##echo done psiblast</span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="diff"> </span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="diff"> # get the psiblast alignment of all the sequences found.</span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="diff"> </span>
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168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-$bindir/psiblast_res_to_fasta_dbpairwise $query.out $query.globalX $iterations $query.unfiltered</span></span>
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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+echo "__SIFT_BINDIR__/psiblast_res_to_fasta_dbpairwise $query.out $query.globalX $iterations $query.unfiltered"</span></span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ __SIFT_BINDIR__/psiblast_res_to_fasta_dbpairwise $query.out $query.globalX $iterations $query.unfiltered</span></span>
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<td class="diff-line-num old old_line" data-linenumber="171" 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">
171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="diff"> if ($status != 0) then</span>
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172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="diff"> exit (-1)</span>
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173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="diff"> endif</span>
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174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="diff"> </span>
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<td class="diff-line-num old old_line" data-linenumber="175" 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">
175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-$bindir/clump_output_alignedseq $query.globalX $tmpdir/$pid.clumped .9 0 >& /dev/null</span></span>
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<td class="diff-line-num old old_line" data-linenumber="176" 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">
176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+echo "__SIFT_BINDIR__/clump_output_alignedseq $query.globalX $TMPDIR/$pid.clumped .9 0 >& /dev/null"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="177" 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">
177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ __SIFT_BINDIR__/clump_output_alignedseq $query.globalX $TMPDIR/$pid.clumped .9 0 >& /dev/null</span></span>
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<td class="diff-line-num old old_line" data-linenumber="178" 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">
178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="diff"> </span>
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<td class="diff-line-num old old_line" data-linenumber="179" 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">
179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-echo "choose seqs time limit exceeded." > $tmpdir/$pid.time.error</span></span>
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<td class="diff-line-num old old_line" data-linenumber="180" 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">
180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+echo "choose seqs time limit exceeded." > $TMPDIR/$pid.time.error</span></span>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="diff"> limit cputime 30m</span>
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<td class="diff-line-num old old_line" data-linenumber="182" 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">
182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="diff"> </span>
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<td class="diff-line-num old old_line" data-linenumber="183" 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">
183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-$bindir/choose_seqs_via_psiblastseedmedian $query.unfiltered $tmpdir/$pid.clumped $query.selectedclumped 1.0 $pid $median_threshold >& /dev/null</span></span>
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<td class="diff-line-num old old_line" data-linenumber="184" 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">
184
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+echo "__SIFT_BINDIR__/choose_seqs_via_psiblastseedmedian $query.unfiltered $TMPDIR/$pid.clumped $query.selectedclumped 1.0 $pid $median_threshold"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="185" 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">
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;">+ __SIFT_BINDIR__/choose_seqs_via_psiblastseedmedian $query.unfiltered $TMPDIR/$pid.clumped $query.selectedclumped 1.0 $pid $median_threshold</span></span>
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<td class="diff-line-num old old_line" data-linenumber="186" 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">
186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="diff"> </span>
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<td class="diff-line-num old old_line" data-linenumber="187" 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">
187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="diff"> if ($status != 0) then</span>
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<td class="diff-line-num old old_line" data-linenumber="188" 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">
188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="diff"> echo "exiting because stauts not equal to 0"</span>
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<td class="diff-line-num old old_line" data-linenumber="189" 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">
189
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="diff"> exit (-1)</span>
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<td class="diff-line-num old old_line" data-linenumber="190" 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">
190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="diff"> endif</span>
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<td class="diff-line-num old old_line" data-linenumber="191" 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">
191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="diff"> unlimit cputime</span>
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<td class="diff-line-num old old_line" data-linenumber="192" 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">
192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-rm -f $tmpdir/$pid.time.error</span></span>
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<td class="diff-line-num old old_line" data-linenumber="193" 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">
193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+rm -f $TMPDIR/$pid.time.error</span></span>
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<td class="diff-line-num old old_line" data-linenumber="194" 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">
194
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="diff"> </span>
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<td class="diff-line-num old old_line" data-linenumber="195" 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">
195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-$bindir/consensus_to_seq $query.selectedclumped $tmpdir/$pid.clumped.consensuskey $tmpdir/$pid.selected >& /dev/null</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="196" 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">
196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+echo "__SIFT_BINDIR__/consensus_to_seq $query.selectedclumped $TMPDIR/$pid.clumped.consensuskey $TMPDIR/$pid.selected >& /dev/null"</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="197" 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">
197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ __SIFT_BINDIR__/consensus_to_seq $query.selectedclumped $TMPDIR/$pid.clumped.consensuskey $TMPDIR/$pid.selected >& /dev/null</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="198" 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">
198
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="199" 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">
199
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<td class="diff-line-num new_line old" data-linenumber="30" 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="LC199" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="200" 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">
200
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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC200" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-$bindir/seqs_from_psiblast_res $query.out $tmpdir/$pid.selected $iterations $query.unfiltered $tmpdir/$pid.alignedfasta $pid</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="201" 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">
201
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<td class="diff-line-num new_line old" data-linenumber="30" 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="LC201" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+echo "__SIFT_BINDIR__/seqs_from_psiblast_res $query.out $TMPDIR/$pid.selected $iterations $query.unfiltered $TMPDIR/$pid.alignedfasta $pid"</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="202" 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">
202
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<td class="diff-line-num new_line old" data-linenumber="30" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC202" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ __SIFT_BINDIR__/seqs_from_psiblast_res $query.out $TMPDIR/$pid.selected $iterations $query.unfiltered $TMPDIR/$pid.alignedfasta $pid</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="203" 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">
203
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<td class="diff-line-num new_line old" data-linenumber="30" 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="LC203" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="204" 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">
204
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<td class="diff-line-num new_line old" data-linenumber="30" 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="LC204" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- rm $tmpdir/$pid.clumped*</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="205" 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">
205
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<td class="diff-line-num new_line old" data-linenumber="30" 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="LC205" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- rm $query.selectedclumped* </span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="206" 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">
206
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<td class="diff-line-num new_line old" data-linenumber="30" 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="LC206" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- rm $tmpdir/$pid.selected</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="207" 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">
207
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- rm $tmpdir/$pid.unaligned</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="208" 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">
208
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<td class="diff-line-num new_line old" data-linenumber="30" 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="LC208" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- rm $query.globalX</span></span>
</pre>
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</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="209" 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">
209
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<td class="diff-line-num new_line old" data-linenumber="30" 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">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC209" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- rm $tmpdir/$pid.psiblastout </span></span>
</pre>
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</tr>
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<td class="diff-line-num old old_line" data-linenumber="210" 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">
210
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<td class="diff-line-num new_line old" data-linenumber="30" 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">
</td>
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- rm $pid.TEMP*</span></span>
</pre>
</td>
</tr>
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<td class="diff-line-num old old_line" data-linenumber="211" 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">
211
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<td class="diff-line-num new_line old" data-linenumber="30" 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">
</td>
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- rm $query</span></span>
</pre>
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</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="212" 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">
212
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<td class="diff-line-num new_line old" data-linenumber="30" 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">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC212" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- rm $query.unfiltered</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="213" 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">
213
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<td class="diff-line-num new_line old" data-linenumber="30" 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">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC213" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+echo "rm -f"</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="214" 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">
214
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<td class="diff-line-num new_line old" data-linenumber="30" 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">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC214" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ rm -f $TMPDIR/$pid.clumped*</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="215" 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">
215
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<td class="diff-line-num new_line old" data-linenumber="30" 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">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC215" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ rm -f $query.selectedclumped*</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="216" 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">
216
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<td class="diff-line-num new_line old" data-linenumber="30" 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">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC216" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ rm -f $TMPDIR/$pid.selected</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="217" 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">
217
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<td class="diff-line-num new_line old" data-linenumber="30" 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">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC217" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ rm -f $TMPDIR/$pid.unaligned</span></span>
</pre>
</td>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ rm -f $query.globalX</span></span>
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ rm -f $TMPDIR/$pid.psiblastout</span></span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ rm -f $pid.TEMP*</span></span>
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ rm -f $query</span></span>
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ rm -f $query.unfiltered</span></span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="diff"> exit (0)</span>
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<pre style="margin: 0;">-<span id="LC224" 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="LC225" 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="LC226" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/bin/SIFT_for_submitting_fasta_seq.csh</span></span>
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227
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/bin/SIFT_for_submitting_fasta_seq.csh</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gh" style="color: #999;">Index: sift/bin/SIFT_for_submitting_NCBI_gi_id.csh</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- sift.orig/bin/SIFT_for_submitting_NCBI_gi_id.csh</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ sift/bin/SIFT_for_submitting_NCBI_gi_id.csh</span></span>
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<pre style="margin: 0;"> <span id="LC34" 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="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/bin/csh</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;">+#!/bin/csh -e</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="diff"> # SIFT.csh</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="diff"> # This program is licensed to you under the Fred</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="diff"> # Hutchinos Cancer Research Center (FHCRC)</span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -10,30 +10,37 @@</span></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="diff"> # Argument 1: the protein sequence file in fasta format</span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="diff"> # Argument 2: the pathname to the protein sequence database</span>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="diff"> # Argument 3: the substitution file (file containing amino acid substitutions to be predicted on. </span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# Argument 4: blast processors</span></span>
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="diff"> ### Set these for your installation</span>
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241
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="diff"> # Location of blastpgp</span>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-setenv NCBI /usr/local/packages/blast-2.2.18/bin/</span></span>
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243
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#setenv NCBI /usr/local/packages/blast-2.2.18/bin/</span></span>
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244
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="diff"> # Location of BLIMPS</span>
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247
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-setenv BLIMPS_DIR /opt/www/sift/sift3.0/blimps/</span></span>
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248
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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249
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# Location of SIFT </span></span>
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250
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-setenv SIFT_DIR /opt/www/sift/sift3.0</span></span>
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251
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+setenv BLIMPS_DIR __MAKE_PREFIX__/share/sift/blimps</span></span>
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252
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="diff"> </span>
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253
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="diff"> # SIFT's output files are written here</span>
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254
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-set tmpdir = /opt/www/sift/sift3.0/tmp</span></span>
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+setenv TMPDIR `mktemp -d` || exit 1</span></span>
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256
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<pre style="margin: 0;">-<span id="LC256" 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="LC257" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+setenv SIFT_BINDIR __SIFT_BINDIR__</span></span>
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258
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<pre style="margin: 0;">-<span id="LC258" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+setenv SIFT_SCRIPTDIR __SIFT_SCRIPTDIR__</span></span>
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259
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+setenv BLASTMAT __MAKE_PREFIX__/share/ncbi/data</span></span>
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260
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num old old_line" data-linenumber="261" 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">
261
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if ( -e "$HOME/.siftrc" ) source "$HOME/.siftrc";</span></span>
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262
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="diff"> ### Shouldn't need to make any more changes, look for output in $tmpsift</span>
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264
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-set bindir = $SIFT_DIR/bin</span></span>
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265
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="diff"> set root_file = $1:r</span>
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266
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="diff"> set tail_of_root = $root_file:t</span>
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267
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-set tmpfasta = $tmpdir/$tail_of_root.alignedfasta</span></span>
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268
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-set tmpsift = $tmpdir/$tail_of_root.SIFTprediction</span></span>
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269
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<td class="diff-line-num old old_line" data-linenumber="270" 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">
270
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-$bindir/seqs_chosen_via_median_info.csh $1 $2 $4</span></span>
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271
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-$bindir/info_on_seqs $tmpfasta $3 $tmpsift</span></span>
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272
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-echo "Output in $tmpsift"</span></span>
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273
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+set tmpfasta = $TMPDIR/$tail_of_root.alignedfasta</span></span>
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<td class="diff-line-num old old_line" data-linenumber="274" 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">
274
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#set tmpsift = $TMPDIR/$tail_of_root.SIFTprediction</span></span>
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275
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+set tmpsift = $tail_of_root.SIFTprediction</span></span>
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<td class="diff-line-num old old_line" data-linenumber="276" 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">
276
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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277
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+echo "$SIFT_SCRIPTDIR/seqs_chosen_via_median_info.csh $1 $2 $4"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="278" 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">
278
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $SIFT_SCRIPTDIR/seqs_chosen_via_median_info.csh $1 $2 $4</span></span>
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<td class="diff-line-num old old_line" data-linenumber="279" 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">
279
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+echo "$SIFT_SCRIPTDIR/info_on_seqs $tmpfasta $3 $tmpsift"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="280" 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">
280
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $SIFT_SCRIPTDIR/info_on_seqs $tmpfasta $3 $tmpsift</span></span>
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<td class="diff-line-num old old_line" data-linenumber="281" 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">
281
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<pre style="margin: 0;">-<span id="LC281" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+rm -rf $TMPDIR</span></span>
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<td class="diff-line-num old old_line" data-linenumber="282" 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">
282
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+echo "Output in ($PWD/)$tmpsift"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="283" 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">
283
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="diff"> </span>
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<td class="diff-line-num old old_line" data-linenumber="284" 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">
284
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="diff"> exit</span>
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<td class="diff-line-num old old_line" data-linenumber="285" 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">
285
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/bin/SIFT_for_submitting_NCBI_gi_id.csh</span></span>
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<td class="diff-line-num old old_line" data-linenumber="286" 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">
286
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/bin/SIFT_for_submitting_NCBI_gi_id.csh</span></span>
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<pre style="margin: 0;">-<span id="LC287" 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="LC288" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/bin/csh</span></span>
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/bin/csh -e</span></span>
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="diff"> # SIFT.csh</span>
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="diff"> # This program is licensed to you under the Fred</span>
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292
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="diff"> # Hutchinos Cancer Research Center (FHCRC)</span>
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -6,53 +6,56 @@</span></span>
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294
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="diff"> # http://blocks.fhcrc.org/sift/license.html and should be attached</span>
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295
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="diff"> # to this software</span>
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296
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<pre style="margin: 0;">-<span id="LC296" class="line" lang="diff"> </span>
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297
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# Argument 1: NCBI protein gi #. Just the number, nothing else. </span></span>
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298
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<pre style="margin: 0;">-<span id="LC298" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# Argument 2: The substitution file (file containing amino acid substitutions to be predicted on. </span></span>
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299
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# Argument 3: Type of sequences to get from NCBI BLink. "BEST" or "ALL" </span></span>
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# BEST is recommended if high-confidence scores can be obtained </span></span>
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301
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# Argument 1: NCBI protein gi #. Just the number, nothing else.</span></span>
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302
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<pre style="margin: 0;">-<span id="LC302" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# Argument 2: The substitution file (file containing amino acid substitutions to be predicted on.</span></span>
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303
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<pre style="margin: 0;">-<span id="LC303" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# Argument 3: Type of sequences to get from NCBI BLink. "BEST" or "ALL"</span></span>
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304
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<pre style="margin: 0;">-<span id="LC304" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# BEST is recommended if high-confidence scores can be obtained</span></span>
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305
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="diff"> </span>
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306
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="diff"> ### Set these for your installation</span>
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307
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="diff"> # Location of blastpgp</span>
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308
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<pre style="margin: 0;">-<span id="LC308" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-setenv NCBI ../../blast</span></span>
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309
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-setenv NCBI /usr/local/blast/</span></span>
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310
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#setenv NCBI ../../blast</span></span>
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311
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="diff"> # Location of BLIMPS</span>
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313
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-setenv BLIMPS_DIR ../blimps</span></span>
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314
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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315
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# Location of SIFT </span></span>
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316
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-setenv SIFT_DIR ../</span></span>
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317
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+setenv BLIMPS_DIR __MAKE_PREFIX__/share/sift/blimps</span></span>
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318
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="diff"> </span>
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319
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="diff"> # SIFT's output files are written here</span>
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320
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-set tmpdir = ../tmp</span></span>
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321
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+setenv TMPDIR `mktemp -d` || exit 1</span></span>
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322
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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323
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+setenv SIFT_SCRIPTDIR __SIFT_SCRIPTDIR__</span></span>
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324
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+setenv BLASTMAT __MAKE_PREFIX__/share/ncbi/data</span></span>
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325
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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326
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<pre style="margin: 0;">-<span id="LC326" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if ( -e "$HOME/.siftrc" ) source "$HOME/.siftrc";</span></span>
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327
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="diff"> </span>
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328
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-### Shouldn't need to make any more changes, look for output in $tmpdir </span></span>
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329
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-set bindir = $SIFT_DIR/bin</span></span>
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330
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+### Shouldn't need to make any more changes, look for output in $tmpdir</span></span>
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331
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<pre style="margin: 0;">-<span id="LC331" class="line" lang="diff"> set gi = $1</span>
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332
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="diff"> set polymorphism_file = $2</span>
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333
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-set outfile = $tmpdir/$1.SIFTprediction</span></span>
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334
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-set bestORall = $3 # if set to BEST, takes best reciprocal hits from BLink, </span></span>
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335
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#set outfile = $TMPDIR/$1.SIFTprediction</span></span>
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336
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<pre style="margin: 0;">-<span id="LC336" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+set outfile = $1.SIFTprediction</span></span>
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<pre style="margin: 0;">-<span id="LC337" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+set bestORall = $3 # if set to BEST, takes best reciprocal hits from BLink,</span></span>
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="diff"> # otherwise it will take all hits from BLINK</span>
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<pre style="margin: 0;">-<span id="LC339" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="diff"> # get unaligned sequences from NCBI</span>
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-set unalignedseqs = $tmpdir/$gi.unaligned</span></span>
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-perl $bindir/perlscripts/get_BLINK_seq.pl $gi $tmpdir/$gi.unaligned $bestORall </span></span>
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<pre style="margin: 0;">-<span id="LC343" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+set unalignedseqs = $TMPDIR/$gi.unaligned</span></span>
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<pre style="margin: 0;">-<span id="LC344" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+$SIFT_SCRIPTDIR/get_BLINK_seq.pl $gi $TMPDIR/$gi.unaligned $bestORall</span></span>
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<pre style="margin: 0;">-<span id="LC345" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="diff"> # getting the alignment from PSI-BLAST, quick and dirty</span>
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<pre style="margin: 0;">-<span id="LC347" class="line" lang="diff"> cat $unalignedseqs | perl -pe 's/\|//' | perl -pe 's/\|/\t/' | perl -pe 's/^\n//' | awk '{if ($1 ~ /^>/) { print $1} else { print;}}' > $unalignedseqs.2</span>
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<pre style="margin: 0;">-<span id="LC348" class="line" lang="diff"> set alignedseqs = $unalignedseqs.aligned</span>
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<pre style="margin: 0;">-<span id="LC349" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- perl $bindir/perlscripts/separate_query_from_rest_of_seqs.pl $unalignedseqs.2 $unalignedseqs.queryseq $unalignedseqs.database</span></span>
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $NCBI/formatdb -i $unalignedseqs.database -o T -p T</span></span>
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<pre style="margin: 0;">-<span id="LC351" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $SIFT_SCRIPTDIR/separate_query_from_rest_of_seqs.pl $unalignedseqs.2 $unalignedseqs.queryseq $unalignedseqs.database</span></span>
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352
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<pre style="margin: 0;">-<span id="LC352" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ formatdb -i $unalignedseqs.database -o T -p T</span></span>
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<pre style="margin: 0;">-<span id="LC353" class="line" lang="diff"> # extremely large evalues and multipass threshold because want to make sure get</span>
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354
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<pre style="margin: 0;">-<span id="LC354" class="line" lang="diff"> #all the</span>
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<pre style="margin: 0;">-<span id="LC355" class="line" lang="diff"> # sequences the user submits</span>
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<pre style="margin: 0;">-<span id="LC356" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $NCBI/blastpgp -d $unalignedseqs.database -i $unalignedseqs.queryseq -o $unalignedseqs.psiblastout -m 0 -j 4 -e 10 -h 1 -b 399</span></span>
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357
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<pre style="margin: 0;">-<span id="LC357" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ blastpgp -d $unalignedseqs.database -i $unalignedseqs.queryseq -o $unalignedseqs.psiblastout -m 0 -j 4 -e 10 -h 1 -b 399</span></span>
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358
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<pre style="margin: 0;">-<span id="LC358" class="line" lang="diff"> echo QUERY > $unalignedseqs.listseq</span>
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359
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<pre style="margin: 0;">-<span id="LC359" class="line" lang="diff"> grep ">" $unalignedseqs.database | cut -d" " -f1 | cut -c2- >> $unalignedseqs.listseq</span>
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $bindir/seqs_from_psiblast_res $unalignedseqs.psiblastout $unalignedseqs.listseq 4 $unalignedseqs.queryseq $alignedseqs $$</span></span>
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<pre style="margin: 0;">-<span id="LC361" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ seqs_from_psiblast_res $unalignedseqs.psiblastout $unalignedseqs.listseq 4 $unalignedseqs.queryseq $alignedseqs $$</span></span>
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<pre style="margin: 0;">-<span id="LC362" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC363" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC364" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# final scoring </span></span>
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<pre style="margin: 0;">-<span id="LC365" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-$bindir/info_on_seqs $alignedseqs $polymorphism_file $outfile </span></span>
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<pre style="margin: 0;">-<span id="LC366" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# final scoring</span></span>
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<pre style="margin: 0;">-<span id="LC367" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+info_on_seqs $alignedseqs $polymorphism_file $outfile</span></span>
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<pre style="margin: 0;">-<span id="LC368" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+rm -rf $TMPDIR</span></span>
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<pre style="margin: 0;">-<span id="LC369" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+echo "Output in ($PWD/)$outfile"</span></span>
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<pre style="margin: 0;">-<span id="LC370" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC371" class="line" lang="diff"> exit</span>
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<pre style="margin: 0;">-<span id="LC372" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC373" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/Alignment.c</span></span>
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<pre style="margin: 0;">-<span id="LC374" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/Alignment.c</span></span>
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<pre style="margin: 0;">-<span id="LC375" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -17,7 +17,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gh" style="color: #999;">Index: sift/src/Alignment.c</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- sift.orig/src/Alignment.c</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ sift/src/Alignment.c</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -17,7 +17,7 @@ query sequence is moved to be the first</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="diff"> #define _ALIGNMENT_C_</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="diff"> #include "PN_convert.c"</span>
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378
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="381" 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="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -381,7 +50,7 @@</td>
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381
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="diff"> </span>
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382
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51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="diff"> #include "Alignment.h"</span>
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383
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52
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="diff"> </span>
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384
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<pre style="margin: 0;">-<span id="LC384" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -478,6 +478,7 @@</span></span>
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<td class="diff-line-num new old_line" data-linenumber="385" 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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<td class="diff-line-num new new_line" data-linenumber="53" 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">
53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -478,6 +478,7 @@<span class="idiff left right"> int flat_master_slave (FILE* fp, Sequenc</span></span></span>
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385
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54
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="diff"> fprintf(errorfp, "ERROR! Why haven't %s and %s been freed?\n", prev_name,</span>
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386
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55
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="diff"> prev_residues);</span>
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387
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56
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="diff"> fprintf (errorfp, "Current %s %s\n", name, residues);</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="389" 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="58" 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">@@ -389,7 +58,7 @@</td>
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389
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58
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="diff"> exit (-1);</span>
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390
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59
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="diff"> }</span>
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<td class="diff-line-num old_line" data-linenumber="391" 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">
391
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60
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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="LC60" class="line" lang="diff"> } /* end of if (line[0] != ' ') */ </span>
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<td class="diff-line-num old old_line" data-linenumber="392" 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">
392
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<td class="diff-line-num new_line old" data-linenumber="61" 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="LC392" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -752,7 +753,8 @@</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -752,7 +753,8 @@<span class="idiff left right"> read_psiblast_header_until_first (FILE*</span></span></span>
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393
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62
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="diff"> }</span>
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394
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63
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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="LC63" class="line" lang="diff"> if (feof (fp)) {</span>
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<td class="diff-line-num old_line" data-linenumber="395" 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">
395
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="diff"> fclose (fp);</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="399" 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="68" 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">@@ -399,7 +68,7 @@</td>
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399
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="diff"> exit (-1);</span>
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400
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69
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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="LC69" class="line" lang="diff"> }</span>
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<td class="diff-line-num old_line" data-linenumber="401" 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">
401
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="diff"> </span>
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<td class="diff-line-num old old_line" data-linenumber="402" 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">
402
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<pre style="margin: 0;">-<span id="LC402" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -792,7 +794,8 @@</span></span>
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<td class="diff-line-num new old_line" data-linenumber="403" 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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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -792,7 +794,8 @@<span class="idiff left right"> read_psiblast_header_until_first_no_erro</span></span></span>
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403
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="diff"> fclose (fp);</span>
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404
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="diff"> if (return_error) {</span>
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405
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="diff"> fprintf (errorfp, "ERROR! PSI-BLAST found no hits. Program terminating.\n");</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="78" 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">@@ -409,7 +78,7 @@</td>
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409
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="diff"> } else {</span>
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410
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="diff"> return (-1);</span>
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411
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="diff"> }</span>
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412
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<td class="diff-line-num new_line old" data-linenumber="81" 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="LC412" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -827,6 +830,7 @@</span></span>
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<td class="diff-line-num new old_line" data-linenumber="413" 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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<td class="diff-line-num new new_line" data-linenumber="81" 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">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -827,6 +830,7 @@<span class="idiff left right"> printf ("finished reading psiblast file\</span></span></span>
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413
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82
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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="LC82" class="line" lang="diff"> if (feof (fp)) {</span>
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<td class="diff-line-num old_line" data-linenumber="414" 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">
414
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<td class="diff-line-num new_line" data-linenumber="83" 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">
83
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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="LC83" class="line" lang="diff"> fclose (fp);</span>
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<td class="diff-line-num old_line" data-linenumber="415" 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">
415
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<td class="diff-line-num new_line" data-linenumber="84" 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">
84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="diff"> fprintf (errorfp, "ERROR! PSI-BLAST found no hits. Program terminating.\n");</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="417" 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="86" 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">@@ -417,7 +86,7 @@</td>
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417
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="diff"> exit (-1);</span>
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418
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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="diff"> }</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="419" 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">
419
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88
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="diff"> sscanf (line, "Results from round %d", &iteration);</span>
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420
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<pre style="margin: 0;">-<span id="LC420" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -12<span class="idiff left right">73,6 +1277,7 @@</span></span></span>
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<td class="diff-line-num new old_line" data-linenumber="421" 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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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -12<span class="idiff left right">13,6 +1217,7 @@ get_index_from_seqs (char name[], Sequen</span></span></span>
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421
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="diff"> }</span>
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422
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="diff"> }</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="423" 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">
423
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<td class="diff-line-num new_line" data-linenumber="92" 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">
92
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="diff"> fprintf (errorfp, "EXITING -- couldn't find %s in get_index_from_seqs\n", name);</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="425" 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="94" 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">@@ -425,7 +94,7 @@</td>
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425
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94
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="diff"> exit (-1);</span>
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426
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95
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="diff"> }</span>
</pre>
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427
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96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="diff"> </span>
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<td class="diff-line-num old old_line" data-linenumber="428" 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">
428
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<td class="diff-line-num new_line old" data-linenumber="97" 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="LC428" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1<span class="idiff left right">405,8 +1410,9 @@</span></span></span>
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<td class="diff-line-num new old_line" data-linenumber="429" 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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<td class="diff-line-num new new_line" data-linenumber="97" 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">
97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1<span class="idiff left right">352,8 +1357,9 @@ psiblast_pairwise (FILE* fp, Sequence *</span></span></span>
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429
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="diff"> sscanf (strptr, "Expect = %lf", &evalue);</span>
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430
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="diff"> } else { </span>
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431
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="diff"> fprintf (errorfp, "Unable to read e-value, parsing incorrect");</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="437" 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="106" 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">@@ -437,7 +106,7 @@</td>
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437
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="diff"> /* printf ("evalue is %lf\n", evalue); */ </span>
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438
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="diff"> /* end get evalue */</span>
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439
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="diff"> </span>
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440
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<td class="diff-line-num new_line old" data-linenumber="109" 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="LC440" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -14<span class="idiff left right">91,6 +1497,7 @@</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="109" 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">
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;">@@ -14<span class="idiff left right">39,6 +1445,7 @@ nonoverlapping (Sequence* seq1, Sequence</span></span></span>
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<td class="diff-line-num old_line" data-linenumber="441" 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">
441
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="diff"> assert (seq1->length == seq2->length);</span>
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442
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="diff"> if (strcmp (seq1->name, seq2->name ) != 0) {</span>
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443
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="diff"> fprintf (errorfp, "seeing whether %s and %s overlap, should be same name\n", seq1->name, seq2->name);</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="445" 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="114" 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">@@ -445,7 +114,7 @@</td>
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445
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="diff"> exit (-1);</span>
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446
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="diff"> }</span>
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447
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="diff"> for (i = 0; i < seq1->length; i++) {</span>
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448
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<pre style="margin: 0;">-<span id="LC448" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -15<span class="idiff left right">95,7 +1602,7 @@</span></span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -15<span class="idiff left right">43,7 +1550,7 @@ read_4lines_of_pairwise (FILE* fp, Seque</span></span></span>
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449
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="diff"> }</span>
</pre>
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450
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="451" 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">
451
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="diff"> if (strstr (line, "Query") == NULL) {</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="454" 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="123" 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">@@ -454,16 +123,7 @@</td>
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454
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123
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="diff"> exit (-1);</span>
</pre>
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455
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124
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="diff"> }</span>
</pre>
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456
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125
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="diff"> strptr = strtok (line, " \t\r\n"); /* this should be Query */</span>
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457
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<pre style="margin: 0;">-<span id="LC457" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1687,7 +1694,7 @@</span></span>
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458
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<pre style="margin: 0;">-<span id="LC458" class="line" lang="diff"> assert (fp != NULL);</span>
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<td class="diff-line-num old old_line" data-linenumber="459" 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">
459
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<pre style="margin: 0;">-<span id="LC459" class="line" lang="diff"> fgets (line, LARGE_BUFF_LENGTH, fp);</span>
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<pre style="margin: 0;">-<span id="LC460" class="line" lang="diff"> if (strstr (line, "Query") == NULL) {</span>
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<pre style="margin: 0;">-<span id="LC461" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- printf ("%s line should have Query:\n");</span></span>
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<pre style="margin: 0;">-<span id="LC462" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf (stderr,"%s line should have Query:\n");</span></span>
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<pre style="margin: 0;">-<span id="LC463" class="line" lang="diff"> exit (-1);</span>
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<pre style="margin: 0;">-<span id="LC464" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC465" class="line" lang="diff"> strptr = strtok (line, " \t\r\n"); /* this should be Query */</span>
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<pre style="margin: 0;">-<span id="LC466" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2107,10 +2114,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2052,10 +2059,10 @@ printf ("entered if statment\n");</span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="diff"> }</span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC129" 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">@@ -476,8 +136,10 @@</td>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="diff"> return no_of_clumps;</span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="diff"> } /* end of cluster */</span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC479" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/blocklist.c</span></span>
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<pre style="margin: 0;">-<span id="LC480" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/blocklist.c</span></span>
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"><span class="gh" style="color: #999;">Index: sift/src/blocklist.c</span></span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- sift.orig/src/blocklist.c</span></span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ sift/src/blocklist.c</span></span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -9,7 +9,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="diff"> #include <string.h></span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="diff"> #include "blocklist.h"</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="487" 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">@@ -487,8 +149,10 @@</td>
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="diff"> </span>
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="diff"> /*======================================================================</span>
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489
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="diff"> routines for a list of blocks</span>
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490
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<pre style="margin: 0;">-<span id="LC490" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/choose_seqs_via_psiblastseedmedian.c</span></span>
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<pre style="margin: 0;">-<span id="LC491" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/choose_seqs_via_psiblastseedmedian.c</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"><span class="gh" style="color: #999;">Index: sift/src/choose_seqs_via_psiblastseedmedian.c</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- sift.orig/src/choose_seqs_via_psiblastseedmedian.c</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ sift/src/choose_seqs_via_psiblastseedmedian.c</span></span>
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492
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156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,6 +1,6 @@</span></span>
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="diff"> /* (C) Copyright 2000, Fred Hutchinson Cancer Research Center */</span>
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494
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="diff"> /* Use, modification or distribution of these programs is subject to */</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="527" 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">@@ -527,7 +191,7 @@</td>
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="diff"> char pid[SMALL_BUFF_LENGTH],</span>
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528
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192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="diff"> double* median_threshold);</span>
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529
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC530" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -53,10 +53,10 @@</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -53,10 +53,10 @@<span class="idiff left right"> main (int argc, char* argv[])</span></span></span>
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531
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="diff"> FILE* outfp; FILE* temp_chk_fp;</span>
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532
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="diff"> FILE* seqfp;</span>
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533
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="diff"> int nseqs, db_type, seq_type;</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">@@ -540,156 +204,7 @@</td>
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540
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204
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="diff"> HashTable seqnamehash;</span>
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541
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="diff"> char seqname[KEY_WIDTH];</span>
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542
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206
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="diff"> char pid[SMALL_BUFF_LENGTH];</span>
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543
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<pre style="margin: 0;">-<span id="LC543" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -77,22 +77,22 @@</span></span>
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<pre style="margin: 0;">-<span id="LC544" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC545" class="line" lang="diff"> init_frq_qij(); /* matrix conversion in order to calculate R */</span>
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<pre style="margin: 0;">-<span id="LC546" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC547" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- getargs (argc, argv, query_seq_file, &seqfp, &outfp, </span></span>
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<pre style="margin: 0;">-<span id="LC548" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ getargs (argc, argv, query_seq_file, &seqfp, &outfp,</span></span>
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<pre style="margin: 0;">-<span id="LC549" class="line" lang="diff"> &clumping_threshold, pid, &median_threshold);</span>
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<pre style="margin: 0;">-<span id="LC550" class="line" lang="diff"> seqnamehash = InitializeTable (10);</span>
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<pre style="margin: 0;">-<span id="LC551" 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="LC552" 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="LC553" class="line" lang="diff"> i = 0;</span>
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<pre style="margin: 0;">-<span id="LC554" class="line" lang="diff"> /**************** READ IN SEQUENCES (to get info comments) ***************/</span>
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<pre style="margin: 0;">-<span id="LC555" class="line" lang="diff"> nseqs = 0;</span>
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<pre style="margin: 0;">-<span id="LC556" class="line" lang="diff"> db_type = type_dbs (seqfp, DbInfo); seq_type = AA_SEQ;</span>
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<pre style="margin: 0;">-<span id="LC557" class="line" lang="diff"> rewind (seqfp);</span>
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<pre style="margin: 0;">-<span id="LC558" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- while ( nseqs < MAXSEQ && </span></span>
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<pre style="margin: 0;">-<span id="LC559" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ while ( nseqs < MAXSEQ &&</span></span>
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<pre style="margin: 0;">-<span id="LC560" class="line" lang="diff"> (seqs[nseqs] = read_a_sequence(seqfp, db_type, seq_type)) != NULL) {</span>
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<pre style="margin: 0;">-<span id="LC561" class="line" lang="diff"> nseqs++;</span>
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<pre style="margin: 0;">-<span id="LC562" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC563" class="line" lang="diff"> fclose (seqfp);</span>
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<pre style="margin: 0;">-<span id="LC564" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC565" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-printf ("clumping teshodl is %.2f\n",clumping_threshold); </span></span>
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<pre style="margin: 0;">-<span id="LC566" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+fprintf( stderr, "clumping teshodl is %.2f\n",clumping_threshold);</span></span>
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<pre style="margin: 0;">-<span id="LC567" class="line" lang="diff"> /**************** GET SEED BLOCK BY PERCENTAGE IDENTITY ******************/</span>
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<pre style="margin: 0;">-<span id="LC568" class="line" lang="diff"> /* cluster_of_seqs = cluster_seqs (clumping_threshold, seqs, nseqs,</span>
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<pre style="margin: 0;">-<span id="LC569" class="line" lang="diff"> &num_clusters);</span>
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570
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<pre style="margin: 0;">-<span id="LC570" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -101,13 +101,13 @@</span></span>
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571
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<pre style="margin: 0;">-<span id="LC571" class="line" lang="diff"> */</span>
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572
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<pre style="margin: 0;">-<span id="LC572" class="line" lang="diff"> </span>
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573
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<pre style="margin: 0;">-<span id="LC573" class="line" lang="diff"> /*only copy query sequence (argumen 3 is 1 =>copy 1rst seq. only )*/</span>
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574
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<pre style="margin: 0;">-<span id="LC574" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- workingblock = make_block (seqs[0]->length, 0, 1, seqs, FALSE); </span></span>
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575
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<pre style="margin: 0;">-<span id="LC575" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ workingblock = make_block (seqs[0]->length, 0, 1, seqs, FALSE);</span></span>
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576
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<pre style="margin: 0;">-<span id="LC576" class="line" lang="diff"> assert (workingblock != NULL);</span>
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577
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<pre style="margin: 0;">-<span id="LC577" class="line" lang="diff"> for (i = 0; i < workingblock->num_sequences; i++) {</span>
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578
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<pre style="margin: 0;">-<span id="LC578" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- printf ("inserting %s in hash\n", workingblock->sequences[i].name);</span></span>
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579
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<pre style="margin: 0;">-<span id="LC579" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf( stderr, "inserting %s in hash\n", workingblock->sequences[i].name);</span></span>
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580
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<pre style="margin: 0;">-<span id="LC580" class="line" lang="diff"> Insert (workingblock->sequences[i].name, seqnamehash);</span>
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581
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<pre style="margin: 0;">-<span id="LC581" class="line" lang="diff"> }</span>
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582
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<pre style="margin: 0;">-<span id="LC582" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- median = calculate_median_information_of_block (workingblock, FALSE, TRUE); </span></span>
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583
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<pre style="margin: 0;">-<span id="LC583" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ median = calculate_median_information_of_block (workingblock, FALSE, TRUE);</span></span>
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584
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<pre style="margin: 0;">-<span id="LC584" class="line" lang="diff"> </span>
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585
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<pre style="margin: 0;">-<span id="LC585" class="line" lang="diff"> /* write the first sequence into a file that will be used as the query</span>
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586
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<pre style="margin: 0;">-<span id="LC586" class="line" lang="diff"> for the psiblast search */</span>
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587
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<pre style="margin: 0;">-<span id="LC587" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -116,20 +116,20 @@</span></span>
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588
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<pre style="margin: 0;">-<span id="LC588" class="line" lang="diff"> write_seq_to_file (query_filename, seqs[0]);</span>
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589
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<pre style="margin: 0;">-<span id="LC589" class="line" lang="diff"> </span>
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590
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<pre style="margin: 0;">-<span id="LC590" class="line" lang="diff"> assert (workingblock != NULL);</span>
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591
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<pre style="margin: 0;">-<span id="LC591" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-printf ("median is %.2f\n", median);</span></span>
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592
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<pre style="margin: 0;">-<span id="LC592" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+fprintf( stderr, "median is %.2f\n", median);</span></span>
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593
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<pre style="margin: 0;">-<span id="LC593" class="line" lang="diff"> /* printf ("finished extracting\n"); */</span>
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<pre style="margin: 0;">-<span id="LC594" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-/* fprintf (outfp, "*********SEED BLOCK********\n"); </span></span>
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<pre style="margin: 0;">-<span id="LC595" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+/* fprintf (outfp, "*********SEED BLOCK********\n");</span></span>
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<pre style="margin: 0;">-<span id="LC596" class="line" lang="diff"> fprintf (outfp, "median %.3f \n", median);</span>
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<pre style="margin: 0;">-<span id="LC597" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- output_block_s (workingblock, outfp, FLOAT_OUTPUT); </span></span>
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<pre style="margin: 0;">-<span id="LC598" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ output_block_s (workingblock, outfp, FLOAT_OUTPUT);</span></span>
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<pre style="margin: 0;">-<span id="LC599" class="line" lang="diff"> fflush (outfp); */</span>
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<pre style="margin: 0;">-<span id="LC600" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- done = FALSE; </span></span>
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<pre style="margin: 0;">-<span id="LC601" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ done = FALSE;</span></span>
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<pre style="margin: 0;">-<span id="LC602" class="line" lang="diff"> /**********ITERATIVE LOOP *************************************/</span>
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<pre style="margin: 0;">-<span id="LC603" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-while ( median > median_threshold && !done) { </span></span>
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<pre style="margin: 0;">-<span id="LC604" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+while ( median > median_threshold && !done) {</span></span>
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<pre style="margin: 0;">-<span id="LC605" class="line" lang="diff"> /* before add next sequence, copy this block, which</span>
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<pre style="margin: 0;">-<span id="LC606" class="line" lang="diff"> we know that passes criterion, to finalblock */</span>
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<pre style="margin: 0;">-<span id="LC607" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC608" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC609" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- /****PSIBLAST CALL do it only every PSIBLAST_TURN round */ </span></span>
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610
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<pre style="margin: 0;">-<span id="LC610" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ /****PSIBLAST CALL do it only every PSIBLAST_TURN round */</span></span>
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611
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<pre style="margin: 0;">-<span id="LC611" class="line" lang="diff"> strcpy (temp_chk_filename, pid);</span>
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<pre style="margin: 0;">-<span id="LC612" class="line" lang="diff"> strcat (temp_chk_filename, ".TEMP");</span>
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613
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<pre style="margin: 0;">-<span id="LC613" class="line" lang="diff"> strcpy (psiblastres_file, pid);</span>
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614
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<pre style="margin: 0;">-<span id="LC614" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -138,31 +138,31 @@</span></span>
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<pre style="margin: 0;">-<span id="LC615" class="line" lang="diff"> strcat (query_database_file, ".TEMP_DB");</span>
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616
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<pre style="margin: 0;">-<span id="LC616" class="line" lang="diff"> </span>
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617
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<pre style="margin: 0;">-<span id="LC617" class="line" lang="diff"> /*strcpy (temp_chk_filename,"tmpout3pid.TEMP"); */</span>
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618
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<pre style="margin: 0;">-<span id="LC618" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- nseqs_written = write_seqs_not_in_hash (query_database_file, </span></span>
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<pre style="margin: 0;">-<span id="LC619" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ nseqs_written = write_seqs_not_in_hash (query_database_file,</span></span>
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620
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<pre style="margin: 0;">-<span id="LC620" class="line" lang="diff"> seqs, nseqs,</span>
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621
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<pre style="margin: 0;">-<span id="LC621" class="line" lang="diff"> seqnamehash);</span>
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622
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<pre style="margin: 0;">-<span id="LC622" class="line" lang="diff"> if (nseqs_written == 0) {</span>
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623
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<pre style="margin: 0;">-<span id="LC623" class="line" lang="diff"> fprintf (stderr, "wrote 0 seqs to database\n");</span>
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<pre style="margin: 0;">-<span id="LC624" class="line" lang="diff"> done = TRUE;</span>
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625
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<pre style="margin: 0;">-<span id="LC625" class="line" lang="diff"> } else {</span>
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<pre style="margin: 0;">-<span id="LC626" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- formatdb_system_call (query_database_file) ; </span></span>
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627
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<pre style="margin: 0;">-<span id="LC627" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ formatdb_system_call (query_database_file) ;</span></span>
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<pre style="margin: 0;">-<span id="LC628" class="line" lang="diff"> if ((temp_chk_fp = fopen (temp_chk_filename, "w")) == NULL) {</span>
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<pre style="margin: 0;">-<span id="LC629" class="line" lang="diff"> fprintf (errorfp, "couldn't open checkpoint file %s when choosing sequences\n", temp_chk_filename);</span>
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<pre style="margin: 0;">-<span id="LC630" class="line" lang="diff"> exit (-1);</span>
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<pre style="margin: 0;">-<span id="LC631" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC632" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- block_to_checkpoint_file (workingblock, temp_chk_fp, logfp); </span></span>
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633
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<pre style="margin: 0;">-<span id="LC633" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fclose (temp_chk_fp); </span></span>
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<pre style="margin: 0;">-<span id="LC634" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- printf ("prior to psiblast system call");</span></span>
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635
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<pre style="margin: 0;">-<span id="LC635" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ block_to_checkpoint_file (workingblock, temp_chk_fp, logfp);</span></span>
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636
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<pre style="margin: 0;">-<span id="LC636" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fclose (temp_chk_fp);</span></span>
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<pre style="margin: 0;">-<span id="LC637" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf( stderr, "prior to psiblast system call");</span></span>
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638
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<pre style="margin: 0;">-<span id="LC638" class="line" lang="diff"> psiblast_system_call (temp_chk_filename, query_database_file,</span>
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<pre style="margin: 0;">-<span id="LC639" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- psiblastres_file, query_filename, logfp); </span></span>
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<pre style="margin: 0;">-<span id="LC640" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- printf ("finished psiblast system call");</span></span>
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<pre style="margin: 0;">-<span id="LC641" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ psiblastres_file, query_filename, logfp);</span></span>
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<pre style="margin: 0;">-<span id="LC642" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf( stderr, "finished psiblast system call");</span></span>
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<pre style="margin: 0;">-<span id="LC643" class="line" lang="diff"> } /* end of if seqs written to database file */</span>
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<pre style="margin: 0;">-<span id="LC644" class="line" lang="diff"> /****END OF PSIBLAST CALL ****/</span>
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<pre style="margin: 0;">-<span id="LC645" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC646" class="line" lang="diff"> /* GET TOP PSIBLAST_TURN HITS ******/</span>
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<pre style="margin: 0;">-<span id="LC647" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for (k = 0; k < PSIBLAST_TURN && !done; k++) { </span></span>
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<pre style="margin: 0;">-<span id="LC648" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- get_top_seq (seqname, seqnamehash, psiblastres_file); </span></span>
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<pre style="margin: 0;">-<span id="LC649" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- printf ( "top sequence is %s\n", seqname); </span></span>
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<pre style="margin: 0;">-<span id="LC650" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for (k = 0; k < PSIBLAST_TURN && !done; k++) {</span></span>
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<pre style="margin: 0;">-<span id="LC651" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ get_top_seq (seqname, seqnamehash, psiblastres_file);</span></span>
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<pre style="margin: 0;">-<span id="LC652" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf( stderr, "top sequence is %s\n", seqname);</span></span>
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<pre style="margin: 0;">-<span id="LC653" class="line" lang="diff"> if (seqname[0] != '\0' && seqname[0] != ' ') {</span>
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<pre style="margin: 0;">-<span id="LC654" class="line" lang="diff"> /**** ADD TOP SEQ to BLOCK *******************/</span>
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<pre style="margin: 0;">-<span id="LC655" class="line" lang="diff"> index = get_index_from_seqs (seqname, seqs, nseqs);</span>
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<pre style="margin: 0;">-<span id="LC656" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -170,28 +170,28 @@</span></span>
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<pre style="margin: 0;">-<span id="LC657" class="line" lang="diff"> /* block not weighted */</span>
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<pre style="margin: 0;">-<span id="LC658" class="line" lang="diff"> add_sequence_to_block (workingblock,seqs[index], FALSE);</span>
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<pre style="margin: 0;">-<span id="LC659" class="line" lang="diff"> if (workingblock->num_sequences == nseqs) {</span>
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<pre style="margin: 0;">-<span id="LC660" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- /* added all the possible sequences to the block </span></span>
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<pre style="margin: 0;">-<span id="LC661" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ /* added all the possible sequences to the block</span></span>
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<pre style="margin: 0;">-<span id="LC662" class="line" lang="diff"> have chosen all of the sequences, done*/</span>
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<pre style="margin: 0;">-<span id="LC663" class="line" lang="diff"> done = TRUE;</span>
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<pre style="margin: 0;">-<span id="LC664" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC665" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Insert (seqname, seqnamehash); /* update hash */ </span></span>
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<pre style="margin: 0;">-<span id="LC666" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Insert (seqname, seqnamehash); /* update hash */</span></span>
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<pre style="margin: 0;">-<span id="LC667" class="line" lang="diff"> } else {</span>
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<pre style="margin: 0;">-<span id="LC668" class="line" lang="diff"> fprintf (stderr, "done\n");</span>
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<pre style="margin: 0;">-<span id="LC669" class="line" lang="diff"> done = TRUE;</span>
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<pre style="margin: 0;">-<span id="LC670" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC671" class="line" lang="diff"> } /* done adding PSIBLAST_TURN sequences ***/</span>
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<pre style="margin: 0;">-<span id="LC672" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC673" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- median = calculate_median_information_of_block (workingblock, </span></span>
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<pre style="margin: 0;">-<span id="LC674" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- FALSE, FALSE); </span></span>
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<pre style="margin: 0;">-<span id="LC675" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ median = calculate_median_information_of_block (workingblock,</span></span>
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<pre style="margin: 0;">-<span id="LC676" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ FALSE, FALSE);</span></span>
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<pre style="margin: 0;">-<span id="LC677" class="line" lang="diff"> fprintf (logfp, "added %s %s median:%.3f median %d seq total\n",</span>
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<pre style="margin: 0;">-<span id="LC678" class="line" lang="diff"> workingblock->sequences[workingblock->num_sequences-1].name,</span>
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<pre style="margin: 0;">-<span id="LC679" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- seqs[index]->info, median, workingblock->num_sequences); </span></span>
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<pre style="margin: 0;">-<span id="LC680" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ seqs[index]->info, median, workingblock->num_sequences);</span></span>
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681
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<pre style="margin: 0;">-<span id="LC681" class="line" lang="diff"> fflush (logfp); fflush (stderr);</span>
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<pre style="margin: 0;">-<span id="LC682" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fflush (errorfp); fflush (outfp); </span></span>
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<pre style="margin: 0;">-<span id="LC683" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fflush (errorfp); fflush (outfp);</span></span>
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<pre style="margin: 0;">-<span id="LC684" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC685" class="line" lang="diff"> /* prepare to run psiblast on next iteration */</span>
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<pre style="margin: 0;">-<span id="LC686" class="line" lang="diff"> fprintf (stderr, "rm search files\n");</span>
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<pre style="margin: 0;">-<span id="LC687" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- rm_file (temp_chk_filename); </span></span>
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<pre style="margin: 0;">-<span id="LC688" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ rm_file (temp_chk_filename);</span></span>
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<pre style="margin: 0;">-<span id="LC689" class="line" lang="diff"> rm_file (psiblastres_file);</span>
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<pre style="margin: 0;">-<span id="LC690" class="line" lang="diff"> strcat (query_database_file, ".*");</span>
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<pre style="margin: 0;">-<span id="LC691" class="line" lang="diff"> rm_file (query_database_file);</span>
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<pre style="margin: 0;">-<span id="LC692" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -208,15 +208,15 @@</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -226,15 +226,15 @@ error file */</span></span>
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693
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208
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="diff"> /* print_block_ids (workingblock, outfp, TRUE); */</span>
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694
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209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="diff"> /* should free memeory, clean up later */</span>
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695
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210
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="diff"> /* fclose (outfp); fclose (errorfp); fclose (logfp);</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="708" 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="223" 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">@@ -708,7 +223,7 @@</td>
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708
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223
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="diff"> FALSE, FALSE);</span>
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709
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224
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="diff"> num_seqs_removed++;</span>
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710
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225
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="diff"> }</span>
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711
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<pre style="margin: 0;">-<span id="LC711" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2<span class="idiff left right">25,30 +225,30 @@</span></span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2<span class="idiff left right">43,30 +243,30 @@ error file */</span></span></span>
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712
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227
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="diff"> </span>
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713
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228
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="diff"> fprintf (logfp, "********FINAL BLOCK ****** ");</span>
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714
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229
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="diff"> fprintf (logfp, "last block : median %.3f with %d sequences\n", median,</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="748" 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="263" 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">@@ -748,7 +263,7 @@</td>
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748
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263
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="diff"> Sequence* seqs[MAXSEQ], int nseqs,</span>
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749
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264
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="diff"> HashTable hash)</span>
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750
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265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="diff"> {</span>
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751
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<pre style="margin: 0;">-<span id="LC751" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2<span class="idiff left right">59,7 +259,7 @@</span></span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2<span class="idiff left right">77,7 +277,7 @@ write_seqs_not_in_hash (char query_datab</span></span></span>
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752
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267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="diff"> </span>
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753
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268
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="diff"> nseqs_written = 0;</span>
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754
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269
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="diff"> if ( (outfp = fopen (query_database_file, "w")) == NULL) {</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="757" 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="272" 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">@@ -757,7 +272,7 @@</td>
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757
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272
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="diff"> query_database_file);</span>
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758
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273
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="diff"> exit (-1);</span>
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759
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274
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC760" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2<span class="idiff left right">73,15 +273,15 @@</span></span></span>
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2<span class="idiff left right">91,15 +291,15 @@ write_seqs_not_in_hash (char query_datab</span></span></span>
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276
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="diff"> </span>
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277
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="diff"> fclose (outfp);</span>
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="diff"> return nseqs_written;</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">@@ -779,38 +294,7 @@</td>
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="diff"> char pid[SMALL_BUFF_LENGTH],</span>
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780
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295
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="diff"> double* median_threshold)</span>
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296
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">-<span id="LC782" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -297,7 +297,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC783" class="line" lang="diff"> if (argc > 1) strcpy (query_seq_file, argv[1]);</span>
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784
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<pre style="margin: 0;">-<span id="LC784" class="line" lang="diff"> else {</span>
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<pre style="margin: 0;">-<span id="LC785" class="line" lang="diff"> printf ("Enter query sequence file\n");</span>
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<pre style="margin: 0;">-<span id="LC786" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- gets (query_seq_file);</span></span>
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<pre style="margin: 0;">-<span id="LC787" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fgets(query_seq_file, LARGE_BUFF_LENGTH, stdin );</span></span>
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788
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<pre style="margin: 0;">-<span id="LC788" class="line" lang="diff"> }</span>
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789
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<pre style="margin: 0;">-<span id="LC789" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC790" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC791" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -306,7 +306,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC792" class="line" lang="diff"> else</span>
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<pre style="margin: 0;">-<span id="LC793" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">-<span id="LC794" class="line" lang="diff"> printf ("Enter sequence file \n");</span>
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<pre style="margin: 0;">-<span id="LC795" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- gets (seqfile);</span></span>
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<pre style="margin: 0;">-<span id="LC796" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fgets(seqfile, LARGE_BUFF_LENGTH, stdin);</span></span>
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<pre style="margin: 0;">-<span id="LC797" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC798" class="line" lang="diff"> if ( (*seqfp = fopen (seqfile, "r")) == NULL )</span>
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799
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<td class="diff-line-num new_line old" data-linenumber="297" 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="LC799" class="line" lang="diff"> {</span>
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800
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<pre style="margin: 0;">-<span id="LC800" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -315,10 +315,10 @@</span></span>
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801
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<pre style="margin: 0;">-<span id="LC801" class="line" lang="diff"> }</span>
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802
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<pre style="margin: 0;">-<span id="LC802" class="line" lang="diff"> </span>
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803
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<pre style="margin: 0;">-<span id="LC803" class="line" lang="diff"> if ( argc > 3) strcpy (outfile, argv[3]);</span>
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804
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<td class="diff-line-num new_line old" data-linenumber="297" 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="LC804" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- else </span></span>
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805
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<td class="diff-line-num new_line old" data-linenumber="297" 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="LC805" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else</span></span>
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<td class="diff-line-num old old_line" data-linenumber="806" 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">
806
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<td class="diff-line-num new_line old" data-linenumber="297" 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="LC806" class="line" lang="diff"> {</span>
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807
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<pre style="margin: 0;">-<span id="LC807" class="line" lang="diff"> printf ("Enter outfile \n");</span>
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<td class="diff-line-num old old_line" data-linenumber="808" 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">
808
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<td class="diff-line-num new_line old" data-linenumber="297" 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="LC808" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- gets (outfile);</span></span>
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809
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<pre style="margin: 0;">-<span id="LC809" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fgets( outfile, LARGE_BUFF_LENGTH, stdin );</span></span>
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<td class="diff-line-num old old_line" data-linenumber="810" 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">
810
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<pre style="margin: 0;">-<span id="LC810" class="line" lang="diff"> }</span>
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811
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<pre style="margin: 0;">-<span id="LC811" class="line" lang="diff"> </span>
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812
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<pre style="margin: 0;">-<span id="LC812" class="line" lang="diff"> strcpy (errorfilename, outfile);</span>
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<td class="diff-line-num old old_line" data-linenumber="813" 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">
813
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<pre style="margin: 0;">-<span id="LC813" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -341,7 +341,7 @@</span></span>
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<td class="diff-line-num new old_line" data-linenumber="814" 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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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -359,7 +359,7 @@ getargs (int argc, char* argv[],</span></span>
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<td class="diff-line-num old_line" data-linenumber="814" 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">
814
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298
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="diff"> }</span>
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<td class="diff-line-num old_line" data-linenumber="815" 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">
815
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<td class="diff-line-num new_line" data-linenumber="299" 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">
299
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="diff"> </span>
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<td class="diff-line-num old_line" data-linenumber="816" 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">
816
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<td class="diff-line-num new_line" data-linenumber="300" 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">
300
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="diff"> if (argc > 4) *clumping_threshold = atof (argv[4]);</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="819" 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="303" 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">@@ -819,21 +303,7 @@</td>
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<td class="diff-line-num old_line" data-linenumber="819" 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">
819
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<td class="diff-line-num new_line" data-linenumber="303" 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">
303
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="diff"> {</span>
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<td class="diff-line-num old_line" data-linenumber="820" 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">
820
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<td class="diff-line-num new_line" data-linenumber="304" 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">
304
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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="LC304" class="line" lang="diff"> printf ("Enter clumping threshold\n");</span>
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<td class="diff-line-num old_line" data-linenumber="821" 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">
821
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<td class="diff-line-num new_line" data-linenumber="305" 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">
305
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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="LC305" class="line" lang="diff"> scanf ("%lf\n", clumping_threshold);</span>
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<td class="diff-line-num old old_line" data-linenumber="822" 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">
822
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<td class="diff-line-num new_line old" data-linenumber="306" 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="LC822" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -351,10 +351,10 @@</span></span>
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<td class="diff-line-num old old_line" data-linenumber="823" 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">
823
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<pre style="margin: 0;">-<span id="LC823" class="line" lang="diff"> if (argc > 5) strcpy (pid, argv[5]);</span>
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<pre style="margin: 0;">-<span id="LC824" class="line" lang="diff"> else {</span>
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825
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<pre style="margin: 0;">-<span id="LC825" class="line" lang="diff"> printf ("Enter process identification number\n");</span>
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826
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<pre style="margin: 0;">-<span id="LC826" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- gets (pid);</span></span>
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827
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<pre style="margin: 0;">-<span id="LC827" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- printf ("gets %s\n", pid);</span></span>
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828
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<pre style="margin: 0;">-<span id="LC828" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fgets( pid, SMALL_BUFF_LENGTH, stdin );</span></span>
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829
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<pre style="margin: 0;">-<span id="LC829" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ printf ("fgets %s\n", pid);</span></span>
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830
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<pre style="margin: 0;">-<span id="LC830" class="line" lang="diff"> }</span>
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831
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<pre style="margin: 0;">-<span id="LC831" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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832
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<pre style="margin: 0;">-<span id="LC832" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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833
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<pre style="margin: 0;">-<span id="LC833" class="line" lang="diff"> if (argc > 6) *median_threshold = atof (argv[6]);</span>
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834
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<pre style="margin: 0;">-<span id="LC834" class="line" lang="diff"> else {</span>
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835
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<pre style="margin: 0;">-<span id="LC835" class="line" lang="diff"> printf ("Enter median threshold\n");</span>
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836
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<pre style="margin: 0;">-<span id="LC836" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -363,10 +363,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -381,10 +381,10 @@ getargs (int argc, char* argv[],</span></span>
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837
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307
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="diff"> }</span>
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838
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308
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="diff"> </span>
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839
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309
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="846" 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="316" 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">@@ -846,9 +316,11 @@</td>
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846
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316
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="diff"> {</span>
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847
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317
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="diff"> FILE* fp;</span>
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848
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318
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="diff"> </span>
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849
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<pre style="margin: 0;">-<span id="LC849" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/clump_output_alignedseq.c</span></span>
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850
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<pre style="margin: 0;">-<span id="LC850" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/clump_output_alignedseq.c</span></span>
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851
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<pre style="margin: 0;">-<span id="LC851" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -25,7 +25,7 @@</span></span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="diff"><span class="gh" style="color: #999;">Index: sift/src/clump_output_alignedseq.c</span></span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- sift.orig/src/clump_output_alignedseq.c</span></span>
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<td class="diff-line-num new new_line" data-linenumber="322" 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">
322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ sift/src/clump_output_alignedseq.c</span></span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -25,7 +25,7 @@ option 1 -- print out sequences that hav</span></span>
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852
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324
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="diff"> #include "Clumping.c"</span>
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853
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325
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="diff"> </span>
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854
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326
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="diff"> #define MINSEQ 2 </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="857" 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="329" 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">@@ -857,55 +329,10 @@</td>
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857
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329
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="diff"> #define INDEX(n, col, row) (col*n - (col*(col+3))/2 - 1 + row)</span>
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858
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330
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="diff"> #define MIN_CLUSTERS 3</span>
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859
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331
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="diff"> </span>
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860
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<pre style="margin: 0;">-<span id="LC860" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -144,7 +144,7 @@</span></span>
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861
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<pre style="margin: 0;">-<span id="LC861" class="line" lang="diff"> else</span>
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862
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<pre style="margin: 0;">-<span id="LC862" class="line" lang="diff"> {</span>
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863
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<pre style="margin: 0;">-<span id="LC863" class="line" lang="diff"> printf ("Enter filename with sequences:\n");</span>
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864
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<pre style="margin: 0;">-<span id="LC864" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- gets (seqfilename);</span></span>
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865
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<pre style="margin: 0;">-<span id="LC865" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fgets( seqfilename, LARGE_BUFF_LENGTH, stdin );</span></span>
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866
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<pre style="margin: 0;">-<span id="LC866" class="line" lang="diff"> }</span>
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867
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<pre style="margin: 0;">-<span id="LC867" class="line" lang="diff"> if ((*seqfp = fopen (seqfilename, "r")) == NULL)</span>
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868
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<pre style="margin: 0;">-<span id="LC868" class="line" lang="diff"> {</span>
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869
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<pre style="margin: 0;">-<span id="LC869" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -156,7 +156,7 @@</span></span>
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870
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<pre style="margin: 0;">-<span id="LC870" class="line" lang="diff"> else</span>
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871
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<pre style="margin: 0;">-<span id="LC871" class="line" lang="diff"> {</span>
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872
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<pre style="margin: 0;">-<span id="LC872" class="line" lang="diff"> printf ("Enter name of outfile\n");</span>
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873
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<pre style="margin: 0;">-<span id="LC873" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- gets (outfilename);</span></span>
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874
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<pre style="margin: 0;">-<span id="LC874" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fgets( outfilename, LARGE_BUFF_LENGTH, stdin );</span></span>
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<pre style="margin: 0;">-<span id="LC875" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC876" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC877" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC878" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/consensus_to_seq.c</span></span>
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<pre style="margin: 0;">-<span id="LC879" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/consensus_to_seq.c</span></span>
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880
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<pre style="margin: 0;">-<span id="LC880" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -120,7 +120,7 @@</span></span>
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881
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<pre style="margin: 0;">-<span id="LC881" class="line" lang="diff"> else </span>
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882
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<pre style="margin: 0;">-<span id="LC882" class="line" lang="diff"> {</span>
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883
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<pre style="margin: 0;">-<span id="LC883" class="line" lang="diff"> printf ("Enter filename with sequences:\n");</span>
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884
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<pre style="margin: 0;">-<span id="LC884" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- gets (seqfilename);</span></span>
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<pre style="margin: 0;">-<span id="LC885" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fgets( seqfilename, LINE_LEN, stdin );</span></span>
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<pre style="margin: 0;">-<span id="LC886" class="line" lang="diff"> }</span>
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887
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<pre style="margin: 0;">-<span id="LC887" class="line" lang="diff"> </span>
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888
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<pre style="margin: 0;">-<span id="LC888" class="line" lang="diff"> if ((*seqfp = fopen (seqfilename, "r")) == NULL)</span>
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889
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<pre style="margin: 0;">-<span id="LC889" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -133,7 +133,7 @@</span></span>
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890
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<pre style="margin: 0;">-<span id="LC890" class="line" lang="diff"> else</span>
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891
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<pre style="margin: 0;">-<span id="LC891" class="line" lang="diff"> {</span>
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892
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<pre style="margin: 0;">-<span id="LC892" class="line" lang="diff"> printf ("Enter file with keys and elements\n");</span>
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893
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<pre style="margin: 0;">-<span id="LC893" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- gets (keyfilename);</span></span>
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894
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<pre style="margin: 0;">-<span id="LC894" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fgets( keyfilename, LINE_LEN, stdin );</span></span>
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895
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<pre style="margin: 0;">-<span id="LC895" class="line" lang="diff"> }</span>
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896
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<pre style="margin: 0;">-<span id="LC896" class="line" lang="diff"> if ((*keyfp = fopen (keyfilename, "r")) == NULL) </span>
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897
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<pre style="margin: 0;">-<span id="LC897" class="line" lang="diff"> {</span>
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898
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<pre style="margin: 0;">-<span id="LC898" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -144,7 +144,7 @@</span></span>
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899
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<pre style="margin: 0;">-<span id="LC899" class="line" lang="diff"> else</span>
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<pre style="margin: 0;">-<span id="LC900" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">-<span id="LC901" class="line" lang="diff"> printf ("Enter name of outfile\n");</span>
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902
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<pre style="margin: 0;">-<span id="LC902" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- gets (outfilename);</span></span>
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<pre style="margin: 0;">-<span id="LC903" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fgets( outfilename, LINE_LEN, stdin );</span></span>
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<pre style="margin: 0;">-<span id="LC904" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC905" class="line" lang="diff"> if ( (*outfp = fopen (outfilename, "w")) == NULL)</span>
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906
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<pre style="margin: 0;">-<span id="LC906" class="line" lang="diff"> {</span>
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907
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<pre style="margin: 0;">-<span id="LC907" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/info_on_seqs.c</span></span>
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<pre style="margin: 0;">-<span id="LC908" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/info_on_seqs.c</span></span>
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="diff"><span class="gh" style="color: #999;">Index: sift/src/info_on_seqs.c</span></span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- sift.orig/src/info_on_seqs.c</span></span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ sift/src/info_on_seqs.c</span></span>
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -11,7 +11,7 @@</span></span>
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337
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="diff"> #include "Psiblast.c"</span>
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911
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338
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<pre style="margin: 0;"> <span id="LC338" class="line" lang="diff"> /* #include "Information.c */</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">@@ -915,7 +342,7 @@</td>
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915
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342
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="diff"> #define LINE_LEN 800</span>
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343
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="diff"> #define FALSE 0</span>
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344
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="diff"> #define TRUE 1</span>
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918
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<pre style="margin: 0;">-<span id="LC918" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">198,10 +198,10 @@</span></span></span>
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345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">200,10 +200,10 @@ output_predictions (AAnode* polymorph_da</span></span></span>
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919
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346
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="diff"> int substitution, original_aa;</span>
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347
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="diff"> int substitution_exists;</span>
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921
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348
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="diff"> int pos;</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">@@ -929,7 +356,7 @@</td>
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929
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356
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="diff"> int block_constructed;</span>
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930
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357
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<pre style="margin: 0;"> <span id="LC357" class="line" lang="diff"> </span>
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931
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358
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<pre style="margin: 0;"> <span id="LC358" class="line" lang="diff"> substitution_exists = FALSE;</span>
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932
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<pre style="margin: 0;">-<span id="LC932" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -33<span class="idiff left right">7,7 +337,7 @@</span></span></span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -33<span class="idiff left right">9,7 +339,7 @@ comments_on_info(Block* oldblock, int po</span></span></span>
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933
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360
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="diff"> fprintf (outfp, "%d\n", residues_stored[pos]);</span>
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934
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361
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<pre style="margin: 0;"> <span id="LC361" class="line" lang="diff"> */</span>
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935
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362
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<pre style="margin: 0;"> <span id="LC362" class="line" lang="diff"> /* the array will be sorted in call for median_of_array*/</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="938" 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="365" 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">@@ -938,7 +365,7 @@</td>
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938
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365
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="diff"> median = median_of_array (info_array, prot_length);</span>
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939
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366
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<pre style="margin: 0;"> <span id="LC366" class="line" lang="diff"> printf ("found mediant %.2f\n", median);</span>
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940
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367
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<pre style="margin: 0;"> <span id="LC367" class="line" lang="diff"> fprintf (outfp, "%.3f\t%d\t%d\n",</span>
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941
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<pre style="margin: 0;">-<span id="LC941" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -35<span class="idiff left right">2,7 +352,7 @@</span></span></span>
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -35<span class="idiff left right">4,7 +354,7 @@ printf ("looking for median\n");</span></span></span>
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942
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369
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="diff"> assert (oldblock->sequences[0].sequence != NULL);</span>
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943
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370
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="diff"> assert (oldblock->sequences != NULL);</span>
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944
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371
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<pre style="margin: 0;"> <span id="LC371" class="line" lang="diff"> assert (oldblock != NULL);</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">@@ -947,52 +374,10 @@</td>
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947
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374
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<pre style="margin: 0;"> <span id="LC374" class="line" lang="diff"> }</span>
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948
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375
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="diff"> </span>
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949
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376
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="diff"> double</span>
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950
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<pre style="margin: 0;">-<span id="LC950" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -524,23 +524,23 @@</span></span>
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951
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<pre style="margin: 0;">-<span id="LC951" class="line" lang="diff"> else</span>
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952
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<pre style="margin: 0;">-<span id="LC952" class="line" lang="diff"> {</span>
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953
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<pre style="margin: 0;">-<span id="LC953" class="line" lang="diff"> printf ("Enter filename with sequences:\n");</span>
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954
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<td class="diff-line-num new_line old" data-linenumber="377" 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="LC954" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- gets (seqfilename);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="955" 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">
955
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<td class="diff-line-num new_line old" data-linenumber="377" 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="LC955" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fgets( seqfilename, LINE_LEN, stdin );</span></span>
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956
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<td class="diff-line-num new_line old" data-linenumber="377" 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="LC956" class="line" lang="diff"> }</span>
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<td class="diff-line-num old old_line" data-linenumber="957" 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">
957
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<td class="diff-line-num new_line old" data-linenumber="377" 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="LC957" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-printf ("fawegwa\n");</span></span>
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<td class="diff-line-num old old_line" data-linenumber="958" 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">
958
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<td class="diff-line-num new_line old" data-linenumber="377" 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="LC958" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+fprintf( stderr, "%s:%d\n", __FILE__, __LINE__ );</span></span>
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<td class="diff-line-num old old_line" data-linenumber="959" 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">
959
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<td class="diff-line-num new_line old" data-linenumber="377" 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="LC959" class="line" lang="diff"> if ((*seqfp = fopen (seqfilename, "r")) == NULL)</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="960" 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">
960
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<td class="diff-line-num new_line old" data-linenumber="377" 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="LC960" class="line" lang="diff"> {</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="961" 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">
961
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<td class="diff-line-num new_line old" data-linenumber="377" 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="LC961" class="line" lang="diff"> printf ("cannot open file %s \n", seqfilename);</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="962" 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">
962
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<td class="diff-line-num new_line old" data-linenumber="377" 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="LC962" class="line" lang="diff"> exit (-1);</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="963" 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">
963
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<td class="diff-line-num new_line old" data-linenumber="377" 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="LC963" class="line" lang="diff"> }</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="964" 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">
964
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<td class="diff-line-num new_line old" data-linenumber="377" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC964" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-printf ("eaegrtjkl\n");</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="965" 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">
965
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<td class="diff-line-num new_line old" data-linenumber="377" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC965" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+fprintf( stderr, "%s:%d\n", __FILE__, __LINE__ );</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="966" 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">
966
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<td class="diff-line-num new_line old" data-linenumber="377" 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="LC966" class="line" lang="diff"> if (argc > 2) strcpy (substfilename, argv[2]);</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="967" 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">
967
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<td class="diff-line-num new_line old" data-linenumber="377" 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="LC967" class="line" lang="diff"> else {</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="968" 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">
968
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<td class="diff-line-num new_line old" data-linenumber="377" 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="LC968" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- printf ("Enter file with substitutions.\n");</span></span>
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<td class="diff-line-num old old_line" data-linenumber="969" 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">
969
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<td class="diff-line-num new_line old" data-linenumber="377" 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">
</td>
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<pre style="margin: 0;">-<span id="LC969" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- printf ("format:\n");</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="970" 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">
970
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<td class="diff-line-num new_line old" data-linenumber="377" 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">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC970" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- printf ("M1Y\n");</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="971" 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">
971
</td>
<td class="diff-line-num new_line old" data-linenumber="377" 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">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC971" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- printf ("S2K\n");</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="972" 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">
972
</td>
<td class="diff-line-num new_line old" data-linenumber="377" 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">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC972" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- printf ("...\n\n");</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="973" 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">
973
</td>
<td class="diff-line-num new_line old" data-linenumber="377" 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">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC973" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- gets (substfilename);</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="974" 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">
974
</td>
<td class="diff-line-num new_line old" data-linenumber="377" 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">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC974" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf( stderr, "Enter file with substitutions.\n");</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="975" 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">
975
</td>
<td class="diff-line-num new_line old" data-linenumber="377" 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">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC975" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf( stderr, "format:\n");</span></span>
</pre>
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</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="976" 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">
976
</td>
<td class="diff-line-num new_line old" data-linenumber="377" 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">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC976" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf( stderr, "M1Y\n");</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="977" 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">
977
</td>
<td class="diff-line-num new_line old" data-linenumber="377" 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">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC977" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf( stderr, "S2K\n");</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="978" 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">
978
</td>
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<pre style="margin: 0;">-<span id="LC978" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf( stderr, "...\n\n");</span></span>
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979
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<pre style="margin: 0;">-<span id="LC979" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fgets( substfilename, LARGE_BUFF_LENGTH, stdin );</span></span>
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980
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<pre style="margin: 0;">-<span id="LC980" class="line" lang="diff"> }</span>
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981
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<pre style="margin: 0;">-<span id="LC981" class="line" lang="diff"> if (substfilename[0] == '-') { *polymorphfp = NULL; }</span>
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982
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<pre style="margin: 0;">-<span id="LC982" class="line" lang="diff"> else if ((*polymorphfp = fopen (substfilename, "r")) == NULL)</span>
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<td class="diff-line-num old old_line" data-linenumber="983" 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">
983
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<pre style="margin: 0;">-<span id="LC983" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -553,8 +553,8 @@</span></span>
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984
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<pre style="margin: 0;">-<span id="LC984" class="line" lang="diff"> if (argc > 3) strcpy (outfilename, argv[3]);</span>
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985
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<pre style="margin: 0;">-<span id="LC985" class="line" lang="diff"> else </span>
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986
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<pre style="margin: 0;">-<span id="LC986" class="line" lang="diff"> {</span>
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987
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<pre style="margin: 0;">-<span id="LC987" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- printf ("Enter name of outfile\n");</span></span>
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988
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<pre style="margin: 0;">-<span id="LC988" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- gets (outfilename);</span></span>
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989
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<pre style="margin: 0;">-<span id="LC989" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf( stderr, "Enter name of outfile\n");</span></span>
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990
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<pre style="margin: 0;">-<span id="LC990" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fgets( outfilename, LARGE_BUFF_LENGTH, stdin );</span></span>
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991
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<pre style="margin: 0;">-<span id="LC991" class="line" lang="diff"> }</span>
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992
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<pre style="margin: 0;">-<span id="LC992" class="line" lang="diff"> </span>
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993
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<pre style="margin: 0;">-<span id="LC993" class="line" lang="diff"> strcpy (errorfilename, outfilename);</span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="diff"><span class="gh" style="color: #999;">Index: sift/src/Makefile</span></span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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994
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379
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- /dev/null</span></span>
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995
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<pre style="margin: 0;">-<span id="LC995" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b</span>/src/Makefile</span></span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">sift</span>/src/Makefile</span></span>
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996
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381
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -0,0 +1,45 @@</span></span>
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997
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382
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<pre style="margin: 0;"> <span id="LC382" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+include-prefix := $(prefix)</span></span>
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998
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383
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+lib-prefix := $(prefix)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1039" 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="424" 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">@@ -1039,9 +424,11 @@</td>
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1039
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424
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<pre style="margin: 0;"> <span id="LC424" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+include deps.mk</span></span>
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1040
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425
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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1041
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426
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# vim:ai:</span></span>
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1042
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<pre style="margin: 0;">-<span id="LC1042" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/Matrix_Info.c</span></span>
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1043
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<pre style="margin: 0;">-<span id="LC1043" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/Matrix_Info.c</span></span>
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1044
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<pre style="margin: 0;">-<span id="LC1044" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -384,7 +384,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="diff"><span class="gh" style="color: #999;">Index: sift/src/Matrix_Info.c</span></span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- sift.orig/src/Matrix_Info.c</span></span>
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430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ sift/src/Matrix_Info.c</span></span>
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -384,7 +384,7 @@ void output_Matrix_Info (Matrix_Info* in</span></span>
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1045
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432
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="diff"> int pos_observed_tolerant, pos_error_tn, pos_notobserved_intolerant,</span>
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1046
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433
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<pre style="margin: 0;"> <span id="LC433" class="line" lang="diff"> pos_error_fp, pos_total;</span>
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1047
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434
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<pre style="margin: 0;"> <span id="LC434" class="line" lang="diff"> char c; int l;</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1049" 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="436" 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">@@ -1049,26 +436,8 @@</td>
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1049
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436
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<pre style="margin: 0;"> <span id="LC436" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ int print_correct, print_incorrect, print_X, print_type = 0;</span></span>
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1050
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437
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<pre style="margin: 0;"> <span id="LC437" class="line" lang="diff"> </span>
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1051
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438
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<pre style="margin: 0;"> <span id="LC438" class="line" lang="diff"> print_correct = 1; print_incorrect = 2; print_X =3; </span>
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1052
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<pre style="margin: 0;">-<span id="LC1052" class="line" lang="diff"> correct = 0; error_fp=0; error_tn = 0, total=0;</span>
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1053
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<pre style="margin: 0;">-<span id="LC1053" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -438,7 +438,7 @@</span></span>
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1054
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<pre style="margin: 0;">-<span id="LC1054" class="line" lang="diff"> observed_tolerant++; pos_observed_tolerant++;</span>
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1055
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<pre style="margin: 0;">-<span id="LC1055" class="line" lang="diff"> print_type = print_correct;</span>
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1056
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<pre style="margin: 0;">-<span id="LC1056" class="line" lang="diff"> }</span>
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1057
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<pre style="margin: 0;">-<span id="LC1057" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- else { printf ("missing somethingdsaff\n"); }</span></span>
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1058
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<pre style="margin: 0;">-<span id="LC1058" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else { fprintf( stderr, "%s:%d missing something\n", __FILE__, __LINE__ ); }</span></span>
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1059
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<td class="diff-line-num new_line old" data-linenumber="439" 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="LC1059" class="line" lang="diff"> } else if (info_matrix->info[aa_atob[c]][l] == not_allowed) {</span>
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1060
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<td class="diff-line-num new_line old" data-linenumber="439" 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="LC1060" class="line" lang="diff"> if ( matrix->weights[aa_atob[c]][l] >= 0 ) </span>
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1061
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<pre style="margin: 0;">-<span id="LC1061" class="line" lang="diff"> { /* ERROR of OBSERVED, but INTOLERANT false positive */</span>
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1062
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<td class="diff-line-num new_line old" data-linenumber="439" 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="LC1062" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -449,7 +449,7 @@</span></span>
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1063
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<td class="diff-line-num new_line old" data-linenumber="439" 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="LC1063" class="line" lang="diff"> notobserved_intolerant++; </span>
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1064
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<pre style="margin: 0;">-<span id="LC1064" class="line" lang="diff"> pos_notobserved_intolerant++;</span>
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1065
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<pre style="margin: 0;">-<span id="LC1065" class="line" lang="diff"> print_type = print_correct;</span>
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<td class="diff-line-num old old_line" data-linenumber="1066" 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">
1066
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<td class="diff-line-num new_line old" data-linenumber="439" 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="LC1066" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- } else {printf ("dfafaw\n"); }</span></span>
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1067
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<pre style="margin: 0;">-<span id="LC1067" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ } else {fprintf( stderr, "%s:%d\n", __FILE__, __LINE__ ); }</span></span>
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1068
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<td class="diff-line-num new_line old" data-linenumber="439" 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="LC1068" class="line" lang="diff"> } else if (info_matrix->info[aa_atob[c]][l] == less_severe) {</span>
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1069
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<pre style="margin: 0;">-<span id="LC1069" class="line" lang="diff"> switch (severity_option) {</span>
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1070
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<pre style="margin: 0;">-<span id="LC1070" class="line" lang="diff"> case 1: /* include +- phenotype with + */</span>
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1071
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<pre style="margin: 0;">-<span id="LC1071" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -520,7 +520,7 @@</span></span>
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439
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="diff"> error_fp=0; error_tn = 0, total=0;</span>
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440
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -520,7 +520,7 @@ void output_Matrix_Info (Matrix_Info* in</span></span>
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1072
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441
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<pre style="margin: 0;"> <span id="LC441" class="line" lang="diff"> pos_error_tn++;</span>
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1073
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442
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<pre style="margin: 0;"> <span id="LC442" class="line" lang="diff"> error_tn++;</span>
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1074
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443
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<pre style="margin: 0;"> <span id="LC443" class="line" lang="diff"> print_type = print_incorrect;</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1076" 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="445" 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">@@ -1076,8 +445,8 @@</td>
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1076
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445
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<pre style="margin: 0;"> <span id="LC445" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ } else {fprintf( stderr, "%s:%d something is wrong\n", __FILE__, __LINE__ );}</span></span>
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1077
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446
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<pre style="margin: 0;"> <span id="LC446" class="line" lang="diff"> break;</span>
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1078
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447
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<pre style="margin: 0;"> <span id="LC447" class="line" lang="diff"> case 2: /* +- phenotype is - */</span>
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1079
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<pre style="margin: 0;">-<span id="LC1079" class="line" lang="diff"> if ( matrix->weights[aa_atob[c]][l] > 0.0) {</span>
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1080
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<pre style="margin: 0;">-<span id="LC1080" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -531,7 +531,7 @@</span></span>
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448
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="diff"> if ( matrix->weights[aa_atob[<span class="idiff left right">(int)</span>c]][l] > 0.0) {</span>
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449
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -531,7 +531,7 @@<span class="idiff left right"> void output_Matrix_Info (Matrix_Info* in</span></span></span>
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1081
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450
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<pre style="margin: 0;"> <span id="LC450" class="line" lang="diff"> pos_notobserved_intolerant++;</span>
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1082
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451
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<pre style="margin: 0;"> <span id="LC451" class="line" lang="diff"> notobserved_intolerant++; </span>
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1083
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452
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<pre style="margin: 0;"> <span id="LC452" class="line" lang="diff"> print_type = print_correct;</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1086" 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="455" 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">@@ -1086,7 +455,7 @@</td>
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1086
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455
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<pre style="margin: 0;"> <span id="LC455" class="line" lang="diff"> break;</span>
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1087
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456
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<pre style="margin: 0;"> <span id="LC456" class="line" lang="diff"> default:</span>
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1088
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457
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<pre style="margin: 0;"> <span id="LC457" class="line" lang="diff"> fprintf(errorfp, "severity option error %d\n", severity_option);</span>
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1089
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<pre style="margin: 0;">-<span id="LC1089" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -612,7 +612,7 @@</span></span>
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458
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -612,7 +612,7 @@<span class="idiff left right"> void output_Matrix_Info_float (Matrix_In</span></span></span>
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1090
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459
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<pre style="margin: 0;"> <span id="LC459" class="line" lang="diff"> int pos_observed_tolerant, pos_error_tn, pos_notobserved_intolerant,</span>
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1091
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460
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<pre style="margin: 0;"> <span id="LC460" class="line" lang="diff"> pos_error_fp, pos_total;</span>
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1092
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461
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<pre style="margin: 0;"> <span id="LC461" class="line" lang="diff"> char c; int l;</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1094" 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="463" 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">@@ -1094,17 +463,8 @@</td>
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1094
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463
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<pre style="margin: 0;"> <span id="LC463" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ int print_correct, print_incorrect, print_X, print_type = 0;</span></span>
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1095
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464
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<pre style="margin: 0;"> <span id="LC464" class="line" lang="diff"> </span>
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1096
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465
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<pre style="margin: 0;"> <span id="LC465" class="line" lang="diff"> print_correct = 1; print_incorrect = 2; print_X =3;</span>
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1097
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<pre style="margin: 0;">-<span id="LC1097" class="line" lang="diff"> correct = 0; error_fp=0; error_tn = 0, total=0;</span>
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1098
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<pre style="margin: 0;">-<span id="LC1098" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -657,7 +657,7 @@</span></span>
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1099
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<pre style="margin: 0;">-<span id="LC1099" class="line" lang="diff"> observed_tolerant++; pos_observed_tolerant++;</span>
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1100
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<pre style="margin: 0;">-<span id="LC1100" class="line" lang="diff"> print_type = print_correct;</span>
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1101
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<pre style="margin: 0;">-<span id="LC1101" class="line" lang="diff"> }</span>
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1102
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<pre style="margin: 0;">-<span id="LC1102" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- else { printf ("missing somethingdsaff\n"); }</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1103" 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">
1103
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<pre style="margin: 0;">-<span id="LC1103" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else { fprintf( stderr, "%s:%d missing something\n", __FILE__, __LINE__ ); }</span></span>
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1104
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<pre style="margin: 0;">-<span id="LC1104" class="line" lang="diff"> } else if (info_matrix->info[aa_atob[c]][l] == not_allowed) {</span>
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1105
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<pre style="margin: 0;">-<span id="LC1105" class="line" lang="diff"> if ( matrix->weights[aa_atob[c]][l] >= 0.01 )</span>
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1106
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<pre style="margin: 0;">-<span id="LC1106" class="line" lang="diff"> { /* ERROR of OBSERVED, but INTOLERANT false positive */</span>
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1107
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<pre style="margin: 0;">-<span id="LC1107" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -735,7 +735,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="diff"> error_fp=0; error_tn = 0, total=0;</span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -735,7 +735,7 @@ void output_Matrix_Info_float (Matrix_In</span></span>
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<pre style="margin: 0;"> <span id="LC468" class="line" lang="diff"> pos_error_tn++;</span>
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469
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<pre style="margin: 0;"> <span id="LC469" class="line" lang="diff"> error_tn++;</span>
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1110
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470
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<pre style="margin: 0;"> <span id="LC470" class="line" lang="diff"> print_type = print_incorrect;</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1112" 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="472" 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">@@ -1112,8 +472,8 @@</td>
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1112
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472
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<pre style="margin: 0;"> <span id="LC472" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ } else {fprintf( stderr, "%s:%d something is wrong\n", __FILE__, __LINE__ );}</span></span>
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1113
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473
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<pre style="margin: 0;"> <span id="LC473" class="line" lang="diff"> break;</span>
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<pre style="margin: 0;"> <span id="LC474" class="line" lang="diff"> case 2: /* +- phenotype is - */</span>
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1115
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<pre style="margin: 0;">-<span id="LC1115" class="line" lang="diff"> if ( matrix->weights[aa_atob[c]][l] > 0.01) {</span>
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1116
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<pre style="margin: 0;">-<span id="LC1116" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -847,10 +847,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="diff"> if ( matrix->weights[aa_atob[<span class="idiff left right">(int) </span>c]][l] > 0.01) {</span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -847,10 +847,10 @@<span class="idiff left right"> void read_matrix_20_aa_body(mfp, matrix)</span></span></span>
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1117
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<pre style="margin: 0;"> <span id="LC477" class="line" lang="diff"> */</span>
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1118
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478
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<pre style="margin: 0;"> <span id="LC478" class="line" lang="diff"> </span>
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1119
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<pre style="margin: 0;"> <span id="LC479" class="line" lang="diff"> len = 0;</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">@@ -1126,7 +486,7 @@</td>
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1126
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<pre style="margin: 0;"> <span id="LC486" class="line" lang="diff"> /* read in the numbers */</span>
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1127
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487
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<pre style="margin: 0;"> <span id="LC487" class="line" lang="diff"> while (fgets(Buffer, LARGE_BUFF_LENGTH, mfp) &&</span>
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1128
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488
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<pre style="margin: 0;"> <span id="LC488" class="line" lang="diff"> !blank_line(Buffer) &&</span>
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1129
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<pre style="margin: 0;">-<span id="LC1129" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -92<span class="idiff left right">4,7 +924,7 @@</span></span></span>
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -92<span class="idiff left right">3,7 +923,7 @@ int</span></span></span>
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<pre style="margin: 0;"> <span id="LC490" class="line" lang="diff"> min_aa_in_column (Matrix * matrix, int pos)</span>
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491
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<pre style="margin: 0;"> <span id="LC491" class="line" lang="diff"> {</span>
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1132
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492
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<pre style="margin: 0;"> <span id="LC492" class="line" lang="diff"> double min;</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">@@ -1135,16 +495,7 @@</td>
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1135
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495
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<pre style="margin: 0;"> <span id="LC495" class="line" lang="diff"> </span>
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1136
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496
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<pre style="margin: 0;"> <span id="LC496" class="line" lang="diff"> min = 1000;</span>
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1137
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497
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<pre style="margin: 0;"> <span id="LC497" class="line" lang="diff"> for (aa = 0; aa < AAS; aa++) {</span>
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1138
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<pre style="margin: 0;">-<span id="LC1138" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1043,7 +1043,7 @@</span></span>
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1139
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<pre style="margin: 0;">-<span id="LC1139" class="line" lang="diff"> case 'W': return 18;</span>
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1140
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<pre style="margin: 0;">-<span id="LC1140" class="line" lang="diff"> case 'Y' : return 19;</span>
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1141
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<pre style="margin: 0;">-<span id="LC1141" class="line" lang="diff"> </span>
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1142
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<pre style="margin: 0;">-<span id="LC1142" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- default: printf ("unknown character %c\n", c );</span></span>
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1143
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<pre style="margin: 0;">-<span id="LC1143" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ default: fprintf( stderr, "unknown character %c\n", c );</span></span>
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1144
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<pre style="margin: 0;">-<span id="LC1144" class="line" lang="diff"> } /* end switch */</span>
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1145
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<pre style="margin: 0;">-<span id="LC1145" class="line" lang="diff"> }</span>
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1146
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<pre style="margin: 0;">-<span id="LC1146" class="line" lang="diff"> </span>
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1147
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<pre style="margin: 0;">-<span id="LC1147" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1060,7 +1060,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1038,7 +1038,7 @@ void output_Matrix_Info_float_uncertaint</span></span>
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<pre style="margin: 0;"> <span id="LC499" class="line" lang="diff"> int pos_observed_tolerant, pos_error_tn, pos_notobserved_intolerant,</span>
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1149
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500
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<pre style="margin: 0;"> <span id="LC500" class="line" lang="diff"> pos_error_fp, pos_total;</span>
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1150
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501
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<pre style="margin: 0;"> <span id="LC501" class="line" lang="diff"> char c; int l;</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">@@ -1153,30 +504,11 @@</td>
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1153
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504
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<pre style="margin: 0;"> <span id="LC504" class="line" lang="diff"> int uncertain_aa, uncertain_tolerant, uncertain_intolerant;</span>
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1154
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505
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<pre style="margin: 0;"> <span id="LC505" class="line" lang="diff"> int pos_uncertain_aa, pos_uncertain_tolerant, pos_uncertain_intolerant;</span>
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1155
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506
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<pre style="margin: 0;"> <span id="LC506" class="line" lang="diff"> int total_correct, total_counted;</span>
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1156
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<pre style="margin: 0;">-<span id="LC1156" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1124,7 +1124,7 @@</span></span>
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1157
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<pre style="margin: 0;">-<span id="LC1157" class="line" lang="diff"> ;</span>
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1158
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<pre style="margin: 0;">-<span id="LC1158" class="line" lang="diff"> print_type = print_correct;</span>
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<td class="diff-line-num old old_line" data-linenumber="1159" 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">
1159
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<pre style="margin: 0;">-<span id="LC1159" class="line" lang="diff"> }</span>
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1160
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<pre style="margin: 0;">-<span id="LC1160" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- else { printf ("missing somethingdsaff\n"); }</span></span>
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1161
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<pre style="margin: 0;">-<span id="LC1161" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else { fprintf( stderr, "%s:%d missing something\n", __FILE__, __LINE__ ); }</span></span>
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1162
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<pre style="margin: 0;">-<span id="LC1162" class="line" lang="diff"> } else if (info_matrix->info[aa_atob[c]][l] == not_allowed) {</span>
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1163
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<pre style="margin: 0;">-<span id="LC1163" class="line" lang="diff"> if ( matrix->weights[aa_atob[c]][l] >= THRESHOLD )</span>
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1164
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<pre style="margin: 0;">-<span id="LC1164" class="line" lang="diff"> { /* ERROR of OBSERVED, but INTOLERANT false positive */</span>
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<td class="diff-line-num old old_line" data-linenumber="1165" 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">
1165
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<pre style="margin: 0;">-<span id="LC1165" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1506,9 +1506,9 @@</span></span>
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1166
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<pre style="margin: 0;">-<span id="LC1166" class="line" lang="diff"> polymorph_data[i]->aa = aa_atob['-'];</span>
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1167
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<pre style="margin: 0;">-<span id="LC1167" class="line" lang="diff"> polymorph_data[i]->next = NULL;</span>
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<td class="diff-line-num old old_line" data-linenumber="1168" 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">
1168
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<pre style="margin: 0;">-<span id="LC1168" class="line" lang="diff"> }</span>
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1169
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<pre style="margin: 0;">-<span id="LC1169" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (infofp == NULL) { printf ("no substitutions read\n");</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1170" 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">
1170
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<pre style="margin: 0;">-<span id="LC1170" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (infofp == NULL) { fprintf( stderr, "no substitutions read\n");</span></span>
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1171
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<pre style="margin: 0;">-<span id="LC1171" class="line" lang="diff"> return polymorph_data;} /* no file to read*/</span>
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<td class="diff-line-num old old_line" data-linenumber="1172" 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">
1172
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<pre style="margin: 0;">-<span id="LC1172" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-printf ("before seg fault?\n");</span></span>
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1173
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<pre style="margin: 0;">-<span id="LC1173" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+fprintf( stderr, "%s:%d before seg fault?\n", __FILE__, __LINE__ );</span></span>
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1174
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<pre style="margin: 0;">-<span id="LC1174" class="line" lang="diff"> while (fgets (line, LARGE_BUFF_LENGTH, infofp) != NULL) {</span>
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1175
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<pre style="margin: 0;">-<span id="LC1175" class="line" lang="diff"> word1[0] = '\0'; word2[0] = '\0';</span>
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<td class="diff-line-num old old_line" data-linenumber="1176" 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">
1176
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<pre style="margin: 0;">-<span id="LC1176" class="line" lang="diff"> stringp = strtok (line, " \r\n\t");</span>
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1177
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<pre style="margin: 0;">-<span id="LC1177" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/PN_blocks.c</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1178" 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">
1178
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<pre style="margin: 0;">-<span id="LC1178" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/PN_blocks.c</span></span>
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1179
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<pre style="margin: 0;">-<span id="LC1179" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -671,7 +671,7 @@</span></span>
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507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="diff"><span class="gh" style="color: #999;">Index: sift/src/PN_blocks.c</span></span>
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- sift.orig/src/PN_blocks.c</span></span>
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510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ sift/src/PN_blocks.c</span></span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -668,7 +668,7 @@ remove_seq0_Xes_from_block (Block* block</span></span>
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1180
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512
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<pre style="margin: 0;"> <span id="LC512" class="line" lang="diff"> Block* newblock;</span>
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1181
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513
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<pre style="margin: 0;"> <span id="LC513" class="line" lang="diff"> Residue* residue_pointer;</span>
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1182
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514
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<pre style="margin: 0;"> <span id="LC514" class="line" lang="diff"> int i, pos;</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="517" 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">@@ -1185,8 +517,10 @@</td>
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1185
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517
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<pre style="margin: 0;"> <span id="LC517" class="line" lang="diff"> </span>
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1186
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518
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<pre style="margin: 0;"> <span id="LC518" class="line" lang="diff"> non_X_length = 0;</span>
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1187
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519
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<pre style="margin: 0;"> <span id="LC519" class="line" lang="diff"> for (i=0; i < block->width; i++) {</span>
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1188
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<pre style="margin: 0;">-<span id="LC1188" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/PN_convert.c</span></span>
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1189
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<pre style="margin: 0;">-<span id="LC1189" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/PN_convert.c</span></span>
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="diff"><span class="gh" style="color: #999;">Index: sift/src/PN_convert.c</span></span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- sift.orig/src/PN_convert.c</span></span>
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523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ sift/src/PN_convert.c</span></span>
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1190
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524
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<pre style="margin: 0;"> <span id="LC524" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,6 +1,6 @@</span></span>
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1191
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525
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<pre style="margin: 0;"> <span id="LC525" class="line" lang="diff"> /* (C) Copyright 2000, Fred Hutchinson Cancer Research Center */</span>
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1192
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526
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<pre style="margin: 0;"> <span id="LC526" class="line" lang="diff"> /* Use, modification or distribution of these programs is subject to */</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1206" 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="540" 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">@@ -1206,7 +540,7 @@</td>
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1206
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540
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<pre style="margin: 0;"> <span id="LC540" class="line" lang="diff"> throughout.</span>
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1207
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541
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<pre style="margin: 0;"> <span id="LC541" class="line" lang="diff"> */</span>
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1208
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542
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<pre style="margin: 0;"> <span id="LC542" class="line" lang="diff"> /* system headers not in global.h */</span>
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1209
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<pre style="margin: 0;">-<span id="LC1209" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -18,6 +18,9 @@</span></span>
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543
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -18,6 +18,9 @@<span class="idiff left right"> throughout.</span></span></span>
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1210
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544
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<pre style="margin: 0;"> <span id="LC544" class="line" lang="diff"> </span>
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1211
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545
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<pre style="margin: 0;"> <span id="LC545" class="line" lang="diff"> #include <assert.h></span>
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1212
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546
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<pre style="margin: 0;"> <span id="LC546" class="line" lang="diff"> #include <math.h></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1216" 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">@@ -1216,7 +550,7 @@</td>
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1216
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550
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<pre style="margin: 0;"> <span id="LC550" class="line" lang="diff"> #include "PN_convert.h"</span>
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1217
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551
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<pre style="margin: 0;"> <span id="LC551" class="line" lang="diff"> #include "queue.c"</span>
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1218
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552
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<pre style="margin: 0;"> <span id="LC552" class="line" lang="diff"> #include "SortList.c"</span>
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1219
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<pre style="margin: 0;">-<span id="LC1219" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -4<span class="idiff left right">7,7 +50,7 @@</span></span></span>
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553
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -4<span class="idiff left right">5,7 +48,7 @@ struct float_qij *Qij;</span></span></span>
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1220
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554
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<pre style="margin: 0;"> <span id="LC554" class="line" lang="diff"> void pb_weights(/*block*/);</span>
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1221
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555
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<pre style="margin: 0;"> <span id="LC555" class="line" lang="diff"> </span>
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1222
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556
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<pre style="margin: 0;"> <span id="LC556" class="line" lang="diff"> /*</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1225" 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="559" 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">@@ -1225,7 +559,7 @@</td>
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1225
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559
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<pre style="margin: 0;"> <span id="LC559" class="line" lang="diff"> * sequence weights.</span>
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1226
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560
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<pre style="margin: 0;"> <span id="LC560" class="line" lang="diff"> */</span>
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1227
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561
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<pre style="margin: 0;"> <span id="LC561" class="line" lang="diff"> </span>
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1228
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<pre style="margin: 0;">-<span id="LC1228" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -13<span class="idiff left right">3,7 +136,7 @@</span></span></span>
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -13<span class="idiff left right">1,7 +134,7 @@ Matrix *PN_block_to_matrix(block, conver</span></span></span>
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1229
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563
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<pre style="margin: 0;"> <span id="LC563" class="line" lang="diff"> break;</span>
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1230
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564
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<pre style="margin: 0;"> <span id="LC564" class="line" lang="diff"> case 22: /* instead of adding RTot * diffaas*/</span>
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1231
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565
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<pre style="margin: 0;"> <span id="LC565" class="line" lang="diff"> /* as in option 20, add RTot * (diffass - 1), thus not adding*/</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1234" 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">@@ -1234,7 +568,7 @@</td>
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1234
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568
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<pre style="margin: 0;"> <span id="LC568" class="line" lang="diff"> /* qij's as pseudocounts */</span>
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1235
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569
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<pre style="margin: 0;"> <span id="LC569" class="line" lang="diff"> PN_altschul_data_dependent_conversion_method (block, matrix, 22);</span>
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1236
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570
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<pre style="margin: 0;"> <span id="LC570" class="line" lang="diff"> break;</span>
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1237
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<pre style="margin: 0;">-<span id="LC1237" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1<span class="idiff left right">41,13 +144,13 @@</span></span></span>
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1<span class="idiff left right">39,13 +142,13 @@ Matrix *PN_block_to_matrix(block, conver</span></span></span>
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572
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<pre style="margin: 0;"> <span id="LC572" class="line" lang="diff"> /* exp. pseudocounts*/</span>
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1239
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<pre style="margin: 0;"> <span id="LC573" class="line" lang="diff"> PN_altschul_data_dependent_conversion_method (block, matrix, 23);</span>
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1240
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574
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<pre style="margin: 0;"> <span id="LC574" class="line" lang="diff"> break;</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">@@ -1250,7 +584,7 @@</td>
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584
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<pre style="margin: 0;"> <span id="LC584" class="line" lang="diff"> PN_altschul_data_dependent_conversion_method (block, matrix, 26);</span>
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1251
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585
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<pre style="margin: 0;"> <span id="LC585" class="line" lang="diff"> break;</span>
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1252
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586
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<pre style="margin: 0;"> <span id="LC586" class="line" lang="diff"> case 27:</span>
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<pre style="margin: 0;">-<span id="LC1253" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -17<span class="idiff left right">2,7 +175,7 @@</span></span></span>
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -17<span class="idiff left right">0,7 +173,7 @@ Matrix *PN_block_to_matrix(block, conver</span></span></span>
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1254
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588
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<pre style="margin: 0;"> <span id="LC588" class="line" lang="diff"> qij_matrix_profile (block, matrix, Qij);</span>
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589
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<pre style="margin: 0;"> <span id="LC589" class="line" lang="diff"> break;</span>
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<pre style="margin: 0;"> <span id="LC590" class="line" lang="diff"> default: /* the default case */</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">@@ -1259,7 +593,7 @@</td>
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1259
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<pre style="margin: 0;"> <span id="LC593" class="line" lang="diff"> "Invalid block to matrix conversion method specified, %d.",</span>
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1260
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594
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<pre style="margin: 0;"> <span id="LC594" class="line" lang="diff"> conversion_method);</span>
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1261
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595
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<pre style="margin: 0;"> <span id="LC595" class="line" lang="diff"> ErrorReport(WARNING_ERR_LVL);</span>
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1262
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<pre style="margin: 0;">-<span id="LC1262" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -21<span class="idiff left right">3,10 +216,10 @@</span></span></span>
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -21<span class="idiff left right">1,10 +214,10 @@ Matrix *PN_block_to_matrix_RTot_par(bloc</span></span></span>
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597
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<pre style="margin: 0;"> <span id="LC597" class="line" lang="diff"> ErrorReport(WARNING_ERR_LVL);</span>
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598
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<pre style="margin: 0;"> <span id="LC598" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC599" class="line" lang="diff"> sprintf(ErrorBuffer, /* ^^^^----------------vvvvvvvvvvvvvvvvvvv */ "Using the default conversion method of Altschul's data-dependent method.\n");</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">@@ -1272,7 +606,7 @@</td>
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606
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<pre style="margin: 0;"> <span id="LC606" class="line" lang="diff"> </span>
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1273
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607
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<pre style="margin: 0;"> <span id="LC607" class="line" lang="diff"> /* return the matrix */</span>
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<pre style="margin: 0;"> <span id="LC608" class="line" lang="diff"> return matrix;</span>
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1275
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<td class="diff-line-num new_line old" data-linenumber="609" 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="LC1275" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2<span class="idiff left right">41,11 +244,11 @@</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="609" 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">
609
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2<span class="idiff left right">39,11 +242,11 @@ static struct working *make_col()</span></span></span>
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1276
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610
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<pre style="margin: 0;"> <span id="LC610" class="line" lang="diff"> {</span>
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<td class="diff-line-num old_line" data-linenumber="1277" 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">
1277
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611
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<pre style="margin: 0;"> <span id="LC611" class="line" lang="diff"> struct working *col;</span>
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<td class="diff-line-num old_line" data-linenumber="1278" 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">
1278
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612
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<pre style="margin: 0;"> <span id="LC612" class="line" lang="diff"> int aa;</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1286" 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="620" 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">@@ -1286,7 +620,7 @@</td>
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1286
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620
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<pre style="margin: 0;"> <span id="LC620" class="line" lang="diff"> col->totcnt = col->totreg = 0.0;</span>
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<td class="diff-line-num old_line" data-linenumber="1287" 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">
1287
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<td class="diff-line-num new_line" data-linenumber="621" 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">
621
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<pre style="margin: 0;"> <span id="LC621" class="line" lang="diff"> for (aa=0; aa < AASALL; aa++) {</span>
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<td class="diff-line-num old_line" data-linenumber="1288" 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">
1288
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<td class="diff-line-num new_line" data-linenumber="622" 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">
622
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<pre style="margin: 0;"> <span id="LC622" class="line" lang="diff"> col->cnt[aa] = col->reg[aa] = 0.0;</span>
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<td class="diff-line-num old old_line" data-linenumber="1289" 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">
1289
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<pre style="margin: 0;">-<span id="LC1289" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -26<span class="idiff left right">2,7 +265,7 @@</span></span></span>
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623
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -26<span class="idiff left right">0,7 +263,7 @@ struct work_pssm *PN_make_pssm(int lengt</span></span></span>
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1290
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624
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<pre style="margin: 0;"> <span id="LC624" class="line" lang="diff"> struct work_pssm *pssm;</span>
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<td class="diff-line-num old_line" data-linenumber="1291" 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">
1291
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625
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<pre style="margin: 0;"> <span id="LC625" class="line" lang="diff"> int pos, aa;</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1292" 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">
1292
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626
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<pre style="margin: 0;"> <span id="LC626" class="line" lang="diff"> double* double_pointer;</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1295" 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="629" 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">@@ -1295,7 +629,7 @@</td>
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1295
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629
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<pre style="margin: 0;"> <span id="LC629" class="line" lang="diff"> CheckMem(</span>
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<td class="diff-line-num old_line" data-linenumber="1296" 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">
1296
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630
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<pre style="margin: 0;"> <span id="LC630" class="line" lang="diff"> pssm = (struct work_pssm *) malloc(sizeof(struct work_pssm))</span>
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<td class="diff-line-num old_line" data-linenumber="1297" 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">
1297
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<td class="diff-line-num new_line" data-linenumber="631" 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">
631
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<pre style="margin: 0;"> <span id="LC631" class="line" lang="diff"> );</span>
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1298
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<td class="diff-line-num new_line old" data-linenumber="632" 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="LC1298" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2<span class="idiff left right">70,7 +273,7 @@</span></span></span>
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632
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2<span class="idiff left right">68,7 +271,7 @@ struct work_pssm *PN_make_pssm(int lengt</span></span></span>
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1299
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633
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<pre style="margin: 0;"> <span id="LC633" class="line" lang="diff"> double_pointer = (double*) calloc (length * AASALL, sizeof (double));</span>
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<td class="diff-line-num old_line" data-linenumber="1300" 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">
1300
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634
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<pre style="margin: 0;"> <span id="LC634" class="line" lang="diff"> pssm->value = (double **) calloc (length, sizeof (double*));</span>
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<td class="diff-line-num old_line" data-linenumber="1301" 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">
1301
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635
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<pre style="margin: 0;"> <span id="LC635" class="line" lang="diff"> pssm->sum = (double *) calloc (length, sizeof (double));</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1304" 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="638" 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">@@ -1304,7 +638,7 @@</td>
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1304
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638
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<pre style="margin: 0;"> <span id="LC638" class="line" lang="diff"> for (pos = 0; pos < length; pos++) {</span>
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<pre style="margin: 0;"> <span id="LC639" class="line" lang="diff"> pssm->value[pos] = &(double_pointer[pos * AASALL]);</span>
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<pre style="margin: 0;"> <span id="LC640" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC1307" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -30<span class="idiff left right">6,7 +309,7 @@</span></span></span>
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -30<span class="idiff left right">4,7 +307,7 @@ void counts_no_gaps (Block* block, struc</span></span></span>
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<pre style="margin: 0;"> <span id="LC642" class="line" lang="diff"> }</span>
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<pre style="margin: 0;"> <span id="LC643" class="line" lang="diff"> } /* end of for */</span>
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<pre style="margin: 0;"> <span id="LC644" class="line" lang="diff"> } /* end of subroutine */</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">@@ -1313,7 +647,7 @@</td>
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<pre style="margin: 0;"> <span id="LC647" class="line" lang="diff"> /*======================================================================*/</span>
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<pre style="margin: 0;"> <span id="LC648" class="line" lang="diff"> static void counts(block, col, pos)</span>
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<pre style="margin: 0;"> <span id="LC649" class="line" lang="diff"> Block *block;</span>
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<pre style="margin: 0;">-<span id="LC1316" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -31<span class="idiff left right">6,7 +319,7 @@</span></span></span>
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -31<span class="idiff left right">4,7 +317,7 @@ static void counts(block, col, pos)</span></span></span>
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<pre style="margin: 0;"> <span id="LC651" class="line" lang="diff"> int seq, aa, aa1;</span>
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<pre style="margin: 0;"> <span id="LC652" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC653" class="line" lang="diff"> col->totcnt = col->totraw = col->totreg = 0.0;</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">@@ -1322,7 +656,7 @@</td>
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<pre style="margin: 0;"> <span id="LC656" class="line" lang="diff"> col->cnt[aa] = col->raw[aa] = col->reg[aa] = 0.0;</span>
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657
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<pre style="margin: 0;"> <span id="LC657" class="line" lang="diff"> }</span>
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<pre style="margin: 0;"> <span id="LC658" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC1325" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -35<span class="idiff left right">8,7 +361,7 @@</span></span></span>
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -35<span class="idiff left right">6,7 +359,7 @@ static int count_residues(col)</span></span></span>
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<pre style="margin: 0;"> <span id="LC660" class="line" lang="diff"> struct working *col;</span>
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661
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<pre style="margin: 0;"> <span id="LC661" class="line" lang="diff"> {</span>
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<pre style="margin: 0;"> <span id="LC662" class="line" lang="diff"> int aa, nr;</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">@@ -1331,7 +665,7 @@</td>
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<pre style="margin: 0;"> <span id="LC665" class="line" lang="diff"> nr = 0;</span>
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<pre style="margin: 0;"> <span id="LC666" class="line" lang="diff"> for (aa = 1; aa < AAS; aa++) {</span>
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<pre style="margin: 0;"> <span id="LC667" class="line" lang="diff"> if (col->cnt[aa] > 0.0) nr++;</span>
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<pre style="margin: 0;">-<span id="LC1334" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -37<span class="idiff left right">5,9 +378,9 @@</span></span></span>
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -37<span class="idiff left right">3,9 +376,9 @@ static void pseudo_alts(col, qij, beta)</span></span></span>
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669
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<pre style="margin: 0;"> <span id="LC669" class="line" lang="diff"> double beta;</span>
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<pre style="margin: 0;"> <span id="LC670" class="line" lang="diff"> {</span>
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<pre style="margin: 0;"> <span id="LC671" class="line" lang="diff"> int aa, row;</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">@@ -1343,7 +677,7 @@</td>
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<pre style="margin: 0;"> <span id="LC677" class="line" lang="diff"> /*---------- get the pseudo counts -------------------------------*/</span>
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<pre style="margin: 0;"> <span id="LC678" class="line" lang="diff"> for (aa=1; aa < AAS; aa++) {</span>
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<pre style="margin: 0;"> <span id="LC679" class="line" lang="diff"> col->reg[aa] = 0.0;</span>
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<pre style="margin: 0;">-<span id="LC1346" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -39<span class="idiff left right">5,7 +398,7 @@</span></span></span>
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -39<span class="idiff left right">3,7 +396,7 @@ static void pseudo_alts(col, qij, beta)</span></span></span>
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<pre style="margin: 0;"> <span id="LC681" class="line" lang="diff"> int</span>
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<pre style="margin: 0;"> <span id="LC682" class="line" lang="diff"> find_min_aa_in_pssm (struct working* col, struct work_pssm* pssm, const int pos)</span>
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<pre style="margin: 0;"> <span id="LC683" 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">@@ -1352,7 +686,7 @@</td>
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<pre style="margin: 0;"> <span id="LC686" class="line" lang="diff"> double min_value;</span>
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<pre style="margin: 0;"> <span id="LC687" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC688" class="line" lang="diff"> min_value = 1000;</span>
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<pre style="margin: 0;">-<span id="LC1355" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -42<span class="idiff left right">2,7 +425,7 @@</span></span></span>
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -42<span class="idiff left right">0,7 +423,7 @@ void range_on_pssm (struct working* col,</span></span></span>
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<pre style="margin: 0;"> <span id="LC690" class="line" lang="diff"> min_aa = find_min_aa_in_pssm(col, pssm, pos);</span>
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<pre style="margin: 0;"> <span id="LC691" class="line" lang="diff"> min = pssm->value[pos][min_aa] * threshold;</span>
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1358
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<td class="diff-line-num new_line" data-linenumber="692" 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">
692
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<pre style="margin: 0;"> <span id="LC692" class="line" lang="diff"> for (aa = 0; aa < AAS; aa++) {</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1361" 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="695" 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">@@ -1361,7 +695,7 @@</td>
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1361
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695
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<pre style="margin: 0;"> <span id="LC695" class="line" lang="diff"> }</span>
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1362
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696
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<pre style="margin: 0;"> <span id="LC696" class="line" lang="diff"> </span>
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1363
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697
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<pre style="margin: 0;"> <span id="LC697" class="line" lang="diff"> </span>
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1364
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<pre style="margin: 0;">-<span id="LC1364" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -43<span class="idiff left right">8,14 +441,14 @@</span></span></span>
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698
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -43<span class="idiff left right">6,14 +439,14 @@ scoring_matrix_profile (Block* block, Ma</span></span></span>
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1365
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699
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<pre style="margin: 0;"> <span id="LC699" class="line" lang="diff"> FILE* matrixfp;</span>
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1366
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700
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<pre style="margin: 0;"> <span id="LC700" class="line" lang="diff"> char matrix_file[LARGE_BUFF_LENGTH];</span>
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1367
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701
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<pre style="margin: 0;"> <span id="LC701" class="line" lang="diff"> int pos, original_aa, aa;</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1380" 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="714" 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">@@ -1380,51 +714,7 @@</td>
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1380
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714
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<pre style="margin: 0;"> <span id="LC714" class="line" lang="diff"> if ( (matrixfp = fopen (matrix_file, "r")) == NULL) {</span>
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1381
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715
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<pre style="margin: 0;"> <span id="LC715" class="line" lang="diff"> fprintf (errorfp, "can't read the matrix %s\n", matrix_file);</span>
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1382
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<td class="diff-line-num new_line" data-linenumber="716" 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">
716
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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="LC716" class="line" lang="diff"> exit (-1);</span>
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1383
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<pre style="margin: 0;">-<span id="LC1383" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -479,7 +482,7 @@</span></span>
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1384
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<pre style="margin: 0;">-<span id="LC1384" class="line" lang="diff"> </span>
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1385
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<pre style="margin: 0;">-<span id="LC1385" class="line" lang="diff"> } /* end of qij_matrix_profile */</span>
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1386
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<pre style="margin: 0;">-<span id="LC1386" class="line" lang="diff"> </span>
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1387
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<pre style="margin: 0;">-<span id="LC1387" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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1388
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<pre style="margin: 0;">-<span id="LC1388" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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1389
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<pre style="margin: 0;">-<span id="LC1389" class="line" lang="diff"> static void Pauline_pseudo_alts (col, qij, epsilon)</span>
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1390
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<pre style="margin: 0;">-<span id="LC1390" class="line" lang="diff"> struct working* col;</span>
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<td class="diff-line-num old old_line" data-linenumber="1391" 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">
1391
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<pre style="margin: 0;">-<span id="LC1391" class="line" lang="diff"> struct float_qij *qij;</span>
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<td class="diff-line-num old old_line" data-linenumber="1392" 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">
1392
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<pre style="margin: 0;">-<span id="LC1392" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -487,7 +490,7 @@</span></span>
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1393
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<pre style="margin: 0;">-<span id="LC1393" class="line" lang="diff"> {</span>
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1394
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<pre style="margin: 0;">-<span id="LC1394" class="line" lang="diff"> int aa, row;</span>
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<pre style="margin: 0;">-<span id="LC1395" class="line" lang="diff"> </span>
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1396
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<pre style="margin: 0;">-<span id="LC1396" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- col->totreg = 0.0; </span></span>
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1397
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<pre style="margin: 0;">-<span id="LC1397" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ col->totreg = 0.0;</span></span>
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1398
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<pre style="margin: 0;">-<span id="LC1398" class="line" lang="diff"> /*---------- get the pseudo counts -------------------------------*/</span>
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1399
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<pre style="margin: 0;">-<span id="LC1399" class="line" lang="diff"> for (aa=1; aa < AAS; aa++) {</span>
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1400
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<pre style="margin: 0;">-<span id="LC1400" class="line" lang="diff"> col->reg[aa] = 0.0;</span>
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1401
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<pre style="margin: 0;">-<span id="LC1401" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -508,13 +511,13 @@</span></span>
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1402
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<pre style="margin: 0;">-<span id="LC1402" class="line" lang="diff"> struct work_pssm *pssm;</span>
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1403
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<pre style="margin: 0;">-<span id="LC1403" class="line" lang="diff"> {</span>
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1404
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<pre style="margin: 0;">-<span id="LC1404" class="line" lang="diff"> int aa;</span>
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1405
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<pre style="margin: 0;">-<span id="LC1405" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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1406
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<pre style="margin: 0;">-<span id="LC1406" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- pssm->sum[pos] = 0.0; </span></span>
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1407
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<pre style="margin: 0;">-<span id="LC1407" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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1408
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<pre style="margin: 0;">-<span id="LC1408" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ pssm->sum[pos] = 0.0;</span></span>
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1409
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<pre style="margin: 0;">-<span id="LC1409" class="line" lang="diff"> for (aa=1; aa < AAS; aa++)</span>
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1410
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<pre style="margin: 0;">-<span id="LC1410" class="line" lang="diff"> {</span>
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1411
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<pre style="margin: 0;">-<span id="LC1411" class="line" lang="diff"> pssm->value[pos][aa] = col->cnt[aa] + col->reg[aa];</span>
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1412
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<pre style="margin: 0;">-<span id="LC1412" class="line" lang="diff"> pssm->value[pos][aa] /= (col->totcnt + col->totreg);</span>
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1413
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<pre style="margin: 0;">-<span id="LC1413" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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1414
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<pre style="margin: 0;">-<span id="LC1414" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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1415
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<pre style="margin: 0;">-<span id="LC1415" class="line" lang="diff"> /* compute the odds ratio */</span>
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1416
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<pre style="margin: 0;">-<span id="LC1416" class="line" lang="diff"> if (freqs[aa] > 0.0) {</span>
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1417
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<pre style="margin: 0;">-<span id="LC1417" class="line" lang="diff"> pssm->value[pos][aa] /= freqs[aa];</span>
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1418
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<pre style="margin: 0;">-<span id="LC1418" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -524,7 +527,7 @@</span></span>
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1419
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<pre style="margin: 0;">-<span id="LC1419" class="line" lang="diff"> if (pssm->value[pos][aa] > 0.0) {</span>
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1420
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<pre style="margin: 0;">-<span id="LC1420" class="line" lang="diff"> pssm->value[pos][aa] = log(pssm->value[pos][aa]);</span>
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1421
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<pre style="margin: 0;">-<span id="LC1421" class="line" lang="diff"> }</span>
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1422
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<pre style="margin: 0;">-<span id="LC1422" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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1423
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<pre style="margin: 0;">-<span id="LC1423" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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1424
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<pre style="margin: 0;">-<span id="LC1424" class="line" lang="diff"> pssm->sum[pos] += pssm->value[pos][aa];</span>
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1425
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<pre style="margin: 0;">-<span id="LC1425" class="line" lang="diff"> }</span>
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1426
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<pre style="margin: 0;">-<span id="LC1426" class="line" lang="diff"> } /* end of log_odds */</span>
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1427
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<pre style="margin: 0;">-<span id="LC1427" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -553,17 +556,17 @@</span></span>
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -502,17 +505,17 @@ static void compute_BZX(frequency, matri</span></span>
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1428
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718
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<pre style="margin: 0;"> <span id="LC718" class="line" lang="diff"> /*</span>
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1429
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719
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<pre style="margin: 0;"> <span id="LC719" class="line" lang="diff"> * find the partitions of D, N, E, and Q for B and Z</span>
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1430
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720
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<pre style="margin: 0;"> <span id="LC720" class="line" lang="diff"> */</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1447" 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="737" 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">@@ -1447,7 +737,7 @@</td>
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1447
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<pre style="margin: 0;"> <span id="LC737" class="line" lang="diff"> (part_D * matrix->weights[aa_atob['D']][col] +</span>
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1448
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738
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<pre style="margin: 0;"> <span id="LC738" class="line" lang="diff"> part_N * matrix->weights[aa_atob['N']][col]);</span>
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1449
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739
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<pre style="margin: 0;"> <span id="LC739" class="line" lang="diff"> matrix->weights[aa_atob['Z']][col] =</span>
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1450
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<pre style="margin: 0;">-<span id="LC1450" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -5<span class="idiff left right">89,7 +592,7 @@</span></span></span>
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<pre style="margin: 0;">+<span id="LC740" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -5<span class="idiff left right">38,7 +541,7 @@ static void compute_BZX(frequency, matri</span></span></span>
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1451
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741
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<pre style="margin: 0;"> <span id="LC741" class="line" lang="diff"> </span>
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1452
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742
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<pre style="margin: 0;"> <span id="LC742" class="line" lang="diff"> /*=========================================================================</span>
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1453
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743
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<pre style="margin: 0;"> <span id="LC743" class="line" lang="diff"> Adds negative minval to give all positive matrix,</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1456" 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="746" 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">@@ -1456,7 +746,7 @@</td>
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1456
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746
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<pre style="margin: 0;"> <span id="LC746" class="line" lang="diff"> NOTE: Not 0 to 100 because "output_matrix" routine might not leave</span>
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1457
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747
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<pre style="margin: 0;"> <span id="LC747" class="line" lang="diff"> enough space.</span>
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1458
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748
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<pre style="margin: 0;"> <span id="LC748" class="line" lang="diff"> ===========================================================================*/</span>
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<pre style="margin: 0;">-<span id="LC1459" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">609,7 +612,7 @@</span></span></span>
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<pre style="margin: 0;">+<span id="LC749" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">558,7 +561,7 @@ static void positive_matrix(freqs, pssm,</span></span></span>
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<pre style="margin: 0;"> <span id="LC750" class="line" lang="diff"> if (pssm->value[pos][aa] > maxval) maxval = pssm->value[pos][aa];</span>
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751
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<pre style="margin: 0;"> <span id="LC751" class="line" lang="diff"> }</span>
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1462
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752
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<pre style="margin: 0;"> <span id="LC752" 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">@@ -1465,7 +755,7 @@</td>
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<pre style="margin: 0;"> <span id="LC755" class="line" lang="diff"> if (minval < 0.0) {</span>
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1466
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<pre style="margin: 0;"> <span id="LC756" class="line" lang="diff"> factor = 99.0 / (maxval - minval);</span>
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1467
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757
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<pre style="margin: 0;"> <span id="LC757" class="line" lang="diff"> }</span>
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1468
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<pre style="margin: 0;">-<span id="LC1468" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">638,7 +641,7 @@</span></span></span>
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<pre style="margin: 0;">+<span id="LC758" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">587,7 +590,7 @@ initialize_cutoff_freqs (double* newfreq</span></span></span>
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759
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<pre style="margin: 0;"> <span id="LC759" class="line" lang="diff"> {</span>
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1470
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760
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<pre style="margin: 0;"> <span id="LC760" class="line" lang="diff"> int aa;</span>
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1471
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761
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<pre style="margin: 0;"> <span id="LC761" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1474" 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">@@ -1474,7 +764,7 @@</td>
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764
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<pre style="margin: 0;"> <span id="LC764" class="line" lang="diff"> assert (oldfreqs[MATRIX_AA_WIDTH] != NULL);</span>
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1475
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765
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<pre style="margin: 0;"> <span id="LC765" class="line" lang="diff"> assert (newfreqs[MATRIX_AA_WIDTH] != NULL);</span>
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1476
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766
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<pre style="margin: 0;"> <span id="LC766" class="line" lang="diff"> */</span>
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<pre style="margin: 0;">-<span id="LC1477" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -6<span class="idiff left right">53,7 +656,7 @@</span></span></span>
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<pre style="margin: 0;">+<span id="LC767" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -6<span class="idiff left right">02,7 +605,7 @@ initialize_cutoff_freqs (double* newfreq</span></span></span>
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768
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<pre style="margin: 0;"> <span id="LC768" class="line" lang="diff"> </span>
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1479
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769
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<pre style="margin: 0;"> <span id="LC769" class="line" lang="diff"> </span>
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770
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<pre style="margin: 0;"> <span id="LC770" class="line" lang="diff"> /* pseudocounts from Altschul's 1997 NAR gapped blast and PSI-BLAST paper */</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1483" 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">@@ -1483,7 +773,7 @@</td>
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1483
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<pre style="margin: 0;"> <span id="LC773" class="line" lang="diff"> psiblast_alts (Block* block, Matrix* matrix, double* freqs, struct float_qij* qij)</span>
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774
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<pre style="margin: 0;"> <span id="LC774" class="line" lang="diff"> {</span>
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<pre style="margin: 0;"> <span id="LC775" class="line" lang="diff"> double beta;</span>
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<pre style="margin: 0;">-<span id="LC1486" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">703,14 +706,14 @@</span></span></span>
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<pre style="margin: 0;">+<span id="LC776" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">652,14 +655,14 @@ psiblast_alts (Block* block, Matrix* mat</span></span></span>
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777
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<pre style="margin: 0;"> <span id="LC777" class="line" lang="diff"> free (pssm->value); free(pssm->sum);</span>
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778
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<pre style="margin: 0;"> <span id="LC778" class="line" lang="diff"> free(pssm);</span>
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779
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<pre style="margin: 0;"> <span id="LC779" 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">@@ -1502,7 +792,7 @@</td>
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<pre style="margin: 0;"> <span id="LC792" class="line" lang="diff"> for (aa = 1; aa < AAS; aa++) {</span>
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<pre style="margin: 0;"> <span id="LC793" class="line" lang="diff"> if (col->cnt[aa] > max) {</span>
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794
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<pre style="margin: 0;"> <span id="LC794" class="line" lang="diff"> max = col->cnt[aa];</span>
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<pre style="margin: 0;">-<span id="LC1505" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">724,7 +727,7 @@</span></span></span>
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">673,7 +676,7 @@ find_max_aa_in_col (struct working* col)</span></span></span>
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796
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<pre style="margin: 0;"> <span id="LC796" class="line" lang="diff"> int</span>
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<pre style="margin: 0;"> <span id="LC797" class="line" lang="diff"> find_max_aa_in_pssm (struct work_pssm* pssm , int pos)</span>
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798
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<pre style="margin: 0;"> <span id="LC798" class="line" lang="diff"> {</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1511" 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="801" 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">@@ -1511,7 +801,7 @@</td>
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801
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<pre style="margin: 0;"> <span id="LC801" class="line" lang="diff"> double max;</span>
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1512
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802
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<pre style="margin: 0;"> <span id="LC802" class="line" lang="diff"> </span>
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803
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<pre style="margin: 0;"> <span id="LC803" class="line" lang="diff"> max = 0.0;</span>
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<pre style="margin: 0;">-<span id="LC1514" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">736,7 +739,7 @@</span></span></span>
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<pre style="margin: 0;">+<span id="LC804" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">685,7 +688,7 @@ find_max_aa_in_pssm (struct work_pssm* p</span></span></span>
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1515
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805
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<pre style="margin: 0;"> <span id="LC805" class="line" lang="diff"> }</span>
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806
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<pre style="margin: 0;"> <span id="LC806" class="line" lang="diff"> return max_aa;</span>
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1517
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807
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<pre style="margin: 0;"> <span id="LC807" class="line" lang="diff"> }</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1520" 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="810" 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">@@ -1520,7 +810,7 @@</td>
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1520
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<td class="diff-line-num new_line" data-linenumber="810" 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">
810
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<pre style="margin: 0;"> <span id="LC810" class="line" lang="diff"> /*==========================================================================</span>
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<td class="diff-line-num old_line" data-linenumber="1521" 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">
1521
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<td class="diff-line-num new_line" data-linenumber="811" 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">
811
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<pre style="margin: 0;"> <span id="LC811" class="line" lang="diff"> Uses Altschul's method of getting pseudo-counts with a qij matrix,</span>
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1522
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<td class="diff-line-num new_line" data-linenumber="812" 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">
812
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<pre style="margin: 0;"> <span id="LC812" class="line" lang="diff"> ===========================================================================*/</span>
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1523
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<td class="diff-line-num new_line old" data-linenumber="813" 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="LC1523" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -7<span class="idiff left right">56,12 +759,12 @@</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="813" 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">
813
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<pre style="margin: 0;">+<span id="LC813" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -7<span class="idiff left right">05,12 +708,12 @@ static void PN_make_alts(block, matrix,</span></span></span>
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<td class="diff-line-num old_line" data-linenumber="1524" 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">
1524
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<td class="diff-line-num new_line" data-linenumber="814" 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">
814
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<pre style="margin: 0;"> <span id="LC814" class="line" lang="diff"> int original_aa;</span>
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<td class="diff-line-num old_line" data-linenumber="1525" 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">
1525
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<td class="diff-line-num new_line" data-linenumber="815" 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">
815
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<pre style="margin: 0;"> <span id="LC815" class="line" lang="diff"> struct dirichlet* diric;</span>
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<td class="diff-line-num old_line" data-linenumber="1526" 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">
1526
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<td class="diff-line-num new_line" data-linenumber="816" 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">
816
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<pre style="margin: 0;"> <span id="LC816" class="line" lang="diff"> int min_aa, max_aa;</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1535" 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="825" 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">@@ -1535,7 +825,7 @@</td>
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1535
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825
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<pre style="margin: 0;"> <span id="LC825" class="line" lang="diff"> char diri_file[LARGE_BUFF_LENGTH];</span>
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<td class="diff-line-num old_line" data-linenumber="1536" 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">
1536
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<td class="diff-line-num new_line" data-linenumber="826" 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">
826
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<pre style="margin: 0;"> <span id="LC826" class="line" lang="diff"> </span>
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<td class="diff-line-num old_line" data-linenumber="1537" 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">
1537
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<td class="diff-line-num new_line" data-linenumber="827" 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">
827
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<pre style="margin: 0;"> <span id="LC827" class="line" lang="diff"> if (scale == 30) {</span>
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<td class="diff-line-num old old_line" data-linenumber="1538" 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">
1538
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<td class="diff-line-num new_line old" data-linenumber="828" 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="LC1538" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -7<span class="idiff left right">74,15 +777,15 @@</span></span></span>
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<td class="diff-line-num new old_line" data-linenumber="1539" 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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828
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<pre style="margin: 0;">+<span id="LC828" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -7<span class="idiff left right">23,15 +726,15 @@ static void PN_make_alts(block, matrix,</span></span></span>
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1539
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829
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<pre style="margin: 0;"> <span id="LC829" class="line" lang="diff"> col = make_col();</span>
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<td class="diff-line-num old_line" data-linenumber="1540" 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">
1540
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<td class="diff-line-num new_line" data-linenumber="830" 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">
830
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<pre style="margin: 0;"> <span id="LC830" class="line" lang="diff"> pssm = PN_make_pssm(block->width);</span>
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<td class="diff-line-num old_line" data-linenumber="1541" 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">
1541
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831
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<pre style="margin: 0;"> <span id="LC831" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1556" 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="846" 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">@@ -1556,7 +846,7 @@</td>
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1556
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846
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<pre style="margin: 0;"> <span id="LC846" class="line" lang="diff"> /*-------------- Do one position at a time -------------------*/</span>
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<td class="diff-line-num old_line" data-linenumber="1557" 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">
1557
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<td class="diff-line-num new_line" data-linenumber="847" 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">
847
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<pre style="margin: 0;"> <span id="LC847" class="line" lang="diff"> for (pos = 0; pos < block->width; pos++)</span>
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<td class="diff-line-num old_line" data-linenumber="1558" 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">
1558
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<td class="diff-line-num new_line" data-linenumber="848" 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">
848
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<pre style="margin: 0;"> <span id="LC848" class="line" lang="diff"> {</span>
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<td class="diff-line-num old old_line" data-linenumber="1559" 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">
1559
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<td class="diff-line-num new_line old" data-linenumber="849" 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="LC1559" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -7<span class="idiff left right">96,8 +799,8 @@</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="849" 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">
849
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<pre style="margin: 0;">+<span id="LC849" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -7<span class="idiff left right">45,8 +748,8 @@ printf ("diri file loaded\n");</span></span></span>
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1560
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<td class="diff-line-num new_line" data-linenumber="850" 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">
850
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<pre style="margin: 0;"> <span id="LC850" class="line" lang="diff"> if (itemp ==1 ) {epsilon = 0; }</span>
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<td class="diff-line-num old_line" data-linenumber="1561" 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">
1561
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<td class="diff-line-num new_line" data-linenumber="851" 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">
851
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<pre style="margin: 0;"> <span id="LC851" class="line" lang="diff"> else {</span>
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1562
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852
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<pre style="margin: 0;"> <span id="LC852" class="line" lang="diff"> original_aa = block->residues[0][pos];</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="857" 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">@@ -1567,7 +857,7 @@</td>
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1567
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857
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<pre style="margin: 0;"> <span id="LC857" class="line" lang="diff"> }</span>
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1568
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858
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<pre style="margin: 0;"> <span id="LC858" class="line" lang="diff"> </span>
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1569
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859
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<pre style="margin: 0;"> <span id="LC859" class="line" lang="diff"> } else if (scale == 20) {</span>
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1570
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<pre style="margin: 0;">-<span id="LC1570" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">813,7 +816,7 @@</span></span></span>
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860
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<pre style="margin: 0;">+<span id="LC860" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">762,7 +765,7 @@ printf ("diri file loaded\n");</span></span></span>
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1571
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861
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<pre style="margin: 0;"> <span id="LC861" class="line" lang="diff"> /*---------- get the pseudo counts -------------------------------*/</span>
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<td class="diff-line-num old_line" data-linenumber="1572" 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">
1572
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<td class="diff-line-num new_line" data-linenumber="862" 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">
862
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<pre style="margin: 0;"> <span id="LC862" class="line" lang="diff"> if (scale == 27 || scale == 29 || scale == 30 || scale == 26) {</span>
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<td class="diff-line-num old_line" data-linenumber="1573" 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">
1573
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863
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<pre style="margin: 0;"> <span id="LC863" class="line" lang="diff"> diri_pseudo = TRUE;</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1576" 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="866" 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">@@ -1576,7 +866,7 @@</td>
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1576
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866
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<pre style="margin: 0;"> <span id="LC866" class="line" lang="diff"> } else {</span>
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1577
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<td class="diff-line-num new_line" data-linenumber="867" 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">
867
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<pre style="margin: 0;"> <span id="LC867" class="line" lang="diff"> pseudo_alts(col, qij, epsilon);</span>
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<td class="diff-line-num old_line" data-linenumber="1578" 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">
1578
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<td class="diff-line-num new_line" data-linenumber="868" 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">
868
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<pre style="margin: 0;"> <span id="LC868" class="line" lang="diff"> }</span>
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1579
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<pre style="margin: 0;">-<span id="LC1579" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">832,8 +835,8 @@</span></span></span>
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869
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<pre style="margin: 0;">+<span id="LC869" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">781,8 +784,8 @@ printf ("diri file loaded\n");</span></span></span>
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1580
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870
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<pre style="margin: 0;"> <span id="LC870" class="line" lang="diff"> </span>
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<td class="diff-line-num old_line" data-linenumber="1581" 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">
1581
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871
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<pre style="margin: 0;"> <span id="LC871" class="line" lang="diff"> /* Count+pseudo proportions; returned if scale == 20 */</span>
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<td class="diff-line-num old_line" data-linenumber="1582" 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">
1582
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872
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<pre style="margin: 0;"> <span id="LC872" class="line" lang="diff"> if (scale <= 20 || scale == 22 || scale == 25 || scale == 23</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1587" 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="877" 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">@@ -1587,7 +877,7 @@</td>
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1587
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877
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<pre style="margin: 0;"> <span id="LC877" class="line" lang="diff"> {</span>
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1588
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878
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<pre style="margin: 0;"> <span id="LC878" class="line" lang="diff"> pssm->value[pos][aa] = col->cnt[aa] + col->reg[aa];</span>
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1589
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879
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<pre style="margin: 0;"> <span id="LC879" class="line" lang="diff"> if ( (col->totcnt + col->totreg) > 0.0)</span>
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1590
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<pre style="margin: 0;">-<span id="LC1590" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -8<span class="idiff left right">90,7 +893,7 @@</span></span></span>
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880
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<pre style="margin: 0;">+<span id="LC880" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -8<span class="idiff left right">39,7 +842,7 @@ printf ("diri file loaded\n");</span></span></span>
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1591
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881
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<pre style="margin: 0;"> <span id="LC881" class="line" lang="diff"> /* by subtracting the min. value for all positions ----- */</span>
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1592
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882
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<pre style="margin: 0;"> <span id="LC882" class="line" lang="diff"> if (!scale) positive_matrix(freqs, pssm, matrix);</span>
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1593
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883
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<pre style="margin: 0;"> <span id="LC883" 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">@@ -1596,7 +886,7 @@</td>
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1596
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886
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<pre style="margin: 0;"> <span id="LC886" class="line" lang="diff"> free (diric);</span>
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1597
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887
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<pre style="margin: 0;"> <span id="LC887" class="line" lang="diff"> free(col);</span>
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1598
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888
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<pre style="margin: 0;"> <span id="LC888" class="line" lang="diff"> free_struct_work_pssm (pssm );</span>
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1599
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<pre style="margin: 0;">-<span id="LC1599" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">903,7 +906,7 @@</span></span></span>
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889
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<pre style="margin: 0;">+<span id="LC889" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">852,7 +855,7 @@ printf ("left make _alts\n");</span></span></span>
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1600
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890
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<pre style="margin: 0;"> <span id="LC890" class="line" lang="diff"> option: diri_pseudocounts</span>
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1601
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891
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<pre style="margin: 0;"> <span id="LC891" class="line" lang="diff"> TRUE: use 13-component Dirichlet</span>
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1602
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892
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<pre style="margin: 0;"> <span id="LC892" class="line" lang="diff"> FALSE use BLOSUM62 qij's</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="895" 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">@@ -1605,7 +895,7 @@</td>
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1605
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895
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<pre style="margin: 0;"> <span id="LC895" class="line" lang="diff"> FALSE - just look at 20 amino acids</span>
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1606
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896
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<pre style="margin: 0;"> <span id="LC896" class="line" lang="diff"> option: exp (m)</span>
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1607
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897
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<pre style="margin: 0;"> <span id="LC897" class="line" lang="diff"> m=0 # of amino acids at pos (default)</span>
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1608
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<pre style="margin: 0;">-<span id="LC1608" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">919,9 +922,9 @@</span></span></span>
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898
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<pre style="margin: 0;">+<span id="LC898" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">868,9 +871,9 @@ SIFT_prediction (Block* block, int diri_</span></span></span>
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1609
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899
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<pre style="margin: 0;"> <span id="LC899" class="line" lang="diff"> Matrix* pssm;</span>
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1610
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900
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<pre style="margin: 0;"> <span id="LC900" class="line" lang="diff"> </span>
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1611
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901
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<pre style="margin: 0;"> <span id="LC901" class="line" lang="diff"> pssm = copy_block_info_to_matrix (block);</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1617" 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="907" 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">@@ -1617,7 +907,7 @@</td>
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1617
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907
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<pre style="margin: 0;"> <span id="LC907" class="line" lang="diff"> exit (-1);</span>
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1618
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908
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<pre style="margin: 0;"> <span id="LC908" class="line" lang="diff"> }</span>
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1619
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909
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<pre style="margin: 0;"> <span id="LC909" class="line" lang="diff"> normalize (block);</span>
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1620
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<pre style="margin: 0;">-<span id="LC1620" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -9<span class="idiff left right">63,13 +966,13 @@</span></span></span>
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910
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<pre style="margin: 0;">+<span id="LC910" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -9<span class="idiff left right">12,13 +915,13 @@ void calculate_counts (Block* block)</span></span></span>
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1621
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911
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<pre style="margin: 0;"> <span id="LC911" class="line" lang="diff"> for (aa = 1; aa < AAS; aa++) {</span>
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1622
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912
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<pre style="margin: 0;"> <span id="LC912" class="line" lang="diff"> printf ("pos %d aa %c counts %.2f weight %.2f\n",</span>
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1623
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913
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<pre style="margin: 0;"> <span id="LC913" class="line" lang="diff"> pos, aa_btoa[aa], col->cnt[aa], col->totcnt);</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="925" 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">@@ -1635,7 +925,7 @@</td>
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1635
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925
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<pre style="margin: 0;"> <span id="LC925" class="line" lang="diff"> int exp_option, int subtract_threshold)</span>
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<td class="diff-line-num old_line" data-linenumber="1636" 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">
1636
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926
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<pre style="margin: 0;"> <span id="LC926" class="line" lang="diff"> {</span>
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1637
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927
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<pre style="margin: 0;"> <span id="LC927" class="line" lang="diff"> double dtemp, dtemp2, epsilon;</span>
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1638
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<td class="diff-line-num new_line old" data-linenumber="928" 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="LC1638" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -9<span class="idiff left right">84,7 +987,7 @@</span></span></span>
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928
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<pre style="margin: 0;">+<span id="LC928" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -9<span class="idiff left right">33,7 +936,7 @@ static void SIFT_alts(Block* block, Matr</span></span></span>
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1639
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929
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<pre style="margin: 0;"> <span id="LC929" class="line" lang="diff"> int div_by_max;</span>
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<td class="diff-line-num old_line" data-linenumber="1640" 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">
1640
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930
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<pre style="margin: 0;"> <span id="LC930" class="line" lang="diff"> int rank_matrix[AAS][AAS];</span>
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<td class="diff-line-num old_line" data-linenumber="1641" 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">
1641
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931
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<pre style="margin: 0;"> <span id="LC931" class="line" lang="diff"> FILE* rfp;</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1644" 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="934" 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">@@ -1644,7 +934,7 @@</td>
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1644
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934
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<pre style="margin: 0;"> <span id="LC934" class="line" lang="diff"> char diri_file[LARGE_BUFF_LENGTH];</span>
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1645
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935
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<pre style="margin: 0;"> <span id="LC935" class="line" lang="diff"> </span>
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<td class="diff-line-num old_line" data-linenumber="1646" 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">
1646
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936
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<pre style="margin: 0;"> <span id="LC936" class="line" lang="diff"> div_by_max = TRUE;</span>
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1647
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<pre style="margin: 0;">-<span id="LC1647" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -9<span class="idiff left right">92,25 +995,25 @@</span></span></span>
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937
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<pre style="margin: 0;">+<span id="LC937" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -9<span class="idiff left right">41,25 +944,25 @@ static void SIFT_alts(Block* block, Matr</span></span></span>
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1648
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938
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<pre style="margin: 0;"> <span id="LC938" class="line" lang="diff"> col = make_col();</span>
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1649
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939
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<pre style="margin: 0;"> <span id="LC939" class="line" lang="diff"> pssm = PN_make_pssm(block->width);</span>
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1650
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940
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<pre style="margin: 0;"> <span id="LC940" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1676" 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">@@ -1676,7 +966,7 @@</td>
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1676
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966
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<pre style="margin: 0;"> <span id="LC966" class="line" lang="diff"> </span>
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1677
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967
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<pre style="margin: 0;"> <span id="LC967" class="line" lang="diff"> /*-------- determine total number of pseudo-counts in column ------*/</span>
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1678
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968
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<pre style="margin: 0;"> <span id="LC968" class="line" lang="diff"> epsilon = 0;</span>
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1679
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<pre style="margin: 0;">-<span id="LC1679" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">1020,24 +1023,24 @@</span></span></span>
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969
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<pre style="margin: 0;">+<span id="LC969" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">969,24 +972,24 @@ static void SIFT_alts(Block* block, Matr</span></span></span>
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970
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<pre style="margin: 0;"> <span id="LC970" class="line" lang="diff"> if (exp_option == 1) {</span>
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1681
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971
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<pre style="margin: 0;"> <span id="LC971" class="line" lang="diff"> /*printf ("pos %d : ", pos); */</span>
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1682
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972
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<pre style="margin: 0;"> <span id="LC972" class="line" lang="diff"> dtemp = similarity_dependent_scale_0(col, rank_matrix, original_aa);</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1710" 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">@@ -1710,7 +1000,7 @@</td>
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1000
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<pre style="margin: 0;"> <span id="LC1000" class="line" lang="diff"> </span>
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1711
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1001
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<pre style="margin: 0;"> <span id="LC1001" class="line" lang="diff"> /*--------- Fill in the matrix entries --------------------*/</span>
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1712
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1002
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<pre style="margin: 0;"> <span id="LC1002" class="line" lang="diff"> pssm->sum[pos] = 0.0;</span>
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1713
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<pre style="margin: 0;">-<span id="LC1713" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -10<span class="idiff left right">58,11 +1061,11 @@</span></span></span>
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1003
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<pre style="margin: 0;">+<span id="LC1003" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -10<span class="idiff left right">07,11 +1010,11 @@ static void SIFT_alts(Block* block, Matr</span></span></span>
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1004
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<pre style="margin: 0;"> <span id="LC1004" class="line" lang="diff"> for (aa = 1; aa < AAS; aa++) {</span>
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1715
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1005
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<pre style="margin: 0;"> <span id="LC1005" class="line" lang="diff"> pssm->value[pos][aa] /= min_freq;</span>
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1716
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1006
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<pre style="margin: 0;"> <span id="LC1006" class="line" lang="diff"> }</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1014" 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">@@ -1724,7 +1014,7 @@</td>
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1014
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<pre style="margin: 0;"> <span id="LC1014" class="line" lang="diff"> }</span>
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1725
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1015
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<pre style="margin: 0;"> <span id="LC1015" class="line" lang="diff"> }</span>
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1726
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1016
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<pre style="margin: 0;"> <span id="LC1016" class="line" lang="diff"> </span>
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1727
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<pre style="margin: 0;">-<span id="LC1727" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -10<span class="idiff left right">78,7 +1081,7 @@</span></span></span>
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1017
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<pre style="margin: 0;">+<span id="LC1017" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -10<span class="idiff left right">27,7 +1030,7 @@ static void SIFT_alts(Block* block, Matr</span></span></span>
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1728
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1018
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<pre style="margin: 0;"> <span id="LC1018" class="line" lang="diff"> if ( (matrix->weights[original_aa][pos] < TOLERANCE_PROB_THRESHOLD</span>
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1729
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1019
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<pre style="margin: 0;"> <span id="LC1019" class="line" lang="diff"> && (!subtract_threshold))</span>
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1730
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1020
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<pre style="margin: 0;"> <span id="LC1020" class="line" lang="diff"> ||</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1733" 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="1023" 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">@@ -1733,7 +1023,7 @@</td>
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1733
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1023
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<pre style="margin: 0;"> <span id="LC1023" class="line" lang="diff"> ) {</span>
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1734
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1024
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<pre style="margin: 0;"> <span id="LC1024" class="line" lang="diff"> printf ("WARNING!!! Amino acid %c at pos %d in your original sequence had score %.3f and was not allowed by the prediction.<BR>\n", aa_btoa[original_aa], pos + 1, matrix->weights[original_aa][pos]);</span>
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1735
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1025
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<pre style="margin: 0;"> <span id="LC1025" class="line" lang="diff"> }</span>
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1736
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<td class="diff-line-num new_line old" data-linenumber="1026" 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="LC1736" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1<span class="idiff left right">111,7 +1114,7 @@</span></span></span>
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1026
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<pre style="margin: 0;">+<span id="LC1026" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1<span class="idiff left right">060,7 +1063,7 @@ void SIFT_alts_test(Block* block, Matrix</span></span></span>
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1737
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1027
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<pre style="margin: 0;"> <span id="LC1027" class="line" lang="diff"> int div_by_max;</span>
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<td class="diff-line-num old_line" data-linenumber="1738" 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">
1738
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1028
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<pre style="margin: 0;"> <span id="LC1028" class="line" lang="diff"> int rank_matrix[AAS][AAS];</span>
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<td class="diff-line-num old_line" data-linenumber="1739" 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">
1739
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1029
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<pre style="margin: 0;"> <span id="LC1029" class="line" lang="diff"> FILE* rfp;</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1742" 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="1032" 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">@@ -1742,7 +1032,7 @@</td>
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1742
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1032
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<pre style="margin: 0;"> <span id="LC1032" class="line" lang="diff"> char diri_file[LARGE_BUFF_LENGTH];</span>
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1743
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1033
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<pre style="margin: 0;"> <span id="LC1033" class="line" lang="diff"> char matrix_file[LARGE_BUFF_LENGTH];</span>
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1744
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1034
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<pre style="margin: 0;"> <span id="LC1034" class="line" lang="diff"> </span>
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1745
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<pre style="margin: 0;">-<span id="LC1745" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1<span class="idiff left right">121,7 +1124,7 @@</span></span></span>
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1035
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<pre style="margin: 0;">+<span id="LC1035" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1<span class="idiff left right">070,7 +1073,7 @@ void SIFT_alts_test(Block* block, Matrix</span></span></span>
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1746
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1036
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<pre style="margin: 0;"> <span id="LC1036" class="line" lang="diff"> col = make_col();</span>
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1747
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1037
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<pre style="margin: 0;"> <span id="LC1037" class="line" lang="diff"> pssm = PN_make_pssm(block->width);</span>
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1748
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1038
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<pre style="margin: 0;"> <span id="LC1038" class="line" lang="diff"> diri_pseudocounts = TRUE;</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1751" 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="1041" 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">@@ -1751,7 +1041,7 @@</td>
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1751
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1041
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<pre style="margin: 0;"> <span id="LC1041" class="line" lang="diff"> </span>
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1752
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1042
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<pre style="margin: 0;"> <span id="LC1042" class="line" lang="diff"> sprintf (diri_file , "%s/docs/default.diri", blimps_dir);</span>
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1753
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1043
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<pre style="margin: 0;"> <span id="LC1043" class="line" lang="diff"> </span>
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1754
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<pre style="margin: 0;">-<span id="LC1754" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1<span class="idiff left right">132,8 +1135,8 @@</span></span></span>
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1044
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<pre style="margin: 0;">+<span id="LC1044" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1<span class="idiff left right">080,8 +1083,8 @@ void SIFT_alts_test(Block* block, Matrix</span></span></span>
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1755
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1045
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<pre style="margin: 0;"> <span id="LC1045" class="line" lang="diff"> </span>
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1756
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1046
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<pre style="margin: 0;"> <span id="LC1046" class="line" lang="diff"> construct_rank_matrix ( rank_matrix);</span>
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1757
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1047
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<pre style="margin: 0;"> <span id="LC1047" class="line" lang="diff"> }</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1760" 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="1050" 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">@@ -1760,9 +1050,9 @@</td>
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1760
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1050
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<pre style="margin: 0;"> <span id="LC1050" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sprintf (matrix_file, "%s/docs/default.qij", blimps_dir );</span></span>
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1761
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1051
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<pre style="margin: 0;"> <span id="LC1051" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ init_frq_qij_for_matrix (matrix_file);</span></span>
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1762
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1052
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<pre style="margin: 0;"> <span id="LC1052" class="line" lang="diff"> </span>
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1763
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<pre style="margin: 0;">-<span id="LC1763" class="line" lang="diff"> /*-------------- Do one position at a time -------------------*/</span>
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1764
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1053
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<pre style="margin: 0;"> <span id="LC1053" class="line" lang="diff"> for (pos = 0; pos < block->width; pos++)</span>
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1765
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<pre style="margin: 0;">-<span id="LC1765" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1262,7 +1265,7 @@</span></span>
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1054
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<pre style="margin: 0;">+<span id="LC1054" class="line" lang="diff"> {</span>
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1055
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<pre style="margin: 0;">+<span id="LC1055" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1200,7 +1203,7 @@ gap_pseudocounts ( struct working* col,</span></span>
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1766
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1056
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<pre style="margin: 0;"> <span id="LC1056" class="line" lang="diff"> </span>
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1767
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1057
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<pre style="margin: 0;"> <span id="LC1057" class="line" lang="diff"> }</span>
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<td class="diff-line-num old_line" data-linenumber="1768" 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">
1768
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1058
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<pre style="margin: 0;"> <span id="LC1058" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1771" 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="1061" 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">@@ -1771,7 +1061,7 @@</td>
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1771
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1061
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<pre style="margin: 0;"> <span id="LC1061" class="line" lang="diff"> ratio_mutated_to_normal (struct working* col, int standard_aa)</span>
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1772
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1062
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<pre style="margin: 0;"> <span id="LC1062" class="line" lang="diff"> {</span>
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1773
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1063
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<pre style="margin: 0;"> <span id="LC1063" class="line" lang="diff"> int aa;</span>
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1774
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<pre style="margin: 0;">-<span id="LC1774" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -12<span class="idiff left right">80,7 +1283,7 @@</span></span></span>
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1064
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<pre style="margin: 0;">+<span id="LC1064" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -12<span class="idiff left right">18,7 +1221,7 @@ assign_gap_positive_scores (Matrix* matr</span></span></span>
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1775
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1065
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<pre style="margin: 0;"> <span id="LC1065" class="line" lang="diff"> {</span>
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1776
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1066
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<pre style="margin: 0;"> <span id="LC1066" class="line" lang="diff"> int gaps;</span>
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1777
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1067
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<pre style="margin: 0;"> <span id="LC1067" class="line" lang="diff"> int seq;</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1780" 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="1070" 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">@@ -1780,7 +1070,7 @@</td>
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1780
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1070
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<pre style="margin: 0;"> <span id="LC1070" class="line" lang="diff"> assert (matrix->block != NULL);</span>
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1781
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1071
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<pre style="margin: 0;"> <span id="LC1071" class="line" lang="diff"> /* printf ("entering gap_positive scores\n"); */</span>
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1782
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1072
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<pre style="margin: 0;"> <span id="LC1072" class="line" lang="diff"> gaps = 0;</span>
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1783
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<pre style="margin: 0;">-<span id="LC1783" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -12<span class="idiff left right">92,7 +1295,7 @@</span></span></span>
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<pre style="margin: 0;">+<span id="LC1073" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -12<span class="idiff left right">30,7 +1233,7 @@ assign_gap_positive_scores (Matrix* matr</span></span></span>
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<pre style="margin: 0;"> <span id="LC1074" class="line" lang="diff"> if (gaps == 0) { /* printf ("no gaps\n"); */return; }</span>
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<pre style="margin: 0;"> <span id="LC1075" class="line" lang="diff"> else { /* printf ("gaps %d\n", gaps) ; */</span>
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1076
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<pre style="margin: 0;"> <span id="LC1076" class="line" lang="diff"> assign_positive_scores_to_column (matrix, pos, gaps); }</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">@@ -1789,7 +1079,7 @@</td>
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<pre style="margin: 0;"> <span id="LC1079" class="line" lang="diff"> } /* end of assign_gap_positive_scores */</span>
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1080
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<pre style="margin: 0;"> <span id="LC1080" class="line" lang="diff"> </span>
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1081
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<pre style="margin: 0;"> <span id="LC1081" class="line" lang="diff"> void</span>
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1792
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<pre style="margin: 0;">-<span id="LC1792" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1<span class="idiff left right">305,7 +1308,7 @@</span></span></span>
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<pre style="margin: 0;">+<span id="LC1082" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1<span class="idiff left right">242,7 +1245,7 @@ assign_positive_scores_to_column (Matrix</span></span></span>
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1083
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<pre style="margin: 0;"> <span id="LC1083" class="line" lang="diff"> for (aa = 1; aa < AAS; aa++) {</span>
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1084
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<pre style="margin: 0;"> <span id="LC1084" class="line" lang="diff"> matrix->weights[aa][pos] = 0.05;</span>
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1085
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<pre style="margin: 0;"> <span id="LC1085" 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">@@ -1798,7 +1088,7 @@</td>
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1088
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<pre style="margin: 0;"> <span id="LC1088" class="line" lang="diff"> </span>
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1089
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<pre style="margin: 0;"> <span id="LC1089" class="line" lang="diff"> /*=========================================================================</span>
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1800
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1090
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<pre style="margin: 0;"> <span id="LC1090" class="line" lang="diff"> Normalize sequence weights to add up to the number of sequences</span>
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<pre style="margin: 0;">-<span id="LC1801" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1<span class="idiff left right">337,11 +1340,11 @@</span></span></span>
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<pre style="margin: 0;">+<span id="LC1091" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1<span class="idiff left right">274,11 +1277,11 @@ PN_altschul_data_dependent_conversion_me</span></span></span>
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<pre style="margin: 0;"> <span id="LC1092" class="line" lang="diff"> }</span>
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1093
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<pre style="margin: 0;"> <span id="LC1093" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC1094" class="line" lang="diff"> /* check to see if the block has sequence weights */</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">@@ -1814,57 +1104,7 @@</td>
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<pre style="margin: 0;"> <span id="LC1104" class="line" lang="diff"> }</span>
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1105
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<pre style="margin: 0;"> <span id="LC1105" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC1106" class="line" lang="diff"> /*</span>
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<pre style="margin: 0;">-<span id="LC1817" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1383,7 +1386,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC1818" class="line" lang="diff"> for (clust=0; clust<block->num_clusters; clust++) {</span>
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<pre style="margin: 0;">-<span id="LC1819" class="line" lang="diff"> weight = 1.0/(double)block->clusters[clust].num_sequences;</span>
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<pre style="margin: 0;">-<span id="LC1820" class="line" lang="diff"> /* fill each sequence in the cluster */</span>
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<pre style="margin: 0;">-<span id="LC1821" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for (seq=seq_num; seq<seq_num+block->clusters[clust].num_sequences; </span></span>
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1822
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<pre style="margin: 0;">-<span id="LC1822" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for (seq=seq_num; seq<seq_num+block->clusters[clust].num_sequences;</span></span>
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1823
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<pre style="margin: 0;">-<span id="LC1823" class="line" lang="diff"> seq++) {</span>
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<pre style="margin: 0;">-<span id="LC1824" class="line" lang="diff"> seq_weight[seq] = weight;</span>
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1825
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<pre style="margin: 0;">-<span id="LC1825" class="line" lang="diff"> }</span>
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1826
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<pre style="margin: 0;">-<span id="LC1826" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1402,7 +1405,7 @@</span></span>
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1827
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<pre style="margin: 0;">-<span id="LC1827" class="line" lang="diff"> * Return codes: a pointer to the sequence weights array.</span>
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<pre style="margin: 0;">-<span id="LC1828" class="line" lang="diff"> * Error codes: NULL if all of the weights in the block are <= zero.</span>
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<pre style="margin: 0;">-<span id="LC1829" class="line" lang="diff"> */</span>
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<pre style="margin: 0;">-<span id="LC1830" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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1831
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<pre style="margin: 0;">-<span id="LC1831" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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1832
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<pre style="margin: 0;">-<span id="LC1832" class="line" lang="diff"> static double *pre_weighted_sequences(block)</span>
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1833
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<pre style="margin: 0;">-<span id="LC1833" class="line" lang="diff"> Block* block;</span>
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1834
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<pre style="margin: 0;">-<span id="LC1834" class="line" lang="diff"> {</span>
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1835
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<pre style="margin: 0;">-<span id="LC1835" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1422,9 +1425,9 @@</span></span>
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1836
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<pre style="margin: 0;">-<span id="LC1836" class="line" lang="diff"> CheckMem(</span>
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1837
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<pre style="margin: 0;">-<span id="LC1837" class="line" lang="diff"> seq_weight = (double *) calloc(block->num_sequences, sizeof(double))</span>
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1838
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<pre style="margin: 0;">-<span id="LC1838" class="line" lang="diff"> );</span>
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1839
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<pre style="margin: 0;">-<span id="LC1839" 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="LC1840" 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="LC1841" class="line" lang="diff"> num_seqs = block->num_sequences;</span>
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<pre style="margin: 0;">-<span id="LC1842" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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1843
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<pre style="margin: 0;">-<span id="LC1843" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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1844
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<pre style="margin: 0;">-<span id="LC1844" class="line" lang="diff"> /* fill each sequence weight from the block */</span>
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1845
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<pre style="margin: 0;">-<span id="LC1845" class="line" lang="diff"> max_weight = 0.0;</span>
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1846
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<pre style="margin: 0;">-<span id="LC1846" class="line" lang="diff"> for (seq=0; seq<num_seqs; seq++) {</span>
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1847
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<pre style="margin: 0;">-<span id="LC1847" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1437,16 +1440,16 @@</span></span>
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1848
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<pre style="margin: 0;">-<span id="LC1848" class="line" lang="diff"> if (max_weight <= 0) {</span>
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1849
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<pre style="margin: 0;">-<span id="LC1849" class="line" lang="diff"> /* all weights were zero */</span>
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1850
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<pre style="margin: 0;">-<span id="LC1850" class="line" lang="diff"> free(seq_weight);</span>
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1851
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<pre style="margin: 0;">-<span id="LC1851" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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1852
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<pre style="margin: 0;">-<span id="LC1852" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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1853
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<pre style="margin: 0;">-<span id="LC1853" class="line" lang="diff"> return NULL; /* the error is handled in the calling function */</span>
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1854
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<pre style="margin: 0;">-<span id="LC1854" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- } </span></span>
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1855
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<pre style="margin: 0;">-<span id="LC1855" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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1856
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<pre style="margin: 0;">-<span id="LC1856" class="line" lang="diff"> </span>
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1857
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<pre style="margin: 0;">-<span id="LC1857" class="line" lang="diff"> return seq_weight;</span>
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1858
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<pre style="margin: 0;">-<span id="LC1858" class="line" lang="diff"> } /* end of pre_weighted_sequences */</span>
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1859
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<pre style="margin: 0;">-<span id="LC1859" class="line" lang="diff"> </span>
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1860
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<pre style="margin: 0;">-<span id="LC1860" class="line" lang="diff"> </span>
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1861
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<pre style="margin: 0;">-<span id="LC1861" class="line" lang="diff"> /*</span>
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1862
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<pre style="margin: 0;">-<span id="LC1862" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- * Matrix construction methods. Build matricies from blocks and </span></span>
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1863
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<pre style="margin: 0;">-<span id="LC1863" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ * Matrix construction methods. Build matricies from blocks and</span></span>
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1864
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<pre style="margin: 0;">-<span id="LC1864" class="line" lang="diff"> * sequence weights.</span>
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1865
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<pre style="margin: 0;">-<span id="LC1865" class="line" lang="diff"> */</span>
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1866
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<pre style="margin: 0;">-<span id="LC1866" class="line" lang="diff"> </span>
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1867
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<pre style="margin: 0;">-<span id="LC1867" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1456,7 +1459,7 @@</span></span>
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1107
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<pre style="margin: 0;">+<span id="LC1107" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1304,7 +1307,7 @@ printf ("exit PN_make_alts\n");</span></span>
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1868
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1108
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<pre style="margin: 0;"> <span id="LC1108" class="line" lang="diff"> */</span>
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1869
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1109
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<pre style="margin: 0;"> <span id="LC1109" class="line" lang="diff"> </span>
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1870
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1110
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<pre style="margin: 0;"> <span id="LC1110" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1873" 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="1113" 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">@@ -1873,7 +1113,7 @@</td>
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1873
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1113
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<pre style="margin: 0;"> <span id="LC1113" class="line" lang="diff"> * basic_matrix_construction</span>
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1874
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1114
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<pre style="margin: 0;"> <span id="LC1114" class="line" lang="diff"> * This is the most general matrix construction method. Each</span>
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1875
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1115
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<pre style="margin: 0;"> <span id="LC1115" class="line" lang="diff"> * occurence of a residue in a sequence contributes the sequence</span>
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1876
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<pre style="margin: 0;">-<span id="LC1876" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1<span class="idiff left right">468,7 +1471,7 @@</span></span></span>
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1116
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<pre style="margin: 0;">+<span id="LC1116" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1<span class="idiff left right">316,7 +1319,7 @@ printf ("exit PN_make_alts\n");</span></span></span>
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1877
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1117
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<pre style="margin: 0;"> <span id="LC1117" class="line" lang="diff"> * X, '-', '*', & non-code scores are read straight from the frequencies</span>
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1878
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1118
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<pre style="margin: 0;"> <span id="LC1118" class="line" lang="diff"> * the frequencies for B and Z are ignored, when a B or Z is encountered</span>
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1879
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1119
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<pre style="margin: 0;"> <span id="LC1119" class="line" lang="diff"> * it is partitioned between D & N or E & Q.</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1882" 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="1122" 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">@@ -1882,7 +1122,7 @@</td>
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1882
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1122
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<pre style="margin: 0;"> <span id="LC1122" class="line" lang="diff"> * D & N and E & Q.</span>
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1883
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1123
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<pre style="margin: 0;"> <span id="LC1123" class="line" lang="diff"> * Parameters:</span>
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1884
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1124
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<pre style="margin: 0;"> <span id="LC1124" class="line" lang="diff"> * Block *block: the block to be converted</span>
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1885
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<pre style="margin: 0;">-<span id="LC1885" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1<span class="idiff left right">512,13 +1515,13 @@</span></span></span>
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1125
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<pre style="margin: 0;">+<span id="LC1125" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1<span class="idiff left right">360,13 +1363,13 @@ static void basic_matrix_construction(bl</span></span></span>
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1886
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1126
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<pre style="margin: 0;"> <span id="LC1126" class="line" lang="diff"> /*</span>
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1887
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1127
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<pre style="margin: 0;"> <span id="LC1127" class="line" lang="diff"> * find the partitions of D, N, E, and Q for B and Z</span>
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1888
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1128
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<pre style="margin: 0;"> <span id="LC1128" class="line" lang="diff"> */</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1900" 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="1140" 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">@@ -1900,7 +1140,7 @@</td>
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1900
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1140
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<pre style="margin: 0;"> <span id="LC1140" class="line" lang="diff"> ( frequency[aa_atob['E']] + frequency[aa_atob['Q']] );</span>
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1901
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1141
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<pre style="margin: 0;"> <span id="LC1141" class="line" lang="diff"> </span>
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1902
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<td class="diff-line-num new_line" data-linenumber="1142" 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">
1142
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<pre style="margin: 0;"> <span id="LC1142" class="line" lang="diff"> </span>
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1903
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<td class="diff-line-num new_line old" data-linenumber="1143" 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="LC1903" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1<span class="idiff left right">553,13 +1556,13 @@</span></span></span>
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<td class="diff-line-num new old_line" data-linenumber="1904" 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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<td class="diff-line-num new new_line" data-linenumber="1143" 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">
1143
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<pre style="margin: 0;">+<span id="LC1143" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1<span class="idiff left right">401,13 +1404,13 @@ static void basic_matrix_construction(bl</span></span></span>
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1904
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<td class="diff-line-num new_line" data-linenumber="1144" 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">
1144
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<pre style="margin: 0;"> <span id="LC1144" class="line" lang="diff"> /* otherwise, if it is B, partition B between D and N */</span>
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<td class="diff-line-num old_line" data-linenumber="1905" 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">
1905
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<td class="diff-line-num new_line" data-linenumber="1145" 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">
1145
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<pre style="margin: 0;"> <span id="LC1145" class="line" lang="diff"> else if (res == aa_atob['B']) {</span>
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<td class="diff-line-num old_line" data-linenumber="1906" 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">
1906
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<td class="diff-line-num new_line" data-linenumber="1146" 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">
1146
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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="LC1146" class="line" lang="diff"> if (frequency[aa_atob['D']] != 0.0) { /* try to protect div by zero */</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1916" 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="1156" 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">@@ -1916,7 +1156,7 @@</td>
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<td class="diff-line-num old_line" data-linenumber="1916" 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">
1916
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<td class="diff-line-num new_line" data-linenumber="1156" 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">
1156
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<pre style="margin: 0;"> <span id="LC1156" class="line" lang="diff"> (part_N * seq_weight[seq]) / frequency[aa_atob['N']];</span>
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<td class="diff-line-num old_line" data-linenumber="1917" 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">
1917
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<td class="diff-line-num new_line" data-linenumber="1157" 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">
1157
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<pre style="margin: 0;"> <span id="LC1157" class="line" lang="diff"> total +=</span>
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<td class="diff-line-num old_line" data-linenumber="1918" 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">
1918
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<td class="diff-line-num new_line" data-linenumber="1158" 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">
1158
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<pre style="margin: 0;"> <span id="LC1158" class="line" lang="diff"> (part_N * seq_weight[seq]) / frequency[aa_atob['N']];</span>
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<td class="diff-line-num old old_line" data-linenumber="1919" 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">
1919
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<td class="diff-line-num new_line old" data-linenumber="1159" 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="LC1919" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1<span class="idiff left right">568,13 +1571,13 @@</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1159" 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">
1159
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<pre style="margin: 0;">+<span id="LC1159" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1<span class="idiff left right">416,13 +1419,13 @@ static void basic_matrix_construction(bl</span></span></span>
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1920
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1160
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<pre style="margin: 0;"> <span id="LC1160" class="line" lang="diff"> /* otherwise, if it is Z, partition Z between E and Q */</span>
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<td class="diff-line-num old_line" data-linenumber="1921" 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">
1921
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<td class="diff-line-num new_line" data-linenumber="1161" 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">
1161
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<pre style="margin: 0;"> <span id="LC1161" class="line" lang="diff"> else if (res == aa_atob['Z']) {</span>
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<td class="diff-line-num old_line" data-linenumber="1922" 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">
1922
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<td class="diff-line-num new_line" data-linenumber="1162" 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">
1162
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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="LC1162" class="line" lang="diff"> if (frequency[aa_atob['E']] != 0.0) { /* try to protect div by zero */</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1932" 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="1172" 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">@@ -1932,7 +1172,7 @@</td>
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<td class="diff-line-num old_line" data-linenumber="1932" 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">
1932
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<td class="diff-line-num new_line" data-linenumber="1172" 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">
1172
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<pre style="margin: 0;"> <span id="LC1172" class="line" lang="diff"> (part_Q * seq_weight[seq]) / frequency[aa_atob['Q']];</span>
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<td class="diff-line-num old_line" data-linenumber="1933" 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">
1933
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<td class="diff-line-num new_line" data-linenumber="1173" 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">
1173
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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="LC1173" class="line" lang="diff"> total +=</span>
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<td class="diff-line-num old_line" data-linenumber="1934" 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">
1934
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<td class="diff-line-num new_line" data-linenumber="1174" 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">
1174
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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="LC1174" class="line" lang="diff"> (part_Q * seq_weight[seq]) / frequency[aa_atob['Q']];</span>
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<td class="diff-line-num old old_line" data-linenumber="1935" 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">
1935
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<td class="diff-line-num new_line old" data-linenumber="1175" 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="LC1935" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1<span class="idiff left right">602,7 +1605,7 @@</span></span></span>
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<td class="diff-line-num new old_line" data-linenumber="1936" 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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<td class="diff-line-num new new_line" data-linenumber="1175" 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">
1175
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<pre style="margin: 0;">+<span id="LC1175" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1<span class="idiff left right">450,7 +1453,7 @@ static void basic_matrix_construction(bl</span></span></span>
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<td class="diff-line-num old_line" data-linenumber="1936" 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">
1936
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<td class="diff-line-num new_line" data-linenumber="1176" 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">
1176
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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="LC1176" class="line" lang="diff"> }</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1937" 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">
1937
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<td class="diff-line-num new_line" data-linenumber="1177" 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">
1177
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<pre style="margin: 0;"> <span id="LC1177" class="line" lang="diff"> </span>
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<td class="diff-line-num old_line" data-linenumber="1938" 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">
1938
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<td class="diff-line-num new_line" data-linenumber="1178" 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">
1178
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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="LC1178" class="line" lang="diff"> /* fill in the matrix for B, Z, X, gap, stop and non */</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1941" 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="1181" 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">@@ -1941,7 +1181,7 @@</td>
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<td class="diff-line-num old_line" data-linenumber="1941" 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">
1941
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<td class="diff-line-num new_line" data-linenumber="1181" 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">
1181
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<pre style="margin: 0;"> <span id="LC1181" class="line" lang="diff"> (part_D * matrix->weights[aa_atob['D']][col] +</span>
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<td class="diff-line-num old_line" data-linenumber="1942" 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">
1942
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<td class="diff-line-num new_line" data-linenumber="1182" 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">
1182
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<pre style="margin: 0;"> <span id="LC1182" class="line" lang="diff"> part_N * matrix->weights[aa_atob['N']][col]);</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1943" 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">
1943
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<td class="diff-line-num new_line" data-linenumber="1183" 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">
1183
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<pre style="margin: 0;"> <span id="LC1183" class="line" lang="diff"> matrix->weights[aa_atob['Z']][col] =</span>
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<td class="diff-line-num old old_line" data-linenumber="1944" 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">
1944
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<td class="diff-line-num new_line old" data-linenumber="1184" 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="LC1944" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1<span class="idiff left right">637,7 +1640,7 @@</span></span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1945" 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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<td class="diff-line-num new new_line" data-linenumber="1184" 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">
1184
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<pre style="margin: 0;">+<span id="LC1184" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1<span class="idiff left right">485,7 +1488,7 @@ get_consensus (Matrix* matrix)</span></span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1945" 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">
1945
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<td class="diff-line-num new_line" data-linenumber="1185" 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">
1185
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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="LC1185" class="line" lang="diff"> int pos;</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1946" 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">
1946
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<td class="diff-line-num new_line" data-linenumber="1186" 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">
1186
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<pre style="margin: 0;"> <span id="LC1186" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1947" 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">
1947
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<td class="diff-line-num new_line" data-linenumber="1187" 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">
1187
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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="LC1187" class="line" lang="diff"> seq = (Sequence *) malloc (sizeof (Sequence));</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1950" 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="1190" 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">@@ -1950,7 +1190,7 @@</td>
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<td class="diff-line-num old_line" data-linenumber="1950" 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">
1950
</td>
<td class="diff-line-num new_line" data-linenumber="1190" 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">
1190
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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="LC1190" class="line" lang="diff"> strcpy (seq->name, "CONSENSUS");</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1951" 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">
1951
</td>
<td class="diff-line-num new_line" data-linenumber="1191" 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">
1191
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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="LC1191" class="line" lang="diff"> seq->info[0] = '\0';</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1952" 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">
1952
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<td class="diff-line-num new_line" data-linenumber="1192" 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">
1192
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1192" class="line" lang="diff"> seq->position = 0;</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1953" 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">
1953
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<td class="diff-line-num new_line old" data-linenumber="1193" 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="LC1953" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1<span class="idiff left right">647,7 +1650,7 @@</span></span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1954" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="1193" 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">
1193
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<pre style="margin: 0;">+<span id="LC1193" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1<span class="idiff left right">495,7 +1498,7 @@ get_consensus (Matrix* matrix)</span></span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1954" 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">
1954
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<td class="diff-line-num new_line" data-linenumber="1194" 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">
1194
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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="LC1194" class="line" lang="diff"> for (pos = 0; pos < matrix->width; pos++) {</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1955" 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">
1955
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<td class="diff-line-num new_line" data-linenumber="1195" 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">
1195
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1195" class="line" lang="diff"> res = find_max_aa_in_pos (matrix, pos);</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1956" 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">
1956
</td>
<td class="diff-line-num new_line" data-linenumber="1196" 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">
1196
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1196" class="line" lang="diff"> seq->sequence[pos] = res;</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1959" 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="1199" 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">@@ -1959,7 +1199,7 @@</td>
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<td class="diff-line-num old_line" data-linenumber="1959" 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">
1959
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<td class="diff-line-num new_line" data-linenumber="1199" 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">
1199
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<pre style="margin: 0;"> <span id="LC1199" class="line" lang="diff"> }</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1960" 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">
1960
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<td class="diff-line-num new_line" data-linenumber="1200" 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">
1200
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1200" class="line" lang="diff"> return seq;</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1961" 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">
1961
</td>
<td class="diff-line-num new_line" data-linenumber="1201" 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">
1201
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1201" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1962" 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">
1962
</td>
<td class="diff-line-num new_line old" data-linenumber="1202" 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">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1962" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1<span class="idiff left right">709,7 +1712,7 @@</span></span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1963" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="1202" 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">
1202
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1202" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1<span class="idiff left right">557,7 +1560,7 @@ cumulative_prob (double col[MATRIX_AA_WI</span></span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1963" 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">
1963
</td>
<td class="diff-line-num new_line" data-linenumber="1203" 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">
1203
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1203" class="line" lang="diff"> {</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1964" 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">
1964
</td>
<td class="diff-line-num new_line" data-linenumber="1204" 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">
1204
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1204" class="line" lang="diff"> int i;</span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1965" 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">
1965
</td>
<td class="diff-line-num new_line" data-linenumber="1205" 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">
1205
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1205" class="line" lang="diff"> double index;</span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1968" 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="1208" 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">@@ -1968,7 +1208,7 @@</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1968" 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">
1968
</td>
<td class="diff-line-num new_line" data-linenumber="1208" 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">
1208
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1208" class="line" lang="diff"> </span>
</pre>
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</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1969" 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">
1969
</td>
<td class="diff-line-num new_line" data-linenumber="1209" 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">
1209
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1209" class="line" lang="diff"> index = 0;</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1970" 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">
1970
</td>
<td class="diff-line-num new_line" data-linenumber="1210" 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">
1210
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1210" class="line" lang="diff"> </span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="1971" 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">
1971
</td>
<td class="diff-line-num new_line old" data-linenumber="1211" 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">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1971" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1<span class="idiff left right">721,7 +1724,7 @@</span></span></span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="1972" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="1211" 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">
1211
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1211" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1<span class="idiff left right">569,7 +1572,7 @@ cumulative_prob (double col[MATRIX_AA_WI</span></span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1972" 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">
1972
</td>
<td class="diff-line-num new_line" data-linenumber="1212" 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">
1212
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1212" class="line" lang="diff"> }</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1973" 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">
1973
</td>
<td class="diff-line-num new_line" data-linenumber="1213" 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">
1213
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1213" class="line" lang="diff"> </span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1974" 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">
1974
</td>
<td class="diff-line-num new_line" data-linenumber="1214" 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">
1214
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1214" class="line" lang="diff"> </span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1977" 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="1217" 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">@@ -1977,7 +1217,7 @@</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1977" 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">
1977
</td>
<td class="diff-line-num new_line" data-linenumber="1217" 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">
1217
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1217" class="line" lang="diff"> MATRIX_AA_WIDTH states ranging from 0 to 1 */</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1978" 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">
1978
</td>
<td class="diff-line-num new_line" data-linenumber="1218" 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">
1218
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1218" class="line" lang="diff"> int</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1979" 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">
1979
</td>
<td class="diff-line-num new_line" data-linenumber="1219" 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">
1219
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1219" class="line" lang="diff"> random_pick (double* P)</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="1980" 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">
1980
</td>
<td class="diff-line-num new_line old" data-linenumber="1220" 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">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1980" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1<span class="idiff left right">732,13 +1735,13 @@</span></span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="1981" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="1220" 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">
1220
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1220" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1<span class="idiff left right">580,13 +1583,13 @@ random_pick (double* P)</span></span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1981" 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">
1981
</td>
<td class="diff-line-num new_line" data-linenumber="1221" 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">
1221
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1221" class="line" lang="diff"> /* printf ("random pick: "); */</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1982" 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">
1982
</td>
<td class="diff-line-num new_line" data-linenumber="1222" 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">
1222
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1222" class="line" lang="diff"> random = (double) rand() / (double) RAND_MAX * 100 ;</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1983" 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">
1983
</td>
<td class="diff-line-num new_line" data-linenumber="1223" 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">
1223
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1223" class="line" lang="diff"> while (random > P[i] && i < MATRIX_AA_WIDTH) {</span>
</pre>
</td>
</tr>
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1993" 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="1233" 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">@@ -1993,7 +1233,7 @@</td>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1993" 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">
1993
</td>
<td class="diff-line-num new_line" data-linenumber="1233" 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">
1233
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1233" class="line" lang="diff"> return (i);</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1994" 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">
1994
</td>
<td class="diff-line-num new_line" data-linenumber="1234" 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">
1234
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1234" class="line" lang="diff"> }</span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1995" 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">
1995
</td>
<td class="diff-line-num new_line" data-linenumber="1235" 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">
1235
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1235" class="line" lang="diff"> }</span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="1996" 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">
1996
</td>
<td class="diff-line-num new_line old" data-linenumber="1236" 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">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1996" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1<span class="idiff left right">924,21 +1927,21 @@</span></span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="1997" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="1236" 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">
1236
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1236" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1<span class="idiff left right">772,21 +1775,21 @@ int scores[24][24];</span></span></span>
</pre>
</td>
</tr>
<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="1997" 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">
1997
</td>
<td class="diff-line-num new_line" data-linenumber="1237" 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">
1237
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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="LC1237" class="line" lang="diff"> </span>
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<td class="diff-line-num old_line" data-linenumber="1998" 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">
1998
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<td class="diff-line-num new_line" data-linenumber="1238" 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">
1238
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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="LC1238" class="line" lang="diff"> /*=====================================================================*/</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1999" 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">
1999
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<td class="diff-line-num new_line" data-linenumber="1239" 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">
1239
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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="LC1239" class="line" lang="diff"> /* This routine initializes the blimps global variables</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2019" 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="1259" 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">@@ -2019,7 +1259,7 @@</td>
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<td class="diff-line-num old_line" data-linenumber="2019" 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">
2019
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<td class="diff-line-num new_line" data-linenumber="1259" 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">
1259
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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="LC1259" class="line" lang="diff"> RTot = LOCAL_QIJ_RTOT;</span>
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<td class="diff-line-num old_line" data-linenumber="2020" 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">
2020
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<td class="diff-line-num new_line" data-linenumber="1260" 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">
1260
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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="LC1260" class="line" lang="diff"> } /* end of frq_qij */</span>
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<td class="diff-line-num old_line" data-linenumber="2021" 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">
2021
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<td class="diff-line-num new_line" data-linenumber="1261" 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">
1261
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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="LC1261" class="line" lang="diff"> </span>
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<td class="diff-line-num old old_line" data-linenumber="2022" 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">
2022
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<td class="diff-line-num new_line old" data-linenumber="1262" 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="LC2022" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1<span class="idiff left right">995,7 +1998,7 @@</span></span></span>
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<td class="diff-line-num new old_line" data-linenumber="2023" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="1262" 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">
1262
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<pre style="margin: 0;">+<span id="LC1262" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1<span class="idiff left right">843,7 +1846,7 @@ void pseudo_diric(struct working* col, s</span></span></span>
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<td class="diff-line-num old_line" data-linenumber="2023" 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">
2023
</td>
<td class="diff-line-num new_line" data-linenumber="1263" 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">
1263
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<pre style="margin: 0;"> <span id="LC1263" class="line" lang="diff"> {</span>
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<td class="diff-line-num old_line" data-linenumber="2024" 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">
2024
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<td class="diff-line-num new_line" data-linenumber="1264" 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">
1264
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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="LC1264" class="line" lang="diff"> col->probj[j] = log(diric->q[j]) + col->probn[j] - denom;</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2025" 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">
2025
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<td class="diff-line-num new_line" data-linenumber="1265" 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">
1265
</td>
<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1265" class="line" lang="diff"> /* printf("j=%d probn[j]=%f probj[j]=%f\n",</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2028" 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="1268" 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">@@ -2028,7 +1268,7 @@</td>
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<td class="diff-line-num old_line" data-linenumber="2028" 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">
2028
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<td class="diff-line-num new_line" data-linenumber="1268" 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">
1268
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<pre style="margin: 0;"> <span id="LC1268" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2029" 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">
2029
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<td class="diff-line-num new_line" data-linenumber="1269" 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">
1269
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<pre style="margin: 0;"> <span id="LC1269" class="line" lang="diff"> }</span>
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<td class="diff-line-num old_line" data-linenumber="2030" 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">
2030
</td>
<td class="diff-line-num new_line" data-linenumber="1270" 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">
1270
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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="LC1270" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2031" 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">
2031
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<td class="diff-line-num new_line old" data-linenumber="1271" 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="LC2031" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">2004,31 +2007,31 @@</span></span></span>
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<td class="diff-line-num new old_line" data-linenumber="2032" 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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<td class="diff-line-num new new_line" data-linenumber="1271" 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">
1271
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<pre style="margin: 0;">+<span id="LC1271" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">1852,31 +1855,31 @@ void pseudo_diric(struct working* col, s</span></span></span>
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<td class="diff-line-num old_line" data-linenumber="2032" 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">
2032
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<td class="diff-line-num new_line" data-linenumber="1272" 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">
1272
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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="LC1272" class="line" lang="diff"> for (aa = 1; aa < AAS; aa++)</span>
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<td class="diff-line-num old_line" data-linenumber="2033" 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">
2033
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<td class="diff-line-num new_line" data-linenumber="1273" 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">
1273
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<pre style="margin: 0;"> <span id="LC1273" class="line" lang="diff"> {</span>
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<td class="diff-line-num old_line" data-linenumber="2034" 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">
2034
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<td class="diff-line-num new_line" data-linenumber="1274" 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">
1274
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<pre style="margin: 0;"> <span id="LC1274" class="line" lang="diff"> for (j = 0; j < diric->ncomp; j++) {</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2067" 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="1307" 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">@@ -2067,7 +1307,7 @@</td>
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2067
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<td class="diff-line-num new_line" data-linenumber="1307" 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">
1307
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<pre style="margin: 0;"> <span id="LC1307" class="line" lang="diff"> double min;</span>
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2068
</td>
<td class="diff-line-num new_line" data-linenumber="1308" 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">
1308
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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="LC1308" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2069" 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">
2069
</td>
<td class="diff-line-num new_line" data-linenumber="1309" 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">
1309
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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="LC1309" class="line" lang="diff"> min = 10000;</span>
</pre>
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2070
</td>
<td class="diff-line-num new_line old" data-linenumber="1310" 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="LC2070" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">2042,10 +2045,10 @@</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1310" 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">
1310
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<pre style="margin: 0;">+<span id="LC1310" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">1890,10 +1893,10 @@ find_min_aa_in_col_reg (struct working*</span></span></span>
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2071
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<td class="diff-line-num new_line" data-linenumber="1311" 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">
1311
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<pre style="margin: 0;"> <span id="LC1311" class="line" lang="diff"> return min_aa;</span>
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<td class="diff-line-num old_line" data-linenumber="2072" 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">
2072
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<td class="diff-line-num new_line" data-linenumber="1312" 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">
1312
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<pre style="margin: 0;"> <span id="LC1312" class="line" lang="diff"> }</span>
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<td class="diff-line-num old_line" data-linenumber="2073" 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">
2073
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<td class="diff-line-num new_line" data-linenumber="1313" 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">
1313
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<pre style="margin: 0;"> <span id="LC1313" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2080" 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="1320" 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">@@ -2080,7 +1320,7 @@</td>
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2080
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<td class="diff-line-num new_line" data-linenumber="1320" 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">
1320
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<pre style="margin: 0;"> <span id="LC1320" class="line" lang="diff"> double min;</span>
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<td class="diff-line-num old_line" data-linenumber="2081" 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">
2081
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<td class="diff-line-num new_line" data-linenumber="1321" 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">
1321
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<pre style="margin: 0;"> <span id="LC1321" class="line" lang="diff"> </span>
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<td class="diff-line-num old_line" data-linenumber="2082" 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">
2082
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<td class="diff-line-num new_line" data-linenumber="1322" 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">
1322
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<pre style="margin: 0;"> <span id="LC1322" class="line" lang="diff"> min = 1000;</span>
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<td class="diff-line-num old old_line" data-linenumber="2083" 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">
2083
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<td class="diff-line-num new_line old" data-linenumber="1323" 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="LC2083" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">2073,7 +2076,7 @@</span></span></span>
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<td class="diff-line-num new old_line" data-linenumber="2084" 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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<td class="diff-line-num new new_line" data-linenumber="1323" 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">
1323
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<pre style="margin: 0;">+<span id="LC1323" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">1921,7 +1924,7 @@ struct dirichlet *load_diri_file (char f</span></span></span>
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<td class="diff-line-num old_line" data-linenumber="2084" 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">
2084
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<td class="diff-line-num new_line" data-linenumber="1324" 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">
1324
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<pre style="margin: 0;"> <span id="LC1324" class="line" lang="diff"> struct dirichlet *diric;</span>
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<td class="diff-line-num old_line" data-linenumber="2085" 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">
2085
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<td class="diff-line-num new_line" data-linenumber="1325" 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">
1325
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<pre style="margin: 0;"> <span id="LC1325" class="line" lang="diff"> double denom;</span>
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<td class="diff-line-num old_line" data-linenumber="2086" 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">
2086
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1326
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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="LC1326" class="line" lang="diff"> double background_frequency[21];</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2089" 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="1329" 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">@@ -2089,7 +1329,7 @@</td>
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<td class="diff-line-num old_line" data-linenumber="2089" 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">
2089
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<td class="diff-line-num new_line" data-linenumber="1329" 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">
1329
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<pre style="margin: 0;"> <span id="LC1329" class="line" lang="diff"> if ((fin = fopen (filename, "r")) == NULL) {</span>
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<td class="diff-line-num old_line" data-linenumber="2090" 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">
2090
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<td class="diff-line-num new_line" data-linenumber="1330" 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">
1330
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<pre style="margin: 0;"> <span id="LC1330" class="line" lang="diff"> fprintf (errorfp, "Cannot open dirichlet file %s\n", filename);</span>
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<td class="diff-line-num old_line" data-linenumber="2091" 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">
2091
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<td class="diff-line-num new_line" data-linenumber="1331" 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">
1331
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<pre style="margin: 0;"> <span id="LC1331" class="line" lang="diff"> exit (-1);</span>
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<td class="diff-line-num old old_line" data-linenumber="2092" 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">
2092
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<td class="diff-line-num new_line old" data-linenumber="1332" 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="LC2092" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">2124,7 +2127,7 @@</span></span></span>
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<td class="diff-line-num new old_line" data-linenumber="2093" 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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<td class="diff-line-num new new_line" data-linenumber="1332" 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">
1332
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<pre style="margin: 0;">+<span id="LC1332" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">1972,7 +1975,7 @@ struct dirichlet *load_diri_file (char f</span></span></span>
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<td class="diff-line-num old_line" data-linenumber="2093" 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">
2093
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<td class="diff-line-num new_line" data-linenumber="1333" 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">
1333
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<pre style="margin: 0;"> <span id="LC1333" class="line" lang="diff"> for (aa = 1; aa < AAS; aa++) {</span>
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<td class="diff-line-num old_line" data-linenumber="2094" 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">
2094
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<td class="diff-line-num new_line" data-linenumber="1334" 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">
1334
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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="LC1334" class="line" lang="diff"> denom = 0.0;</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2095" 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">
2095
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<td class="diff-line-num new_line" data-linenumber="1335" 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">
1335
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<pre style="margin: 0;"> <span id="LC1335" class="line" lang="diff"> for (i = 0; i < numc; i++) {</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2098" 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="1338" 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">@@ -2098,7 +1338,7 @@</td>
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2098
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1338
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<pre style="margin: 0;"> <span id="LC1338" class="line" lang="diff"> diric->altot[i]);</span>
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<td class="diff-line-num old_line" data-linenumber="2099" 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">
2099
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<td class="diff-line-num new_line" data-linenumber="1339" 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">
1339
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<pre style="margin: 0;"> <span id="LC1339" class="line" lang="diff"> }</span>
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<td class="diff-line-num old_line" data-linenumber="2100" 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">
2100
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<td class="diff-line-num new_line" data-linenumber="1340" 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">
1340
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<pre style="margin: 0;"> <span id="LC1340" class="line" lang="diff"> background_frequency[aa] = denom;</span>
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2101
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<pre style="margin: 0;">-<span id="LC2101" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">2132,7 +2135,7 @@</span></span></span>
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1341
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<pre style="margin: 0;">+<span id="LC1341" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">1980,7 +1983,7 @@ struct dirichlet *load_diri_file (char f</span></span></span>
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2102
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1342
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<pre style="margin: 0;"> <span id="LC1342" class="line" lang="diff"> for (i =0; i < numc; i++) {</span>
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2103
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1343
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<pre style="margin: 0;"> <span id="LC1343" class="line" lang="diff"> /* printf ("Component %d ratio of aa relative to background \n", i); */</span>
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2104
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1344
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<pre style="margin: 0;"> <span id="LC1344" class="line" lang="diff"> for (aa = 1; aa < AAS; aa++) {</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2107" 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="1347" 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">@@ -2107,7 +1347,7 @@</td>
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2107
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1347
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<pre style="margin: 0;"> <span id="LC1347" class="line" lang="diff"> diric->alpha[i][aa]/(diric->altot[i] * background_frequency[aa]);</span>
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2108
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1348
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<pre style="margin: 0;"> <span id="LC1348" class="line" lang="diff"> }</span>
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2109
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1349
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<pre style="margin: 0;"> <span id="LC1349" class="line" lang="diff"> }</span>
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2110
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<pre style="margin: 0;">-<span id="LC2110" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">2142,7 +2145,7 @@</span></span></span>
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1350
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<pre style="margin: 0;">+<span id="LC1350" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">1990,7 +1993,7 @@ struct dirichlet *load_diri_file (char f</span></span></span>
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2111
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1351
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<pre style="margin: 0;"> <span id="LC1351" class="line" lang="diff"> </span>
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2112
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1352
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<pre style="margin: 0;"> <span id="LC1352" class="line" lang="diff"> </span>
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2113
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1353
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<pre style="margin: 0;"> <span id="LC1353" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2116" 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="1356" 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">@@ -2116,7 +1356,7 @@</td>
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2116
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1356
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<pre style="margin: 0;"> <span id="LC1356" class="line" lang="diff"> cutoff_target_freq (double* cutoff_freq, int original_aa, struct float_qij *qij)</span>
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2117
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1357
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<pre style="margin: 0;"> <span id="LC1357" class="line" lang="diff"> {</span>
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2118
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1358
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<pre style="margin: 0;"> <span id="LC1358" class="line" lang="diff"> </span>
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2119
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<pre style="margin: 0;">-<span id="LC2119" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2<span class="idiff left right">160,8 +2163,9 @@</span></span></span>
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1359
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<pre style="margin: 0;">+<span id="LC1359" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2<span class="idiff left right">008,8 +2011,9 @@ cutoff_target_freq (double* cutoff_freq,</span></span></span>
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2120
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1360
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<pre style="margin: 0;"> <span id="LC1360" class="line" lang="diff"> void init_frq_qij()</span>
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<td class="diff-line-num old_line" data-linenumber="2121" 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">
2121
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1361
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<pre style="margin: 0;"> <span id="LC1361" class="line" lang="diff"> {</span>
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2122
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1362
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<pre style="margin: 0;"> <span id="LC1362" class="line" lang="diff"> FILE *fqij;</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2128" 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="1368" 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">@@ -2128,7 +1368,7 @@</td>
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2128
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1368
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<pre style="margin: 0;"> <span id="LC1368" class="line" lang="diff"> /*"/howard/servers/blimps/blimps";*/ /* getenv("BLIMPS_DIR"); */</span>
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2129
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<td class="diff-line-num new_line" data-linenumber="1369" 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">
1369
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<pre style="margin: 0;"> <span id="LC1369" class="line" lang="diff"> if (blimps_dir != NULL)</span>
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2130
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1370
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<pre style="margin: 0;"> <span id="LC1370" class="line" lang="diff"> {</span>
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2131
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<td class="diff-line-num new_line old" data-linenumber="1371" 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="LC2131" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2<span class="idiff left right">177,6 +2181,13 @@</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="1371" 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">
1371
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<pre style="margin: 0;">+<span id="LC1371" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2<span class="idiff left right">025,6 +2029,13 @@ void init_frq_qij()</span></span></span>
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2132
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1372
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<pre style="margin: 0;"> <span id="LC1372" class="line" lang="diff"> Qij = NULL;</span>
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<td class="diff-line-num old_line" data-linenumber="2133" 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">
2133
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1373
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<pre style="margin: 0;"> <span id="LC1373" class="line" lang="diff"> if ( (fqij=fopen(qijname, "r")) != NULL)</span>
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<td class="diff-line-num old_line" data-linenumber="2134" 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">
2134
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1374
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<pre style="margin: 0;"> <span id="LC1374" class="line" lang="diff"> { Qij = load_qij(fqij); fclose(fqij); }</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2142" 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="1382" 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">@@ -2142,7 +1382,7 @@</td>
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2142
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1382
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<pre style="margin: 0;"> <span id="LC1382" class="line" lang="diff"> RTot = LOCAL_QIJ_RTOT;</span>
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2143
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1383
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<pre style="margin: 0;"> <span id="LC1383" class="line" lang="diff"> } /* end of frq_qij */</span>
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2144
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1384
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<pre style="margin: 0;"> <span id="LC1384" class="line" lang="diff"> </span>
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2145
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<pre style="margin: 0;">-<span id="LC2145" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2<span class="idiff left right">195,7 +2206,7 @@</span></span></span>
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1385
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<pre style="margin: 0;">+<span id="LC1385" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2<span class="idiff left right">043,7 +2054,7 @@ similarity_dependent_scale_0 (struct wor</span></span></span>
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2146
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1386
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<pre style="margin: 0;"> <span id="LC1386" class="line" lang="diff"> original_aa = max_aa; /* change to max aa 10/24/00 */</span>
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2147
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1387
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<pre style="margin: 0;"> <span id="LC1387" class="line" lang="diff"> </span>
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2148
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1388
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<pre style="margin: 0;"> <span id="LC1388" class="line" lang="diff"> n = 0;</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2151" 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="1391" 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">@@ -2151,7 +1391,7 @@</td>
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2151
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1391
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<pre style="margin: 0;"> <span id="LC1391" class="line" lang="diff"> for (aa = 1; aa <= 20 ; aa++) {</span>
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2152
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<td class="diff-line-num new_line" data-linenumber="1392" 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">
1392
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<pre style="margin: 0;"> <span id="LC1392" class="line" lang="diff"> if (col->cnt[aa] > 0.0) {</span>
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2153
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1393
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<pre style="margin: 0;"> <span id="LC1393" class="line" lang="diff"> n++;</span>
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2154
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<td class="diff-line-num new_line old" data-linenumber="1394" 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="LC2154" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2<span class="idiff left right">217,20 +2228,20 @@</span></span></span>
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1394
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<pre style="margin: 0;">+<span id="LC1394" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2<span class="idiff left right">065,20 +2076,20 @@ construct_rank_matrix (int rank_matrix[A</span></span></span>
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2155
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1395
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<pre style="margin: 0;"> <span id="LC1395" class="line" lang="diff"> struct float_qij* rank_Qij;</span>
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2156
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1396
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<pre style="margin: 0;"> <span id="LC1396" class="line" lang="diff"> FILE* qijfp;</span>
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2157
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1397
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<pre style="margin: 0;"> <span id="LC1397" class="line" lang="diff"> int aa;</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1417" 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">@@ -2177,7 +1417,7 @@</td>
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2177
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1417
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<pre style="margin: 0;"> <span id="LC1417" class="line" lang="diff"> </span>
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2178
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1418
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<pre style="margin: 0;"> <span id="LC1418" class="line" lang="diff"> for (original_aa = 0; original_aa < AAS; original_aa++) {</span>
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2179
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1419
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<pre style="margin: 0;"> <span id="LC1419" class="line" lang="diff"> copy_values_to_ranklist (aalist, original_aa, rank_Qij);</span>
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2180
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<td class="diff-line-num new_line old" data-linenumber="1420" 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="LC2180" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2<span class="idiff left right">248,14 +2259,14 @@</span></span></span>
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1420
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<pre style="margin: 0;">+<span id="LC1420" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2<span class="idiff left right">096,14 +2107,14 @@ assign_ranks (int rank_matrix[AAS][AAS],</span></span></span>
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2181
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1421
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<pre style="margin: 0;"> <span id="LC1421" class="line" lang="diff"> </span>
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<td class="diff-line-num old_line" data-linenumber="2182" 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">
2182
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1422
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<pre style="margin: 0;"> <span id="LC1422" class="line" lang="diff"> for (rank = 0; rank < AAS; rank++) {</span>
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2183
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1423
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<pre style="margin: 0;"> <span id="LC1423" class="line" lang="diff"> aa = aalist[rank].aa;</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2194" 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="1434" 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">@@ -2194,7 +1434,7 @@</td>
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2194
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1434
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<pre style="margin: 0;"> <span id="LC1434" class="line" lang="diff"> struct float_qij* rankQij) {</span>
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2195
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1435
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<pre style="margin: 0;"> <span id="LC1435" class="line" lang="diff"> </span>
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2196
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1436
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<pre style="margin: 0;"> <span id="LC1436" class="line" lang="diff"> int aa;</span>
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2197
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<pre style="margin: 0;">-<span id="LC2197" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2<span class="idiff left right">263,8 +2274,8 @@</span></span></span>
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1437
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<pre style="margin: 0;">+<span id="LC1437" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2<span class="idiff left right">111,8 +2122,8 @@ copy_values_to_ranklist (struct rank_cel</span></span></span>
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2198
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1438
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<pre style="margin: 0;"> <span id="LC1438" class="line" lang="diff"> /* 01/03/00 rankQij has -1 for gap, which will mess up</span>
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2199
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1439
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<pre style="margin: 0;"> <span id="LC1439" class="line" lang="diff"> ranks. Assign it a really negative value so it will have</span>
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2200
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1440
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<pre style="margin: 0;"> <span id="LC1440" class="line" lang="diff"> the lowest rank */</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1445" 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">@@ -2205,7 +1445,7 @@</td>
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2205
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1445
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<pre style="margin: 0;"> <span id="LC1445" class="line" lang="diff"> aalist[0].value = -50;</span>
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2206
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1446
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<pre style="margin: 0;"> <span id="LC1446" class="line" lang="diff"> </span>
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2207
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1447
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<pre style="margin: 0;"> <span id="LC1447" class="line" lang="diff"> for (aa = 1; aa < AAS; aa++) {</span>
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2208
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<pre style="margin: 0;">-<span id="LC2208" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2<span class="idiff left right">332,7 +2343,7 @@</span></span></span>
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1448
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<pre style="margin: 0;">+<span id="LC1448" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2<span class="idiff left right">180,7 +2191,7 @@ number_of_real_aminoacids (Block* block,</span></span></span>
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2209
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1449
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<pre style="margin: 0;"> <span id="LC1449" class="line" lang="diff"> </span>
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2210
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1450
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<pre style="margin: 0;"> <span id="LC1450" class="line" lang="diff"> count = 0;</span>
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2211
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<td class="diff-line-num new_line" data-linenumber="1451" 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">
1451
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<pre style="margin: 0;"> <span id="LC1451" class="line" lang="diff"> for (seq = 0; seq < block->num_sequences; seq++) {</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2214" 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="1454" 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">@@ -2214,7 +1454,7 @@</td>
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2214
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1454
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<pre style="margin: 0;"> <span id="LC1454" class="line" lang="diff"> block->residues[seq][pos] <=20) {</span>
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<td class="diff-line-num old_line" data-linenumber="2215" 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">
2215
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1455
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<pre style="margin: 0;"> <span id="LC1455" class="line" lang="diff"> count++;</span>
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<td class="diff-line-num old_line" data-linenumber="2216" 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">
2216
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<td class="diff-line-num new_line" data-linenumber="1456" 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">
1456
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<pre style="margin: 0;"> <span id="LC1456" class="line" lang="diff"> }</span>
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<td class="diff-line-num old old_line" data-linenumber="2217" 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">
2217
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<td class="diff-line-num new_line old" data-linenumber="1457" 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="LC2217" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2<span class="idiff left right">341,7 +2352,7 @@</span></span></span>
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<td class="diff-line-num new old_line" data-linenumber="2218" 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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<td class="diff-line-num new new_line" data-linenumber="1457" 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">
1457
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<pre style="margin: 0;">+<span id="LC1457" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2<span class="idiff left right">189,7 +2200,7 @@ number_of_real_aminoacids (Block* block,</span></span></span>
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<td class="diff-line-num old_line" data-linenumber="2218" 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">
2218
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<td class="diff-line-num new_line" data-linenumber="1458" 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">
1458
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<pre style="margin: 0;"> <span id="LC1458" class="line" lang="diff"> } /* end of number_of_real_aminoacids */</span>
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<td class="diff-line-num old_line" data-linenumber="2219" 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">
2219
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<td class="diff-line-num new_line" data-linenumber="1459" 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">
1459
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<pre style="margin: 0;"> <span id="LC1459" class="line" lang="diff"> </span>
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<td class="diff-line-num old_line" data-linenumber="2220" 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">
2220
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1460
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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="LC1460" class="line" lang="diff"> double*</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2223" 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="1463" 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">@@ -2223,7 +1463,7 @@</td>
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<td class="diff-line-num old_line" data-linenumber="2223" 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">
2223
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1463
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<pre style="margin: 0;"> <span id="LC1463" class="line" lang="diff"> {</span>
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<td class="diff-line-num old_line" data-linenumber="2224" 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">
2224
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<td class="diff-line-num new_line" data-linenumber="1464" 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">
1464
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<pre style="margin: 0;"> <span id="LC1464" class="line" lang="diff"> double* fraction_stored;</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2225" 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">
2225
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<td class="diff-line-num new_line" data-linenumber="1465" 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">
1465
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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="LC1465" class="line" lang="diff"> double percent_obsaa_div_seq;</span>
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<td class="diff-line-num old old_line" data-linenumber="2226" 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">
2226
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<pre style="margin: 0;">-<span id="LC2226" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2<span class="idiff left right">371,15 +2382,15 @@</span></span></span>
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<td class="diff-line-num new old_line" data-linenumber="2227" 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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<td class="diff-line-num new new_line" data-linenumber="1466" 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">
1466
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<pre style="margin: 0;">+<span id="LC1466" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -2<span class="idiff left right">219,15 +2230,15 @@ calculate_basic_aa_stored (Block* block)</span></span></span>
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<td class="diff-line-num old_line" data-linenumber="2227" 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">
2227
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1467
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<pre style="margin: 0;"> <span id="LC1467" class="line" lang="diff"> }</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2228" 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">
2228
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1468
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<pre style="margin: 0;"> <span id="LC1468" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2229" 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">
2229
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1469
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<pre style="margin: 0;"> <span id="LC1469" class="line" lang="diff"> void</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2242" 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="1482" 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">@@ -2242,9 +1482,11 @@</td>
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2242
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1482
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<pre style="margin: 0;"> <span id="LC1482" class="line" lang="diff"> </span>
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<td class="diff-line-num old_line" data-linenumber="2243" 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">
2243
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1483
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<pre style="margin: 0;"> <span id="LC1483" class="line" lang="diff"> }</span>
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<td class="diff-line-num old_line" data-linenumber="2244" 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">
2244
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1484
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<pre style="margin: 0;"> <span id="LC1484" class="line" lang="diff"> </span>
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2245
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<pre style="margin: 0;">-<span id="LC2245" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/Protdist.c</span></span>
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2246
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<pre style="margin: 0;">-<span id="LC2246" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/Protdist.c</span></span>
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2247
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<td class="diff-line-num new_line old" data-linenumber="1485" 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="LC2247" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -124,7 +124,7 @@</span></span>
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1485
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<pre style="margin: 0;">+<span id="LC1485" class="line" lang="diff"><span class="gh" style="color: #999;">Index: sift/src/Protdist.c</span></span>
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1486
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<pre style="margin: 0;">+<span id="LC1486" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1487" 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">
1487
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<pre style="margin: 0;">+<span id="LC1487" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- sift.orig/src/Protdist.c</span></span>
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1488
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<pre style="margin: 0;">+<span id="LC1488" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ sift/src/Protdist.c</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1489" 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">
1489
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<pre style="margin: 0;">+<span id="LC1489" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -124,7 +124,7 @@ seq_with_max_dist (struct score_pair* pa</span></span>
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2248
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1490
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<pre style="margin: 0;"> <span id="LC1490" class="line" lang="diff"> {</span>
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2249
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1491
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<pre style="margin: 0;"> <span id="LC1491" class="line" lang="diff"> double max_dist;</span>
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<td class="diff-line-num old_line" data-linenumber="2250" 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">
2250
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1492
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<pre style="margin: 0;"> <span id="LC1492" class="line" lang="diff"> int i;</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1495" 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">@@ -2253,8 +1495,10 @@</td>
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2253
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1495
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<pre style="margin: 0;"> <span id="LC1495" class="line" lang="diff"> </span>
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2254
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1496
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<pre style="margin: 0;"> <span id="LC1496" class="line" lang="diff"> max_dist = 0;</span>
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2255
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1497
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<pre style="margin: 0;"> <span id="LC1497" class="line" lang="diff"> </span>
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2256
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<pre style="margin: 0;">-<span id="LC2256" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/Psiblast.c</span></span>
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2257
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<pre style="margin: 0;">-<span id="LC2257" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/Psiblast.c</span></span>
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1498
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<pre style="margin: 0;">+<span id="LC1498" class="line" lang="diff"><span class="gh" style="color: #999;">Index: sift/src/Psiblast.c</span></span>
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1499
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<pre style="margin: 0;">+<span id="LC1499" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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1500
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<pre style="margin: 0;">+<span id="LC1500" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- sift.orig/src/Psiblast.c</span></span>
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1501
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<pre style="margin: 0;">+<span id="LC1501" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ sift/src/Psiblast.c</span></span>
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<pre style="margin: 0;"> <span id="LC1502" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,6 +1,6 @@</span></span>
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2259
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<pre style="margin: 0;"> <span id="LC1503" class="line" lang="diff"> /* (C) Copyright 2000, Fred Hutchinson Cancer Research Center */</span>
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<td class="diff-line-num old_line" data-linenumber="2260" 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="LC1504" class="line" lang="diff"> /* Use, modification or distribution of these programs is subject to */</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2263" 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="1507" 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">@@ -2263,15 +1507,7 @@</td>
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<pre style="margin: 0;"> <span id="LC1507" class="line" lang="diff"> </span>
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1508
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<pre style="margin: 0;"> <span id="LC1508" class="line" lang="diff"> #ifndef _PSIBLAST_C_</span>
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2265
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1509
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<pre style="margin: 0;"> <span id="LC1509" class="line" lang="diff"> #define _PSIBLAST_C_</span>
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<pre style="margin: 0;">-<span id="LC2266" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -9,6 +9,7 @@</span></span>
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2267
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<pre style="margin: 0;">-<span id="LC2267" class="line" lang="diff"> #include "Alignment.c" /* for the function read_psiblast_header_until_first*/</span>
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2268
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<pre style="margin: 0;">-<span id="LC2268" class="line" lang="diff"> #include "PN_convert.c"</span>
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2269
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<pre style="margin: 0;">-<span id="LC2269" class="line" lang="diff"> #include "stringhash.c"</span>
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2270
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<pre style="margin: 0;">-<span id="LC2270" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include <inttypes.h></span></span>
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2271
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<pre style="margin: 0;">-<span id="LC2271" class="line" lang="diff"> </span>
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2272
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<pre style="margin: 0;">-<span id="LC2272" class="line" lang="diff"> void process_sequence_line(Sequence* seq, char* buff);</span>
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2273
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<pre style="margin: 0;">-<span id="LC2273" class="line" lang="diff"> </span>
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2274
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<pre style="margin: 0;">-<span id="LC2274" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -18,7 +19,7 @@</span></span>
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1510
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<pre style="margin: 0;">+<span id="LC1510" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -20,7 +20,7 @@ read_psiblast_entry ( FILE* fp, char Buf</span></span>
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2275
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1511
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<pre style="margin: 0;"> <span id="LC1511" class="line" lang="diff"> /* passing first line in entry that begins with >seq_id in Buffer */</span>
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2276
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1512
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<pre style="margin: 0;"> <span id="LC1512" class="line" lang="diff"> Aligned_Pair* alignment, *new_alignment;</span>
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2277
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1513
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<pre style="margin: 0;"> <span id="LC1513" class="line" lang="diff"> Aligned_Pair * cursor;</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2280" 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="1516" 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">@@ -2280,7 +1516,7 @@</td>
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2280
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1516
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<pre style="margin: 0;"> <span id="LC1516" class="line" lang="diff"> alignment = initialize_Aligned_Pair (Buffer);</span>
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2281
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1517
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<pre style="margin: 0;"> <span id="LC1517" class="line" lang="diff"> cursor = alignment;</span>
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2282
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1518
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<pre style="margin: 0;"> <span id="LC1518" class="line" lang="diff"> </span>
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2283
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<pre style="margin: 0;">-<span id="LC2283" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -3<span class="idiff left right">3,14 +34,14 @@</span></span></span>
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1519
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<pre style="margin: 0;">+<span id="LC1519" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -3<span class="idiff left right">5,14 +35,14 @@ read_psiblast_entry ( FILE* fp, char Buf</span></span></span>
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2284
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1520
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<pre style="margin: 0;"> <span id="LC1520" class="line" lang="diff"> new_alignment =initialize_Aligned_Pair (Buffer);</span>
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2285
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1521
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<pre style="margin: 0;"> <span id="LC1521" class="line" lang="diff"> cursor->next = new_alignment;</span>
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2286
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1522
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<pre style="margin: 0;"> <span id="LC1522" class="line" lang="diff"> cursor = new_alignment;</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2297" 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="1533" 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">@@ -2297,7 +1533,7 @@</td>
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2297
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1533
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<pre style="margin: 0;"> <span id="LC1533" class="line" lang="diff"> {</span>
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2298
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1534
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<pre style="margin: 0;"> <span id="LC1534" class="line" lang="diff"> Aligned_Pair* alignment;</span>
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<td class="diff-line-num old_line" data-linenumber="2299" 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">
2299
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<td class="diff-line-num new_line" data-linenumber="1535" 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">
1535
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<pre style="margin: 0;"> <span id="LC1535" class="line" lang="diff"> char* stringptr;</span>
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2300
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<td class="diff-line-num new_line old" data-linenumber="1536" 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="LC2300" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">68,7 +69,7 @@</span></span></span>
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1536
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<pre style="margin: 0;">+<span id="LC1536" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">70,7 +70,7 @@ initialize_Aligned_Pair (char Buffer[LAR</span></span></span>
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2301
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1537
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<pre style="margin: 0;"> <span id="LC1537" class="line" lang="diff"> } /* end of initialize_Aligned_Pair*/</span>
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2302
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1538
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<pre style="margin: 0;"> <span id="LC1538" class="line" lang="diff"> </span>
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2303
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1539
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<pre style="margin: 0;"> <span id="LC1539" class="line" lang="diff"> void</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1542" 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">@@ -2306,7 +1542,7 @@</td>
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2306
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1542
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<pre style="margin: 0;"> <span id="LC1542" class="line" lang="diff"> char Buffer[LARGE_BUFF_LENGTH], FILE* fp)</span>
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2307
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<td class="diff-line-num new_line" data-linenumber="1543" 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">
1543
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<pre style="margin: 0;"> <span id="LC1543" class="line" lang="diff"> {</span>
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2308
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1544
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<pre style="margin: 0;"> <span id="LC1544" class="line" lang="diff"> char* buff;</span>
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2309
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<pre style="margin: 0;">-<span id="LC2309" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -16<span class="idiff left right">5,7 +166,7 @@</span></span></span>
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1545
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<pre style="margin: 0;">+<span id="LC1545" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -16<span class="idiff left right">7,7 +167,7 @@ void process_sequence_line(Sequence* seq</span></span></span>
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2310
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1546
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<pre style="margin: 0;"> <span id="LC1546" class="line" lang="diff"> /* Note: The buff may have characters that are not residues, this is */</span>
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<td class="diff-line-num old_line" data-linenumber="2311" 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">
2311
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1547
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<pre style="margin: 0;"> <span id="LC1547" class="line" lang="diff"> /* ok, there will just be a little extra space */</span>
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<td class="diff-line-num old_line" data-linenumber="2312" 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">
2312
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1548
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<pre style="margin: 0;"> <span id="LC1548" class="line" lang="diff"> while ((saved_length + estimated_length) > seq->max_length) {</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2315" 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="1551" 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">@@ -2315,7 +1551,7 @@</td>
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2315
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1551
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<pre style="margin: 0;"> <span id="LC1551" class="line" lang="diff"> }</span>
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2316
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1552
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<pre style="margin: 0;"> <span id="LC1552" class="line" lang="diff"> </span>
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2317
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1553
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<pre style="margin: 0;"> <span id="LC1553" class="line" lang="diff"> /* temporarily increase the room to put the sequence into */</span>
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<td class="diff-line-num old old_line" data-linenumber="2318" 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">
2318
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<pre style="margin: 0;">-<span id="LC2318" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -19<span class="idiff left right">2,23 +193,23 @@</span></span></span>
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<td class="diff-line-num new old_line" data-linenumber="2319" 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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1554
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<pre style="margin: 0;">+<span id="LC1554" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -19<span class="idiff left right">4,23 +194,23 @@ free_aligned_pair (Aligned_Pair* alignme</span></span></span>
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2319
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1555
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<pre style="margin: 0;"> <span id="LC1555" class="line" lang="diff"> free (alignment);</span>
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2320
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1556
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<pre style="margin: 0;"> <span id="LC1556" class="line" lang="diff"> }</span>
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2321
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1557
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<pre style="margin: 0;"> <span id="LC1557" class="line" lang="diff"> alignment = NULL;</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2347" 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="1583" 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">@@ -2347,77 +1583,7 @@</td>
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1583
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<pre style="margin: 0;"> <span id="LC1583" class="line" lang="diff"> for (pos = 0; pos < block->width; pos++)</span>
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1584
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<pre style="margin: 0;"> <span id="LC1584" class="line" lang="diff"> {</span>
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1585
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<pre style="margin: 0;"> <span id="LC1585" class="line" lang="diff"> ctemp[0] = toupper (aa_btoa[block->sequences[0].sequence[pos]]);</span>
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2350
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<pre style="margin: 0;">-<span id="LC2350" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -222,24 +223,24 @@</span></span>
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2351
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<pre style="margin: 0;">-<span id="LC2351" class="line" lang="diff"> }</span>
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2352
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<pre style="margin: 0;">-<span id="LC2352" class="line" lang="diff"> }</span>
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2353
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<pre style="margin: 0;">-<span id="LC2353" class="line" lang="diff"> free_matrix (pssm);</span>
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2354
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<pre style="margin: 0;">-<span id="LC2354" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-printf ("finished converting to checkpointsuccessful\n");</span></span>
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2355
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<pre style="margin: 0;">-<span id="LC2355" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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2356
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<pre style="margin: 0;">-<span id="LC2356" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+fprintf( stderr, "finished converting to checkpoint successful\n");</span></span>
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2357
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<pre style="margin: 0;">-<span id="LC2357" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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2358
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<pre style="margin: 0;">-<span id="LC2358" class="line" lang="diff"> } /* end block_to_checkpoint_file */</span>
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2359
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<pre style="margin: 0;">-<span id="LC2359" class="line" lang="diff"> </span>
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2360
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<pre style="margin: 0;">-<span id="LC2360" class="line" lang="diff"> void</span>
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2361
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<pre style="margin: 0;">-<span id="LC2361" class="line" lang="diff"> psiblast_system_call (char chkpoint_filename[], char database[],</span>
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2362
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<pre style="margin: 0;">-<span id="LC2362" class="line" lang="diff"> char result_file[], char query_seq_file[], FILE* outfp)</span>
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2363
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<pre style="margin: 0;">-<span id="LC2363" class="line" lang="diff"> {</span>
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2364
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<pre style="margin: 0;">-<span id="LC2364" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ int ret;</span></span>
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2365
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<pre style="margin: 0;">-<span id="LC2365" class="line" lang="diff"> char command_line[LARGE_BUFF_LENGTH * 4];</span>
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2366
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<pre style="margin: 0;">-<span id="LC2366" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char* ncbi_dir;</span></span>
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2367
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<pre style="margin: 0;">-<span id="LC2367" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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2368
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<pre style="margin: 0;">-<span id="LC2368" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ncbi_dir = getenv ("NCBI");</span></span>
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2369
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<pre style="margin: 0;">-<span id="LC2369" class="line" lang="diff"> </span>
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2370
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<pre style="margin: 0;">-<span id="LC2370" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sprintf (command_line, "%s/blastpgp -d %s -i %s -o %s -m 6 -R %s\n",</span></span>
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2371
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<pre style="margin: 0;">-<span id="LC2371" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ncbi_dir, database, query_seq_file, result_file, </span></span>
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2372
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<pre style="margin: 0;">-<span id="LC2372" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sprintf (command_line, "blastpgp -d %s -i %s -o %s -m 6 -R %s",</span></span>
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2373
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<pre style="margin: 0;">-<span id="LC2373" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ database, query_seq_file, result_file,</span></span>
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2374
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<pre style="margin: 0;">-<span id="LC2374" class="line" lang="diff"> chkpoint_filename);</span>
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2375
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<pre style="margin: 0;">-<span id="LC2375" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- system (command_line);</span></span>
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2376
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<pre style="margin: 0;">-<span id="LC2376" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf( stderr, "%s:%d About to call '%s'\n", __FILE__, __LINE__, command_line );</span></span>
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2377
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<pre style="margin: 0;">-<span id="LC2377" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ret = system (command_line);</span></span>
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2378
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<pre style="margin: 0;">-<span id="LC2378" class="line" lang="diff"> </span>
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2379
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<pre style="margin: 0;">-<span id="LC2379" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if( ret ) { fprintf( stderr, "%s:%d Error calling '%s'!\n", __FILE__, __LINE__, command_line ); exit(-1); }</span></span>
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2380
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<pre style="margin: 0;">-<span id="LC2380" class="line" lang="diff"> }</span>
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2381
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<pre style="margin: 0;">-<span id="LC2381" class="line" lang="diff"> </span>
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2382
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<pre style="margin: 0;">-<span id="LC2382" class="line" lang="diff"> void</span>
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2383
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<pre style="margin: 0;">-<span id="LC2383" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -247,29 +248,27 @@</span></span>
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2384
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<pre style="margin: 0;">-<span id="LC2384" class="line" lang="diff"> {</span>
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2385
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<pre style="margin: 0;">-<span id="LC2385" class="line" lang="diff"> char command_line[LARGE_BUFF_LENGTH];</span>
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2386
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<pre style="margin: 0;">-<span id="LC2386" class="line" lang="diff"> </span>
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2387
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<pre style="margin: 0;">-<span id="LC2387" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sprintf (command_line, "rm -f %s\n", filename);</span></span>
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2388
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<pre style="margin: 0;">-<span id="LC2388" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- system ("unalias rm");</span></span>
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2389
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<pre style="margin: 0;">-<span id="LC2389" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sprintf (command_line, "\\rm -f %s\n", filename);</span></span>
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2390
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<pre style="margin: 0;">-<span id="LC2390" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ //system ("unalias rm");</span></span>
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2391
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<pre style="margin: 0;">-<span id="LC2391" class="line" lang="diff"> system (command_line);</span>
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2392
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<pre style="margin: 0;">-<span id="LC2392" class="line" lang="diff"> }</span>
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2393
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<pre style="margin: 0;">-<span id="LC2393" class="line" lang="diff"> </span>
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2394
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<pre style="margin: 0;">-<span id="LC2394" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-void </span></span>
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2395
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<pre style="margin: 0;">-<span id="LC2395" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+void</span></span>
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2396
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<pre style="margin: 0;">-<span id="LC2396" class="line" lang="diff"> formatdb_system_call (char database[])</span>
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2397
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<pre style="margin: 0;">-<span id="LC2397" class="line" lang="diff"> {</span>
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2398
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<pre style="margin: 0;">-<span id="LC2398" class="line" lang="diff"> char command_line[LARGE_BUFF_LENGTH *2];</span>
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2399
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<pre style="margin: 0;">-<span id="LC2399" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char* ncbi_dir;</span></span>
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2400
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<pre style="margin: 0;">-<span id="LC2400" class="line" lang="diff"> </span>
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2401
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<pre style="margin: 0;">-<span id="LC2401" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ncbi_dir = getenv ("NCBI");</span></span>
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2402
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<pre style="margin: 0;">-<span id="LC2402" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sprintf (command_line, "%s/formatdb -i %s -o T -p T\n", ncbi_dir, database);</span></span>
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2403
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<pre style="margin: 0;">-<span id="LC2403" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- printf ("formatting database command_line %s\n", command_line);</span></span>
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2404
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<td class="diff-line-num new_line old" data-linenumber="1586" 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="LC2404" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sprintf (command_line, "formatdb -i %s -o T -p T\n", database);</span></span>
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2405
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<td class="diff-line-num new_line old" data-linenumber="1586" 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="LC2405" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf( stderr, "formatting database command_line %s\n", command_line);</span></span>
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2406
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<pre style="margin: 0;">-<span id="LC2406" class="line" lang="diff"> system (command_line);</span>
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2407
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<pre style="margin: 0;">-<span id="LC2407" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- printf ("finished formatting database\n");</span></span>
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2408
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<pre style="margin: 0;">-<span id="LC2408" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf( stderr, "finished formatting database\n");</span></span>
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2409
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<pre style="margin: 0;">-<span id="LC2409" class="line" lang="diff"> } /* end formatdb_system_call */</span>
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2410
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<pre style="margin: 0;">-<span id="LC2410" class="line" lang="diff"> </span>
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2411
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<pre style="margin: 0;">-<span id="LC2411" class="line" lang="diff"> /* opens psiblast result file and reads the top-scoring matches. The top match</span>
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2412
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<pre style="margin: 0;">-<span id="LC2412" class="line" lang="diff"> that isn't already in the sequence name hash is returned in next_seq_to_add.</span>
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2413
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<pre style="margin: 0;">-<span id="LC2413" class="line" lang="diff"> */</span>
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2414
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<pre style="margin: 0;">-<span id="LC2414" class="line" lang="diff"> void</span>
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2415
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<pre style="margin: 0;">-<span id="LC2415" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-get_top_seq (char next_seq_to_add[], HashTable namehash, </span></span>
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2416
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<pre style="margin: 0;">-<span id="LC2416" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+get_top_seq (char next_seq_to_add[], HashTable namehash,</span></span>
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2417
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<pre style="margin: 0;">-<span id="LC2417" class="line" lang="diff"> char psiblastres_file[])</span>
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2418
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<pre style="margin: 0;">-<span id="LC2418" class="line" lang="diff"> {</span>
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2419
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<pre style="margin: 0;">-<span id="LC2419" class="line" lang="diff"> FILE* psiblastfp;</span>
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2420
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<pre style="margin: 0;">-<span id="LC2420" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -286,7 +285,7 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1586" 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">
1586
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<pre style="margin: 0;">+<span id="LC1586" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -313,7 +313,7 @@ get_top_seq (char next_seq_to_add[], Has</span></span>
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2421
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1587
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<pre style="margin: 0;"> <span id="LC1587" class="line" lang="diff"> </span>
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2422
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1588
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<pre style="margin: 0;"> <span id="LC1588" class="line" lang="diff"> </span>
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2423
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1589
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<pre style="margin: 0;"> <span id="LC1589" class="line" lang="diff"> if (read_psiblast_header_until_first_no_error (psiblastfp, FALSE) == -1) {</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2426" 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="1592" 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">@@ -2426,7 +1592,7 @@</td>
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2426
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1592
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<pre style="margin: 0;"> <span id="LC1592" class="line" lang="diff"> } else {</span>
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<td class="diff-line-num old_line" data-linenumber="2427" 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">
2427
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1593
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<pre style="margin: 0;"> <span id="LC1593" class="line" lang="diff"> </span>
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<td class="diff-line-num old_line" data-linenumber="2428" 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">
2428
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1594
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<pre style="margin: 0;"> <span id="LC1594" class="line" lang="diff"> fgets (line, LINE_LEN, psiblastfp);</span>
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<td class="diff-line-num old old_line" data-linenumber="2429" 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">
2429
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<td class="diff-line-num new_line old" data-linenumber="1595" 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="LC2429" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">295,24 +294,24 @@</span></span></span>
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1595
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<pre style="margin: 0;">+<span id="LC1595" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -<span class="idiff left right">322,24 +322,24 @@ get_top_seq (char next_seq_to_add[], Has</span></span></span>
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2430
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1596
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<pre style="margin: 0;"> <span id="LC1596" class="line" lang="diff"> assert ( strlen(strptr) < KEY_WIDTH);</span>
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<td class="diff-line-num old_line" data-linenumber="2431" 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">
2431
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1597
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<pre style="margin: 0;"> <span id="LC1597" class="line" lang="diff"> strncpy (name, strptr, KEY_WIDTH);</span>
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<td class="diff-line-num old_line" data-linenumber="2432" 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">
2432
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1598
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<pre style="margin: 0;"> <span id="LC1598" class="line" lang="diff"> name[KEY_WIDTH-1] = '\0';</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2455" 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="1621" 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">@@ -2455,10 +1621,12 @@</td>
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2455
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1621
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<pre style="margin: 0;"> <span id="LC1621" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num old_line" data-linenumber="2456" 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">
2456
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<td class="diff-line-num new_line" data-linenumber="1622" 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">
1622
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<pre style="margin: 0;"> <span id="LC1622" class="line" lang="diff"> } /* end get_top_seq */</span>
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2457
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1623
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<pre style="margin: 0;"> <span id="LC1623" class="line" lang="diff"> </span>
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2458
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<pre style="margin: 0;">-<span id="LC2458" class="line" lang="diff"> #endif</span>
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<td class="diff-line-num old old_line" data-linenumber="2459" 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">
2459
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<pre style="margin: 0;">-<span id="LC2459" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/psiblast_res_to_fasta_dbpairwise.c</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2460" 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">
2460
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<td class="diff-line-num new_line old" data-linenumber="1624" 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="LC2460" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/psiblast_res_to_fasta_dbpairwise.c</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2461" 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">
2461
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<td class="diff-line-num new_line old" data-linenumber="1624" 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="LC2461" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -32,8 +32,8 @@</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2462" 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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1624
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<pre style="margin: 0;">+<span id="LC1624" class="line" lang="diff"> char* substring(Sequence* seq, int begin, int len)</span>
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<td class="diff-line-num new old_line" data-linenumber="2462" 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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<td class="diff-line-num new new_line" data-linenumber="1625" 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">
1625
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<pre style="margin: 0;">+<span id="LC1625" class="line" lang="diff"><span class="gh" style="color: #999;">Index: sift/src/psiblast_res_to_fasta_dbpairwise.c</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1626" 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">
1626
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<pre style="margin: 0;">+<span id="LC1626" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2462" 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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1627
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<pre style="margin: 0;">+<span id="LC1627" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- sift.orig/src/psiblast_res_to_fasta_dbpairwise.c</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1628" 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">
1628
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<pre style="margin: 0;">+<span id="LC1628" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ sift/src/psiblast_res_to_fasta_dbpairwise.c</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1629" 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">
1629
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<pre style="margin: 0;">+<span id="LC1629" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -32,8 +32,8 @@ Output2: Sequences found with residues f</span></span>
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2462
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1630
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<pre style="margin: 0;"> <span id="LC1630" class="line" lang="diff"> #include "Protdist.c"</span>
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2463
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1631
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<pre style="margin: 0;"> <span id="LC1631" class="line" lang="diff"> #include "Psiblast.c"</span>
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2464
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1632
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<pre style="margin: 0;"> <span id="LC1632" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2469" 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="1637" 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">@@ -2469,7 +1637,7 @@</td>
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2469
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1637
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<pre style="margin: 0;"> <span id="LC1637" class="line" lang="diff"> #define LINE_LEN 800</span>
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2470
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1638
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<pre style="margin: 0;"> <span id="LC1638" class="line" lang="diff"> #define FALSE 0</span>
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2471
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1639
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<pre style="margin: 0;"> <span id="LC1639" class="line" lang="diff"> #define TRUE 1</span>
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2472
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<pre style="margin: 0;">-<span id="LC2472" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -113,17 +113,17 @@</span></span>
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1640
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<pre style="margin: 0;">+<span id="LC1640" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -113,17 +113,17 @@<span class="idiff left right"> int main</span></span></span>
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2473
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1641
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<pre style="margin: 0;"> <span id="LC1641" class="line" lang="diff"> </span>
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2474
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1642
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<pre style="margin: 0;"> <span id="LC1642" class="line" lang="diff"> free_seqs (alignedseqs, nseqs);</span>
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2475
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1643
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<pre style="margin: 0;"> <span id="LC1643" class="line" lang="diff"> if (nseqs < MIN_SEQ) {</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2493" 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="1661" 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">@@ -2493,49 +1661,7 @@</td>
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2493
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1661
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<pre style="margin: 0;"> <span id="LC1661" class="line" lang="diff"> } /* end main */</span>
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2494
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1662
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<pre style="margin: 0;"> <span id="LC1662" class="line" lang="diff"> </span>
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2495
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1663
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<pre style="margin: 0;"> <span id="LC1663" class="line" lang="diff"> void getargs (int argc, char* argv[], FILE** psiblastfp, </span>
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2496
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<pre style="margin: 0;">-<span id="LC2496" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -147,33 +147,33 @@</span></span>
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2497
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<pre style="margin: 0;">-<span id="LC2497" class="line" lang="diff"> else</span>
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2498
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<pre style="margin: 0;">-<span id="LC2498" class="line" lang="diff"> {</span>
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2499
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<pre style="margin: 0;">-<span id="LC2499" class="line" lang="diff"> printf ("Enter name of psiblast outfile with pairwise alignments:\n");</span>
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2500
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<pre style="margin: 0;">-<span id="LC2500" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- gets (psiblastfilename);</span></span>
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2501
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<pre style="margin: 0;">-<span id="LC2501" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fgets( psiblastfilename, LARGE_BUFF_LENGTH, stdin );</span></span>
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2502
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<pre style="margin: 0;">-<span id="LC2502" class="line" lang="diff"> }</span>
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2503
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<td class="diff-line-num new_line old" data-linenumber="1664" 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="LC2503" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2504" 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">
2504
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<td class="diff-line-num new_line old" data-linenumber="1664" 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="LC2504" class="line" lang="diff"> if ((*psiblastfp = fopen (psiblastfilename, "r")) == NULL)</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2505" 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">
2505
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<td class="diff-line-num new_line old" data-linenumber="1664" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2505" class="line" lang="diff"> {</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2506" 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">
2506
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<td class="diff-line-num new_line old" data-linenumber="1664" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2506" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- printf ("cannot open file %s \n", psiblastfilename);</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2507" 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">
2507
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<td class="diff-line-num new_line old" data-linenumber="1664" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2507" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf(stderr, "cannot open file %s \n", psiblastfilename);</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2508" 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">
2508
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<td class="diff-line-num new_line old" data-linenumber="1664" 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="LC2508" class="line" lang="diff"> exit (-1);</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2509" 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">
2509
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<td class="diff-line-num new_line old" data-linenumber="1664" 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">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2509" class="line" lang="diff"> }</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2510" 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">
2510
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<td class="diff-line-num new_line old" data-linenumber="1664" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2510" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2511" 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">
2511
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<td class="diff-line-num new_line old" data-linenumber="1664" 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="LC2511" class="line" lang="diff"> if (argc > 2) strcpy (queryaligned_outfilename, argv[2]);</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2512" 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">
2512
</td>
<td class="diff-line-num new_line old" data-linenumber="1664" 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">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2512" class="line" lang="diff"> else</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="2513" 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">
2513
</td>
<td class="diff-line-num new_line old" data-linenumber="1664" 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">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2513" class="line" lang="diff"> {</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="2514" 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">
2514
</td>
<td class="diff-line-num new_line old" data-linenumber="1664" 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">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2514" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- printf ("Enter name of output file for which the psiblast \n");</span></span>
</pre>
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</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="2515" 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">
2515
</td>
<td class="diff-line-num new_line old" data-linenumber="1664" 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">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2515" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- printf ("alignment to the query will be printed out in \n");</span></span>
</pre>
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</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="2516" 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">
2516
</td>
<td class="diff-line-num new_line old" data-linenumber="1664" 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">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2516" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- printf ("fasta format\n");</span></span>
</pre>
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</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="2517" 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">
2517
</td>
<td class="diff-line-num new_line old" data-linenumber="1664" 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">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2517" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- gets (queryaligned_outfilename);</span></span>
</pre>
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</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="2518" 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">
2518
</td>
<td class="diff-line-num new_line old" data-linenumber="1664" 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">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2518" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf( stderr, "Enter name of output file for which the psiblast \n");</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="2519" 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">
2519
</td>
<td class="diff-line-num new_line old" data-linenumber="1664" 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">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2519" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf( stderr, "alignment to the query will be printed out in \n");</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="2520" 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">
2520
</td>
<td class="diff-line-num new_line old" data-linenumber="1664" 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">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2520" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf( stderr, "fasta format\n");</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="2521" 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">
2521
</td>
<td class="diff-line-num new_line old" data-linenumber="1664" 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">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2521" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fgets( queryaligned_outfilename, LARGE_BUFF_LENGTH, stdin );</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="2522" 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">
2522
</td>
<td class="diff-line-num new_line old" data-linenumber="1664" 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">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2522" class="line" lang="diff"> }</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="2523" 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">
2523
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<td class="diff-line-num new_line old" data-linenumber="1664" 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">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2523" class="line" lang="diff"> </span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="2524" 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">
2524
</td>
<td class="diff-line-num new_line old" data-linenumber="1664" 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">
</td>
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<pre style="margin: 0;">-<span id="LC2524" class="line" lang="diff"> if ((*outfpqueryalign = fopen (queryaligned_outfilename, "w")) == NULL)</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="2525" 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">
2525
</td>
<td class="diff-line-num new_line old" data-linenumber="1664" 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">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2525" class="line" lang="diff"> {</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="2526" 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">
2526
</td>
<td class="diff-line-num new_line old" data-linenumber="1664" 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">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2526" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- printf ("cannot open file %s\n", queryaligned_outfilename);</span></span>
</pre>
</td>
</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="2527" 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">
2527
</td>
<td class="diff-line-num new_line old" data-linenumber="1664" 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">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2527" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf( stderr, "cannot open file %s\n", queryaligned_outfilename);</span></span>
</pre>
</td>
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2528
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<pre style="margin: 0;">-<span id="LC2528" class="line" lang="diff"> exit (-1);</span>
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2529
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<pre style="margin: 0;">-<span id="LC2529" class="line" lang="diff"> }</span>
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2530
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<pre style="margin: 0;">-<span id="LC2530" class="line" lang="diff"> strcpy (errorfilename, queryaligned_outfilename);</span>
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2531
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<pre style="margin: 0;">-<span id="LC2531" class="line" lang="diff"> strcat (errorfilename, ".error");</span>
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<td class="diff-line-num old old_line" data-linenumber="2532" 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">
2532
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<td class="diff-line-num new_line old" data-linenumber="1664" 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="LC2532" class="line" lang="diff"> if ((errorfp = fopen (errorfilename, "w")) == NULL) {</span>
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<td class="diff-line-num old old_line" data-linenumber="2533" 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">
2533
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<td class="diff-line-num new_line old" data-linenumber="1664" 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="LC2533" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- printf ("couldn't open file %s\n", errorfilename);</span></span>
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2534
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<td class="diff-line-num new_line old" data-linenumber="1664" 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="LC2534" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf (stderr, "couldn't open file %s\n", errorfilename);</span></span>
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2535
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<td class="diff-line-num new_line old" data-linenumber="1664" 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="LC2535" class="line" lang="diff"> exit (-1);</span>
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<td class="diff-line-num old old_line" data-linenumber="2536" 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">
2536
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<pre style="margin: 0;">-<span id="LC2536" class="line" lang="diff"> }</span>
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<td class="diff-line-num old old_line" data-linenumber="2537" 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">
2537
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<pre style="margin: 0;">-<span id="LC2537" class="line" lang="diff"> </span>
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<td class="diff-line-num old old_line" data-linenumber="2538" 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">
2538
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<pre style="margin: 0;">-<span id="LC2538" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -201,6 +201,7 @@</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2539" 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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1664
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<pre style="margin: 0;">+<span id="LC1664" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -201,6 +201,7 @@ read_sequence_from_filename (char filena</span></span>
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<td class="diff-line-num old_line" data-linenumber="2539" 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">
2539
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1665
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<pre style="margin: 0;"> <span id="LC1665" class="line" lang="diff"> Sequence* seq;</span>
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<td class="diff-line-num old_line" data-linenumber="2540" 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">
2540
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1666
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<pre style="margin: 0;"> <span id="LC1666" class="line" lang="diff"> </span>
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<td class="diff-line-num old_line" data-linenumber="2541" 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">
2541
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<td class="diff-line-num new_line" data-linenumber="1667" 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">
1667
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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="LC1667" class="line" lang="diff"> if ((fp = fopen (filename, "r")) == NULL) {</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2543" 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="1669" 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">@@ -2543,9 +1669,11 @@</td>
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2543
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1669
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<pre style="margin: 0;"> <span id="LC1669" class="line" lang="diff"> fprintf (errorfp, "couldn't open %s in processing PSIBLAST results\n", filename);</span>
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2544
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1670
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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="LC1670" class="line" lang="diff"> exit (-1);</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2545" 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">
2545
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1671
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<pre style="margin: 0;"> <span id="LC1671" class="line" lang="diff"> }</span>
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2546
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<pre style="margin: 0;">-<span id="LC2546" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/seqs_from_psiblast_res.c</span></span>
</pre>
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2547
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<pre style="margin: 0;">-<span id="LC2547" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/seqs_from_psiblast_res.c</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2548" 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">
2548
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<pre style="margin: 0;">-<span id="LC2548" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -23,7 +23,7 @@</span></span>
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1672
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<pre style="margin: 0;">+<span id="LC1672" class="line" lang="diff"><span class="gh" style="color: #999;">Index: sift/src/seqs_from_psiblast_res.c</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1673" 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">
1673
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<pre style="margin: 0;">+<span id="LC1673" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1674" 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">
1674
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<pre style="margin: 0;">+<span id="LC1674" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- sift.orig/src/seqs_from_psiblast_res.c</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1675" 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">
1675
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<pre style="margin: 0;">+<span id="LC1675" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ sift/src/seqs_from_psiblast_res.c</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1676" 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">
1676
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<pre style="margin: 0;">+<span id="LC1676" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -23,7 +23,7 @@ and prints out the complete sequence fro</span></span>
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2549
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<td class="diff-line-num new_line" data-linenumber="1677" 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">
1677
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<pre style="margin: 0;"> <span id="LC1677" class="line" lang="diff"> #include "stringhash.c"</span>
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<td class="diff-line-num old_line" data-linenumber="2550" 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">
2550
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<td class="diff-line-num new_line" data-linenumber="1678" 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">
1678
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<pre style="margin: 0;"> <span id="LC1678" class="line" lang="diff"> #include "Psiblast.c"</span>
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<td class="diff-line-num old_line" data-linenumber="2551" 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">
2551
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<td class="diff-line-num new_line" data-linenumber="1679" 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">
1679
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<pre style="margin: 0;"> <span id="LC1679" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2554" 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="1682" 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">@@ -2554,32 +1682,10 @@</td>
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2554
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<td class="diff-line-num new_line" data-linenumber="1682" 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">
1682
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<pre style="margin: 0;"> <span id="LC1682" class="line" lang="diff"> #define LINE_LEN 800</span>
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<td class="diff-line-num old_line" data-linenumber="2555" 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">
2555
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<td class="diff-line-num new_line" data-linenumber="1683" 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">
1683
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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="LC1683" class="line" lang="diff"> #define FALSE 0</span>
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<td class="diff-line-num old_line" data-linenumber="2556" 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">
2556
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<td class="diff-line-num new_line" data-linenumber="1684" 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">
1684
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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="LC1684" class="line" lang="diff"> #define TRUE 1</span>
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<td class="diff-line-num old old_line" data-linenumber="2557" 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">
2557
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<td class="diff-line-num new_line old" data-linenumber="1685" 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="LC2557" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -154,8 +154,8 @@</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2558" 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">
2558
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<td class="diff-line-num new_line old" data-linenumber="1685" 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="LC2558" class="line" lang="diff"> if (argc > 1) strcpy (psiblastfilename, argv[1]);</span>
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<td class="diff-line-num old old_line" data-linenumber="2559" 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">
2559
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<td class="diff-line-num new_line old" data-linenumber="1685" 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="LC2559" class="line" lang="diff"> else</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2560" 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">
2560
</td>
<td class="diff-line-num new_line old" data-linenumber="1685" 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="LC2560" class="line" lang="diff"> {</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2561" 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">
2561
</td>
<td class="diff-line-num new_line old" data-linenumber="1685" 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="LC2561" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- printf ("Enter name of psiblast outfile with pairwise alignments:\n");</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2562" 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">
2562
</td>
<td class="diff-line-num new_line old" data-linenumber="1685" 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="LC2562" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- gets (psiblastfilename);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2563" 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">
2563
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<td class="diff-line-num new_line old" data-linenumber="1685" 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="LC2563" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf( stderr, "Enter name of psiblast outfile with pairwise alignments:\n");</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2564" 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">
2564
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<td class="diff-line-num new_line old" data-linenumber="1685" 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="LC2564" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fgets( psiblastfilename, LARGE_BUFF_LENGTH, stdin );</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2565" 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">
2565
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<td class="diff-line-num new_line old" data-linenumber="1685" 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="LC2565" class="line" lang="diff"> }</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2566" 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">
2566
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<td class="diff-line-num new_line old" data-linenumber="1685" 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="LC2566" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2567" 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">
2567
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<td class="diff-line-num new_line old" data-linenumber="1685" 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="LC2567" class="line" lang="diff"> if ((*psiblastfp = fopen (psiblastfilename, "r")) == NULL)</span>
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<td class="diff-line-num old old_line" data-linenumber="2568" 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">
2568
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<td class="diff-line-num new_line old" data-linenumber="1685" 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="LC2568" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -167,9 +167,9 @@</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2569" 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">
2569
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<td class="diff-line-num new_line old" data-linenumber="1685" 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="LC2569" class="line" lang="diff"> if (argc > 2) strcpy (seqfilename, argv[2]);</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2570" 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">
2570
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<td class="diff-line-num new_line old" data-linenumber="1685" 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="LC2570" class="line" lang="diff"> else</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2571" 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">
2571
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<td class="diff-line-num new_line old" data-linenumber="1685" 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="LC2571" class="line" lang="diff"> {</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2572" 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">
2572
</td>
<td class="diff-line-num new_line old" data-linenumber="1685" 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="LC2572" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- printf ("Enter name of seq file for which the psiblast \n");</span></span>
</pre>
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2573
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<pre style="margin: 0;">-<span id="LC2573" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- printf ("sequences will be printed \n");</span></span>
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2574
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<pre style="margin: 0;">-<span id="LC2574" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- gets (seqfilename);</span></span>
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2575
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<pre style="margin: 0;">-<span id="LC2575" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf( stderr, "Enter name of seq file for which the psiblast \n");</span></span>
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2576
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<pre style="margin: 0;">-<span id="LC2576" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fprintf( stderr, "sequences will be printed \n");</span></span>
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2577
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<pre style="margin: 0;">-<span id="LC2577" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fgets( seqfilename, LARGE_BUFF_LENGTH, stdin );</span></span>
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2578
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<pre style="margin: 0;">-<span id="LC2578" class="line" lang="diff"> }</span>
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2579
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<pre style="margin: 0;">-<span id="LC2579" class="line" lang="diff"> </span>
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2580
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<pre style="margin: 0;">-<span id="LC2580" class="line" lang="diff"> if ((*seqfp = fopen (seqfilename, "r")) == NULL)</span>
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1685
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<pre style="margin: 0;">+<span id="LC1685" class="line" lang="diff"><span class="gh" style="color: #999;">Index: sift/src/sift_blimps.h</span></span>
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1686
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<pre style="margin: 0;">+<span id="LC1686" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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2581
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1687
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<pre style="margin: 0;"> <span id="LC1687" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- /dev/null</span></span>
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2582
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<pre style="margin: 0;">-<span id="LC2582" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b</span>/src/sift_blimps.h</span></span>
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<pre style="margin: 0;">+<span id="LC1688" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">sift</span>/src/sift_blimps.h</span></span>
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2583
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1689
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<pre style="margin: 0;"> <span id="LC1689" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -0,0 +1,12 @@</span></span>
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2584
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1690
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<pre style="margin: 0;"> <span id="LC1690" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#ifndef SIFT_BLIMPS_H</span></span>
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2585
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1691
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<pre style="margin: 0;"> <span id="LC1691" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#define SIFT_BLIMPS_H</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2593" 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="1699" 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">@@ -2593,9 +1699,11 @@</td>
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2593
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1699
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<pre style="margin: 0;"> <span id="LC1699" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+}</span></span>
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2594
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1700
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<pre style="margin: 0;"> <span id="LC1700" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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2595
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1701
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<pre style="margin: 0;"> <span id="LC1701" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#endif</span></span>
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2596
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<pre style="margin: 0;">-<span id="LC2596" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/SortList.c</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2597" 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">
2597
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<pre style="margin: 0;">-<span id="LC2597" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/SortList.c</span></span>
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2598
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<pre style="margin: 0;">-<span id="LC2598" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -13,7 +13,7 @@</span></span>
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1702
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<pre style="margin: 0;">+<span id="LC1702" class="line" lang="diff"><span class="gh" style="color: #999;">Index: sift/src/SortList.c</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1703" 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">
1703
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<pre style="margin: 0;">+<span id="LC1703" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1704" 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">
1704
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<pre style="margin: 0;">+<span id="LC1704" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- sift.orig/src/SortList.c</span></span>
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1705
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<pre style="margin: 0;">+<span id="LC1705" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ sift/src/SortList.c</span></span>
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1706
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<pre style="margin: 0;">+<span id="LC1706" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -13,7 +13,7 @@ int</span></span>
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2599
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1707
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<pre style="margin: 0;"> <span id="LC1707" class="line" lang="diff"> lowest_scoring_aa (Matrix* matrix, int pos)</span>
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2600
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1708
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<pre style="margin: 0;"> <span id="LC1708" class="line" lang="diff"> {</span>
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<td class="diff-line-num old_line" data-linenumber="2601" 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">
2601
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<td class="diff-line-num new_line" data-linenumber="1709" 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">
1709
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<pre style="margin: 0;"> <span id="LC1709" class="line" lang="diff"> struct working* col;</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2604" 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="1712" 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">@@ -2604,8 +1712,10 @@</td>
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2604
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1712
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<pre style="margin: 0;"> <span id="LC1712" class="line" lang="diff"> double min;</span>
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2605
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1713
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<pre style="margin: 0;"> <span id="LC1713" class="line" lang="diff"> </span>
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<td class="diff-line-num old_line" data-linenumber="2606" 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">
2606
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<td class="diff-line-num new_line" data-linenumber="1714" 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">
1714
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<pre style="margin: 0;"> <span id="LC1714" class="line" lang="diff"> min = 10000;</span>
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1715
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<pre style="margin: 0;">+<span id="LC1715" class="line" lang="diff"><span class="gh" style="color: #999;">Index: sift/SIFT_for_submitting_fasta_seq.csh.pod</span></span>
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1716
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<pre style="margin: 0;">+<span id="LC1716" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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2607
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1717
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<pre style="margin: 0;"> <span id="LC1717" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- /dev/null</span></span>
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2608
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<td class="diff-line-num new_line old" data-linenumber="1718" 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="LC2608" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b</span>/SIFT_for_submitting_fasta_seq.csh.pod</span></span>
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1718
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<pre style="margin: 0;">+<span id="LC1718" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">sift</span>/SIFT_for_submitting_fasta_seq.csh.pod</span></span>
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2609
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<td class="diff-line-num new_line" data-linenumber="1719" 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">
1719
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<pre style="margin: 0;"> <span id="LC1719" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -0,0 +1,55 @@</span></span>
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2610
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<td class="diff-line-num new_line" data-linenumber="1720" 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">
1720
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<pre style="margin: 0;"> <span id="LC1720" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+=head1 NAME</span></span>
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<td class="diff-line-num old_line" data-linenumber="2611" 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">
2611
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<td class="diff-line-num new_line" data-linenumber="1721" 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">
1721
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<pre style="margin: 0;"> <span id="LC1721" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2662" 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="1772" 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">@@ -2662,131 +1772,11 @@</td>
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2662
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<td class="diff-line-num new_line" data-linenumber="1772" 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">
1772
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<pre style="margin: 0;"> <span id="LC1772" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+=head1 SEE ALSO</span></span>
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<td class="diff-line-num old_line" data-linenumber="2663" 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">
2663
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<td class="diff-line-num new_line" data-linenumber="1773" 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">
1773
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<pre style="margin: 0;"> <span id="LC1773" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num old_line" data-linenumber="2664" 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">
2664
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<td class="diff-line-num new_line" data-linenumber="1774" 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">
1774
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<pre style="margin: 0;"> <span id="LC1774" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+L<info_on_seqs></span></span>
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2665
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2665" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/bin/Classify_SNPs_Indels.pl</span></span>
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2666
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2666" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/bin/Classify_SNPs_Indels.pl</span></span>
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2667
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2667" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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2668
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2668" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/local/bin/perl</span></span>
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2669
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2669" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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2670
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2670" class="line" lang="diff"> $SIFT_HOME = $ENV{'SIFT_HOME'};</span>
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2671
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2671" class="line" lang="diff"> $bin = "$SIFT_HOME/bin";</span>
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2672
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2672" class="line" lang="diff"> </span>
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2673
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2673" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/bin/SIFT_intersect_cds.pl</span></span>
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2674
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2674" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/bin/SIFT_intersect_cds.pl</span></span>
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2675
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2675" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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2676
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2676" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/local/bin/perl</span></span>
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2677
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2677" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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2678
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2678" class="line" lang="diff"> $| = 1;</span>
</pre>
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2679
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<pre style="margin: 0;">-<span id="LC2679" class="line" lang="diff"> use Getopt::Std;</span>
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<td class="diff-line-num old old_line" data-linenumber="2680" 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">
2680
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2680" class="line" lang="diff"> use File::Basename;</span>
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<td class="diff-line-num old old_line" data-linenumber="2681" 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">
2681
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<pre style="margin: 0;">-<span id="LC2681" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/bin/SNPClassifier/Classify_SNPs.pl</span></span>
</pre>
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2682
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2682" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/bin/SNPClassifier/Classify_SNPs.pl</span></span>
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2683
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2683" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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2684
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2684" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/local/bin/perl</span></span>
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2685
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<pre style="margin: 0;">-<span id="LC2685" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2686" 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">
2686
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2686" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2687" 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">
2687
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2687" class="line" lang="diff"> ###############################################################################</span>
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<td class="diff-line-num old old_line" data-linenumber="2688" 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">
2688
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<pre style="margin: 0;">-<span id="LC2688" class="line" lang="diff"> # #</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2689" 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">
2689
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2689" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/bin/SNPClassifier/Extract_Coding_Info.pl</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2690" 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">
2690
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2690" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/bin/SNPClassifier/Extract_Coding_Info.pl</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2691" 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">
2691
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<pre style="margin: 0;">-<span id="LC2691" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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2692
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<pre style="margin: 0;">-<span id="LC2692" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/local/bin/perl</span></span>
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2693
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<pre style="margin: 0;">-<span id="LC2693" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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2694
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2694" class="line" lang="diff"> </span>
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2695
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2695" class="line" lang="diff"> ###############################################################################</span>
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2696
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<pre style="margin: 0;">-<span id="LC2696" class="line" lang="diff"> # #</span>
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<td class="diff-line-num old old_line" data-linenumber="2697" 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">
2697
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<pre style="margin: 0;">-<span id="LC2697" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/bin/detect_indel.pl</span></span>
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2698
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<pre style="margin: 0;">-<span id="LC2698" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/bin/detect_indel.pl</span></span>
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2699
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<pre style="margin: 0;">-<span id="LC2699" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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2700
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<pre style="margin: 0;">-<span id="LC2700" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/local/bin/perl -w</span></span>
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2701
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<pre style="margin: 0;">-<span id="LC2701" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl -w</span></span>
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2702
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<pre style="margin: 0;">-<span id="LC2702" class="line" lang="diff"> use strict;</span>
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2703
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<pre style="margin: 0;">-<span id="LC2703" class="line" lang="diff"> </span>
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2704
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<pre style="margin: 0;">-<span id="LC2704" class="line" lang="diff"> # This program is licensed to you under the Fred</span>
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<td class="diff-line-num old old_line" data-linenumber="2705" 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">
2705
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<pre style="margin: 0;">-<span id="LC2705" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/bin/detect_repeat.pl</span></span>
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2706
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<pre style="margin: 0;">-<span id="LC2706" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/bin/detect_repeat.pl</span></span>
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2707
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<pre style="margin: 0;">-<span id="LC2707" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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2708
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<pre style="margin: 0;">-<span id="LC2708" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/local/bin/perl </span></span>
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<td class="diff-line-num old old_line" data-linenumber="2709" 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">
2709
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<pre style="margin: 0;">-<span id="LC2709" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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2710
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<pre style="margin: 0;">-<span id="LC2710" class="line" lang="diff"> </span>
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2711
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<pre style="margin: 0;">-<span id="LC2711" class="line" lang="diff"> # This program is licensed to you under the Fred</span>
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<td class="diff-line-num old old_line" data-linenumber="2712" 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">
2712
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<pre style="margin: 0;">-<span id="LC2712" class="line" lang="diff"> # Hutchinos Cancer Research Center (FHCRC)</span>
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<td class="diff-line-num old old_line" data-linenumber="2713" 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">
2713
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<pre style="margin: 0;">-<span id="LC2713" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/bin/get_sequences.pl</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2714" 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">
2714
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<pre style="margin: 0;">-<span id="LC2714" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/bin/get_sequences.pl</span></span>
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2715
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<pre style="margin: 0;">-<span id="LC2715" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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2716
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<pre style="margin: 0;">-<span id="LC2716" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#! /opt/local/bin/perl5 -w</span></span>
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2717
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2717" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl -w</span></span>
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2718
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<pre style="margin: 0;">-<span id="LC2718" class="line" lang="diff"> </span>
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2719
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<pre style="margin: 0;">-<span id="LC2719" class="line" lang="diff"> #####################################################################</span>
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<td class="diff-line-num old old_line" data-linenumber="2720" 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">
2720
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<pre style="margin: 0;">-<span id="LC2720" class="line" lang="diff"> #</span>
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<td class="diff-line-num old old_line" data-linenumber="2721" 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">
2721
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<pre style="margin: 0;">-<span id="LC2721" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/bin/indelfile_to_gff.pl</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2722" 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">
2722
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2722" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/bin/indelfile_to_gff.pl</span></span>
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2723
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2723" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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2724
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2724" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/local/bin/perl</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2725" 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">
2725
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2725" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2726" 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">
2726
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2726" class="line" lang="diff"> # This program is licensed to you under the Fred</span>
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<td class="diff-line-num old old_line" data-linenumber="2727" 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">
2727
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<pre style="margin: 0;">-<span id="LC2727" class="line" lang="diff"> # Hutchinos Cancer Research Center (FHCRC)</span>
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<td class="diff-line-num old old_line" data-linenumber="2728" 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">
2728
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2728" class="line" lang="diff"> # NONCOMMERICAL LICENSE. A copy of the license may be found at</span>
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<td class="diff-line-num old old_line" data-linenumber="2729" 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">
2729
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<pre style="margin: 0;">-<span id="LC2729" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/bin/map_coords_to_bin.pl</span></span>
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2730
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<pre style="margin: 0;">-<span id="LC2730" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/bin/map_coords_to_bin.pl</span></span>
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2731
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<pre style="margin: 0;">-<span id="LC2731" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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2732
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2732" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/local/bin/perl</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2733" 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">
2733
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<pre style="margin: 0;">-<span id="LC2733" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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2734
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<pre style="margin: 0;">-<span id="LC2734" class="line" lang="diff"> </span>
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2735
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<pre style="margin: 0;">-<span id="LC2735" class="line" lang="diff"> # This program is licensed to you under the Fred</span>
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<td class="diff-line-num old old_line" data-linenumber="2736" 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">
2736
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<pre style="margin: 0;">-<span id="LC2736" class="line" lang="diff"> # Hutchinos Cancer Research Center (FHCRC)</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2737" 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">
2737
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<pre style="margin: 0;">-<span id="LC2737" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/bin/map_coords_to_bin_indels.pl</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2738" 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">
2738
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<pre style="margin: 0;">-<span id="LC2738" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/bin/map_coords_to_bin_indels.pl</span></span>
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2739
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<pre style="margin: 0;">-<span id="LC2739" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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2740
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<pre style="margin: 0;">-<span id="LC2740" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/local/bin/perl</span></span>
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2741
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<pre style="margin: 0;">-<span id="LC2741" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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2742
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<pre style="margin: 0;">-<span id="LC2742" class="line" lang="diff"> </span>
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2743
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<pre style="margin: 0;">-<span id="LC2743" class="line" lang="diff"> </span>
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2744
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<pre style="margin: 0;">-<span id="LC2744" class="line" lang="diff"> # This program is licensed to you under the Fred</span>
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<td class="diff-line-num old old_line" data-linenumber="2745" 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">
2745
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<pre style="margin: 0;">-<span id="LC2745" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/bin/model_transcript.pl</span></span>
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2746
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2746" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/bin/model_transcript.pl</span></span>
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2747
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2747" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2748" 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">
2748
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2748" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/local/bin/perl -w</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2749" 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">
2749
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2749" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl -w</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2750" 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">
2750
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2750" class="line" lang="diff"> use strict;</span>
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<td class="diff-line-num old old_line" data-linenumber="2751" 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">
2751
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<pre style="margin: 0;">-<span id="LC2751" class="line" lang="diff"> use DBI;</span>
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<td class="diff-line-num old old_line" data-linenumber="2752" 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">
2752
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<pre style="margin: 0;">-<span id="LC2752" class="line" lang="diff"> my $SIFT_HOME = $ENV{'SIFT_HOME'};</span>
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<td class="diff-line-num old old_line" data-linenumber="2753" 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">
2753
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2753" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/bin/reformat_chrfile.pl</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2754" 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">
2754
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<pre style="margin: 0;">-<span id="LC2754" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/bin/reformat_chrfile.pl</span></span>
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2755
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<pre style="margin: 0;">-<span id="LC2755" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
</pre>
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2756
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<pre style="margin: 0;">-<span id="LC2756" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/local/bin/perl </span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2757" 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">
2757
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<pre style="margin: 0;">-<span id="LC2757" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2758" 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">
2758
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<pre style="margin: 0;">-<span id="LC2758" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2759" 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">
2759
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<pre style="margin: 0;">-<span id="LC2759" class="line" lang="diff"> # This program is licensed to you under the Fred</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2760" 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">
2760
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<pre style="margin: 0;">-<span id="LC2760" class="line" lang="diff"> # Hutchinos Cancer Research Center (FHCRC)</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2761" 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">
2761
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<pre style="margin: 0;">-<span id="LC2761" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/bin/sift_feed_to_chr_coords_batch.pl</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2762" 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">
2762
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<pre style="margin: 0;">-<span id="LC2762" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/bin/sift_feed_to_chr_coords_batch.pl</span></span>
</pre>
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2763
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<pre style="margin: 0;">-<span id="LC2763" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
</pre>
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2764
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<pre style="margin: 0;">-<span id="LC2764" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/local/bin/perl</span></span>
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2765
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2765" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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2766
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2766" class="line" lang="diff"> my $SIFT_HOME = $ENV{'SIFT_HOME'};</span>
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2767
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2767" class="line" lang="diff"> my $bin = "$SIFT_HOME/bin";</span>
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2768
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2768" class="line" lang="diff"> </span>
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<td class="diff-line-num old old_line" data-linenumber="2769" 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">
2769
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2769" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/bin/snv_db_engine.pl</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2770" 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">
2770
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2770" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/bin/snv_db_engine.pl</span></span>
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2771
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2771" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2772" 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">
2772
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2772" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/local/bin/perl</span></span>
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2773
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2773" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2774" 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">
2774
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2774" class="line" lang="diff"> use Class::Struct;</span>
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2775
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<pre style="margin: 0;">-<span id="LC2775" class="line" lang="diff"> </span>
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2776
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2776" class="line" lang="diff"> #</span>
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<td class="diff-line-num old old_line" data-linenumber="2777" 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">
2777
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<pre style="margin: 0;">-<span id="LC2777" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -17,7 +17,8 @@</span></span>
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2778
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<pre style="margin: 0;">-<span id="LC2778" class="line" lang="diff"> system("umask 006");</span>
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<td class="diff-line-num old old_line" data-linenumber="2779" 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">
2779
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<pre style="margin: 0;">-<span id="LC2779" class="line" lang="diff"> my $bin = "$SIFT_HOME/bin";</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2780" 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">
2780
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<pre style="margin: 0;">-<span id="LC2780" class="line" lang="diff"> $snp_classifier = "$bin/Classify_SNPs.pl";</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2781" 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">
2781
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<pre style="margin: 0;">-<span id="LC2781" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-require 'SIFT_subroutines.pm';</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2782" 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">
2782
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<pre style="margin: 0;">-<span id="LC2782" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+use lib '/usr/lib/sift/bin';</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2783" 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">
2783
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<pre style="margin: 0;">-<span id="LC2783" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+use SIFT_subroutines;</span></span>
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2784
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<pre style="margin: 0;">-<span id="LC2784" class="line" lang="diff"> my $tmp = $ARGV[0];</span>
</pre>
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2785
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<pre style="margin: 0;">-<span id="LC2785" class="line" lang="diff"> my $Variation_db_dir = $ARGV[1];</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2786" 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">
2786
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<pre style="margin: 0;">-<span id="LC2786" class="line" lang="diff"> my $master_pid = $ARGV[2];</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2787" 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">
2787
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<pre style="margin: 0;">-<span id="LC2787" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/Clumping.c</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2788" 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">
2788
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<td class="diff-line-num new_line old" data-linenumber="1775" 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="LC2788" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/Clumping.c</span></span>
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2789
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<pre style="margin: 0;">-<span id="LC2789" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -183,7 +183,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC1775" class="line" lang="diff"><span class="gh" style="color: #999;">Index: sift/src/Clumping.c</span></span>
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1776
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<pre style="margin: 0;">+<span id="LC1776" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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1777
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<pre style="margin: 0;">+<span id="LC1777" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- sift.orig/src/Clumping.c</span></span>
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1778
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<pre style="margin: 0;">+<span id="LC1778" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ sift/src/Clumping.c</span></span>
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1779
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<pre style="margin: 0;">+<span id="LC1779" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -175,7 +175,7 @@ printf ("entered if statment\n");</span></span>
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2790
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1780
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<pre style="margin: 0;"> <span id="LC1780" class="line" lang="diff"> printf ("Clumped %d sequences into %d clusters\n", nseq, iclus);</span>
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2791
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1781
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<pre style="margin: 0;"> <span id="LC1781" class="line" lang="diff"> /* keep this print because get # of clustersin awk statement */</span>
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2792
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1782
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<pre style="margin: 0;"> <span id="LC1782" class="line" lang="diff"> free(pairs);</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2795" 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="1785" 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">@@ -2795,7 +1785,7 @@</td>
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2795
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1785
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<pre style="margin: 0;"> <span id="LC1785" class="line" lang="diff"> return clusters_of_seqs;</span>
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2796
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1786
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<pre style="margin: 0;"> <span id="LC1786" class="line" lang="diff"> } /* end of cluster */</span>
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2797
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1787
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<pre style="margin: 0;"> <span id="LC1787" class="line" lang="diff"> </span>
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2798
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<pre style="margin: 0;">-<span id="LC2798" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -4<span class="idiff left right">40,7 +440,7 @@</span></span></span>
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<pre style="margin: 0;">+<span id="LC1788" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -4<span class="idiff left right">32,7 +432,7 @@ printf ("entered if statment\n");</span></span></span>
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2799
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1789
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<pre style="margin: 0;"> <span id="LC1789" class="line" lang="diff"> printf ("Clumped %d sequences into %d clusters\n", nseq, i2);</span>
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2800
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1790
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<pre style="margin: 0;"> <span id="LC1790" class="line" lang="diff"> /* keep this print because get # of clustersin awk statement */</span>
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2801
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1791
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<pre style="margin: 0;"> <span id="LC1791" class="line" lang="diff"> free(pairs);</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2804" 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="1794" 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">@@ -2804,8 +1794,10 @@</td>
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2804
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1794
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<pre style="margin: 0;"> <span id="LC1794" class="line" lang="diff"> return no_of_clumps;</span>
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2805
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1795
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<pre style="margin: 0;"> <span id="LC1795" class="line" lang="diff"> } /* end of cluster */</span>
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2806
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1796
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<pre style="margin: 0;"> <span id="LC1796" class="line" lang="diff"> </span>
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1797
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<pre style="margin: 0;">+<span id="LC1797" class="line" lang="diff"><span class="gh" style="color: #999;">Index: sift/info_on_seqs.pod</span></span>
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1798
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<pre style="margin: 0;">+<span id="LC1798" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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2807
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1799
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<pre style="margin: 0;"> <span id="LC1799" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- /dev/null</span></span>
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2808
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<pre style="margin: 0;">-<span id="LC2808" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b</span>/info_on_seqs.pod</span></span>
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<pre style="margin: 0;">+<span id="LC1800" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">sift</span>/info_on_seqs.pod</span></span>
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<pre style="margin: 0;"> <span id="LC1801" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -0,0 +1,46 @@</span></span>
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1802
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<pre style="margin: 0;"> <span id="LC1802" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+=head1 NAME</span></span>
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1803
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<pre style="margin: 0;"> <span id="LC1803" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<a href="https://salsa.debian.org/med-team/sift/commit/4a2c15772a02139e4e87f8c5aaf901d8ea9f4cad#c53a6a0c5788a03f80ac1101bb0f08d31eb8249a"><strong>debian/patches/jarfile</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff">Author: Laszlo Kajan <lkajan@rostlab.org></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff">Description: path to IntersectFeatures.jar</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"> IntersectFeatures.jar file now in /usr/share, patch for calling script.</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/bin/IntersectLocations.sh</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/bin/IntersectLocations.sh</span></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,3 +1,3 @@</span></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"> #!/bin/sh</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-bin="/usr/local/projects/SIFT/sift4.0/bin/"</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+bin="/usr/share/sift"</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> java -Xmx500m -jar $bin/IntersectFeatures.jar $1 $2 $3 $4 $5</span></pre>
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<a href="https://salsa.debian.org/med-team/sift/commit/4a2c15772a02139e4e87f8c5aaf901d8ea9f4cad#5053077081e60564d2ba8d7dfed0c73e49a574a4"><strong>debian/patches/ld-as-needed</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">@@ -10,18 +10,20 @@ Description: src/Makefile patch</td>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> same result.</span>
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11
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff">Author: Michael Bienia <geser@ubuntu.com></span>
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12
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff">Author: Laszlo Kajan <lkajan@rostlab.org></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;">--- a/src/Makefile</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;">+++ b/src/Makefile</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -9,8 +9,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gh" style="color: #999;">Index: sift/src/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- sift.orig/src/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ sift/src/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -9,8 +9,10 @@ BIN := choose_seqs_via_psiblastseedmedia</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> seqs_from_psiblast_res</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"> CC := gcc</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CFLAGS := -I$(include-prefix)/include/blimps -O2 -D__MAKE_PREFIX__=\"$(prefix)\" $(CFLAGS)</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;">-LDFLAGS := -L$(lib-prefix)/lib -lblimps $(LDFLAGS)</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CPPFLAGS <span class="idiff left right">:</span>= $(shell dpkg-buildflags --get CPPFLAGS)</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CFLAGS <span class="idiff left right">:= $(shell dpkg-buildflags --get CFLAGS)</span> -Wno-unused-result -I$(include-prefix)/include/blimps -O2 -D__MAKE_PREFIX__=\"$(prefix)\"</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;">+LDFLAGS <span class="idiff left right">:= $(shell dpkg-buildflags --get LDFLAGS)</span> -L$(lib-prefix)/lib</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+LDLIBS <span class="idiff left right">:</span>= -lblimps -lm</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;">+CPPFLAGS <span class="idiff left right">?</span>= $(shell dpkg-buildflags --get CPPFLAGS)</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CFLAGS <span class="idiff left right">+=</span> -Wno-unused-result -I$(include-prefix)/include/blimps -O2 -D__MAKE_PREFIX__=\"$(prefix)\"</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+LDFLAGS <span class="idiff left right">+=</span> -L$(lib-prefix)/lib</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;">+LDLIBS <span class="idiff left right"> +</span>= -lblimps -lm</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="diff"> all: bin</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/sift/commit/4a2c15772a02139e4e87f8c5aaf901d8ea9f4cad#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">fix_perl_interpreter_and_lib_path</span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">ld-as-needed</span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">fix_gcc_warnings</span></pre>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">jarfile</span></pre>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">#!/usr/bin/make -f</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"># Uncomment this to turn on verbose mode.</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">#export DH_VERBOSE=1</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">export DH_VERBOSE = 1</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS = hardening=+all</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">export DEB_CFLAGS_MAINT_APPEND = -Wall -pedantic</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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5
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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6
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">PACKAGE:=sift</span>
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7
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">DESTDIR:=$(CURDIR)/debian/$(PACKAGE)</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">VERSION:=<span class="idiff left right">4.0.3b</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">VERSION:=<span class="idiff left right">6.2.1</span></span>
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9
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">prefix:=/usr</span>
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10
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">pkgdatadir:=$(prefix)/share/$(PACKAGE)</span>
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11
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="38" 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">@@ -38,6 +42,14 @@ override_dh_auto_clean:</td>
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38
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42
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext"> rm -f bin/process_alignment</span>
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39
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43
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"> rm -f bin/psiblast_res_to_fasta_dbpairwise</span>
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40
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"> rm -f bin/seqs_from_psiblast_res</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> rm -f src/choose_seqs_via_psiblastseedmedian</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> rm -f src/clump_output_alignedseq</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> rm -f src/consensus_to_seq</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> rm -f src/deps.mk</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> rm -f src/info_on_seqs</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> rm -f src/psiblast_res_to_fasta_dbpairwise</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> rm -f src/seqs_from_psiblast_res</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> find . -name "*.o" -delete</span>
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53
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext">override_dh_auto_build: man</span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext"> make -j$(parallel) -C src prefix=$(prefix) VERSION=$(VERSION) deps.mk && \</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -49,24 +61,43 @@ override_dh_auto_install:</td>
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49
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext">override_dh_install:</span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext"> # lkajan: fastaseqs comes from the blimps package, this source does not have rules for creating it</span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext"> dh_install -X.svn -X.swp -XIntersectFeatures.jar -XManuals -Xfastaseqs -Xlinux -Xsolaris bin $(prefix)/lib/sift/</span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext"> dh_install bin/IntersectFeatures.jar $(pkgdatadir)/</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> <span class="idiff left right">#</span>dh_install bin/IntersectFeatures.jar $(pkgdatadir)/</span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext"> dh_install -X.svn -X.swp blimps/docs $(prefix)/share/sift/blimps/</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="plaintext"> #Links are created by debian/links</span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="plaintext"> for f in SIFT_for_submitting_fasta_seq.csh SIFT_for_submitting_NCBI_gi_id.csh; do \</span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="plaintext"> sed --in-place -e 's|\b__MAKE_PREFIX__\b|$(prefix)|g;s|__SIFT_SCRIPTDIR__|$(SIFT_SCRIPTDIR)|g;s|__SIFT_BINDIR__|$(SIFT_BINDIR)|g;' $(DESTDIR)$(SIFT_SCRIPTDIR)/$$f; \</span>
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57
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="plaintext"> done;</span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext"> for f in seqs_chosen_via_median_info.csh SIFT_for_submitting_fasta_seq.csh SIFT_for_submitting_NCBI_gi_id.csh; do \</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> </span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"> for f in seqs_chosen_via_median_info.csh \</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"> SIFT_for_submitting_fasta_seq.csh \</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"> SIFT_for_submitting_NCBI_gi_id.csh; \</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"> do \</span>
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59
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="plaintext"> sed --in-place -e 's|\b__MAKE_PREFIX__\b|$(prefix)|g;s|__SIFT_SCRIPTDIR__|$(SIFT_SCRIPTDIR)|g;s|__SIFT_BINDIR__|$(SIFT_BINDIR)|g;' $(DESTDIR)$(SIFT_SCRIPTDIR)/$$f; \</span>
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60
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="plaintext"> done;</span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext"> <span class="idiff left right">chmod +x $(DESTDIR)$(prefix)/lib/sift/bin/perlscripts/separate_query_from_rest_of_seqs.pl</span></span>
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<td class="diff-line-num new new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"> </span>
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62
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="plaintext"> # look out: DNA_PROT_SUBROUTINES.pl is really a module (should be pm)!</span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext"> for f in SIFT_subroutines.pm DNA_PROT_SUBROUTINES.pl; do \</span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext"> chmod -x $(DESTDIR)$(prefix)/lib/sift/bin/$$f; \</span>
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<td class="diff-line-num new new_line" data-linenumber="80" 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">
80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"> # Update: Not existing at all in 6.2.1</span>
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<td class="diff-line-num new new_line" data-linenumber="81" 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">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"> for f in SIFT_subroutines.pm \</span>
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<td class="diff-line-num new new_line" data-linenumber="82" 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">
82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext"> DNA_PROT_SUBROUTINES.pl \</span>
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<td class="diff-line-num new new_line" data-linenumber="83" 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">
83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext"> perlscripts/get_BLINK_seq.pl \</span>
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<td class="diff-line-num new new_line" data-linenumber="84" 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">
84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext"> perlscripts/separate_query_from_rest_of_seqs.pl \</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext"> perlscripts/separate_query_from_database.pl; \</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext"> do \</span>
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<td class="diff-line-num new new_line" data-linenumber="87" 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">
87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext"> ff="$(DESTDIR)$(prefix)/lib/sift/bin/$$f"; \</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext"> if [ -r "$$ff" ]; then \</span>
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<td class="diff-line-num new new_line" data-linenumber="89" 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">
89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext"> sed -i '1s%/usr/local/bin/%/usr/bin/%' $$ff; \</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext"> chmod +x $$ff; \</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext"> fi; \</span>
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65
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<td class="diff-line-num new_line" data-linenumber="92" 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">
92
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="plaintext"> done;</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext"> </span>
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<td class="diff-line-num old_line" data-linenumber="66" 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">
66
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<td class="diff-line-num new_line" data-linenumber="94" 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">
94
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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="LC94" class="line" lang="plaintext"> for f in IntersectFeatures.jar; do \</span>
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<td class="diff-line-num old old_line" data-linenumber="67" 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">
67
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<td class="diff-line-num new_line old" data-linenumber="95" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC67" class="line" lang="plaintext"> chmod -x $(DESTDIR)$(pkgdatadir)/$$f; \</span>
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<td class="diff-line-num new old_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
95
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext"> if [ -r "$(DESTDIR)$(pkgdatadir)/$$f" ]; then \</span>
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<td class="diff-line-num new old_line" data-linenumber="68" 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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<td class="diff-line-num new new_line" data-linenumber="96" 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">
96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"> chmod -x $(DESTDIR)$(pkgdatadir)/$$f; \</span>
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<td class="diff-line-num new old_line" data-linenumber="68" 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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<td class="diff-line-num new new_line" data-linenumber="97" 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">
97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext"> fi; \</span>
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<td class="diff-line-num old_line" data-linenumber="68" 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">
68
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<td class="diff-line-num new_line" data-linenumber="98" 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">
98
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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="LC98" class="line" lang="plaintext"> done;</span>
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69
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<td class="diff-line-num new_line" data-linenumber="99" 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">
99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="70" 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">
70
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<td class="diff-line-num new_line" data-linenumber="100" 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">
100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="plaintext">get-orig-source:</span>
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<td class="diff-line-num old_line" data-linenumber="71" 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">
71
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<td class="diff-line-num new_line" data-linenumber="101" 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">
101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="plaintext"> mkdir -p ../tarballs</span>
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<td class="diff-line-num old_line" data-linenumber="72" 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">
72
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<td class="diff-line-num new_line" data-linenumber="102" 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">
102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="plaintext"> uscan --verbose --force-download --destdir=../tarballs</span>
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<td class="diff-line-num new old_line" data-linenumber="73" 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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<td class="diff-line-num new new_line" data-linenumber="103" 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">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext"></span></pre>
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<li id="85ccdeeb03055211183e48520592d9a93592b330">
<a href="https://salsa.debian.org/med-team/sift/commit/4a2c15772a02139e4e87f8c5aaf901d8ea9f4cad#85ccdeeb03055211183e48520592d9a93592b330"><strong>debian/source/lintian-overrides</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">sift source: source-includes-file-in-files-excluded bin/choose_seqs_via_psiblastseedmedian</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">sift source: source-includes-file-in-files-excluded bin/clump_output_alignedseq</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">sift source: source-includes-file-in-files-excluded bin/consensus_to_seq</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">sift source: source-includes-file-in-files-excluded bin/info_on_seqs</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">sift source: source-includes-file-in-files-excluded bin/psiblast_res_to_fasta_dbpairwise</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">sift source: source-includes-file-in-files-excluded bin/seqs_from_psiblast_res</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span></pre>
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