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<h3>
Fabian Klötzl pushed to branch master
at <a href="https://salsa.debian.org/med-team/theseus">Debian Med / theseus</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/theseus/commit/d3c09ec35a991316e6cd59f0c848b59d207a434e">d3c09ec3</a></strong>
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<span>by Fabian Klötzl</span>
<i>at 2018-09-10T10:38:15Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix issues uncovered by gcc 8
</pre>
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<strong><a href="https://salsa.debian.org/med-team/theseus/commit/bbe22ea999b2d1933f45d8676876ecab9ffbae5a">bbe22ea9</a></strong>
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<span>by Fabian Klötzl</span>
<i>at 2018-09-10T10:38:53Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">create lib directory during build
</pre>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#bd09bf5875aeccbd9c5ae4c70d112093e3bf2590">
<span class="new-file">
+
debian/patches/0003-fix-issues-uncovered-by-gcc8.patch
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</a>
</li>
<li class="file-stats">
<a href="#200e4ccacc6026e14964a051d24712f4768fcf65">
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+
debian/patches/0004-create-lib-dir.patch
</span>
</a>
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/theseus/compare/fc973f3ea997f1857ddaec2e4001727b0b301a63...bbe22ea999b2d1933f45d8676876ecab9ffbae5a#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">theseus (3.3.0-7) UNRELEASED; 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"> * Non-maintainer upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Fix string bugs uncovered by gcc8</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Closes: #908459</span>
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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"> -- Fabian Kloetzl <kloetzl@evolbio.mpg.de> Mon, 10 Sep 2018 09:56:01 +0000</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">theseus (3.3.0-6) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * Move packaging from SVN to Git</span>
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<li id="bd09bf5875aeccbd9c5ae4c70d112093e3bf2590">
<a href="https://salsa.debian.org/med-team/theseus/compare/fc973f3ea997f1857ddaec2e4001727b0b301a63...bbe22ea999b2d1933f45d8676876ecab9ffbae5a#bd09bf5875aeccbd9c5ae4c70d112093e3bf2590"><strong>debian/patches/0003-fix-issues-uncovered-by-gcc8.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">From: =?utf-8?q?Fabian_Kl=C3=B6tzl?= <fabian@kloetzl.info></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Date: Mon, 10 Sep 2018 07:51:18 +0000</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Subject: fix issues uncovered by gcc8</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">---</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> MultiPose2MSA.c | 17 ++++++++---------</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> PCAstats.c | 4 ++--</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> RandCds.c | 11 +++++------</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> StructAlign.c | 2 +-</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> libDLTutils/DLTutils.c | 4 ++--</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> libmsa/msa.c | 8 ++++----</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> make.inc | 2 +-</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> pdbIO.c | 44 ++++++++++++++++++--------------------------</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> pdbMalloc.c | 2 +-</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> pdbUtils.c | 18 ++++++++----------</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> theseus.c | 15 +++++++--------</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> 11 files changed, 57 insertions(+), 70 deletions(-)</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/MultiPose2MSA.c b/MultiPose2MSA.c</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gh" style="color: #999;">index 47f93dc..2cc4442 100644</span></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;">--- a/MultiPose2MSA.c</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;">+++ b/MultiPose2MSA.c</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -178,7 +178,7 @@ Align2segID(PDBCdsArray *pdbA)</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> while(cdsi->resSeq[k] == resSeq)</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> {</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;">- strncpy(cdsi->segID[k], alnindex, 4);</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;">+ strcpy(cdsi->segID[k], alnindex);</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> //printf("\n%s %4d %4d %s %4d %c %5d", cdsi->segID[k], i, k, alnindex, resSeq, seq[j], cdsi->vlen);</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> //fflush(NULL);</span>
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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"><span class="gu" style="color: #800080; font-weight: 600;">@@ -635,7 +635,7 @@ GetCdsFrAlignment(PDBCdsArray *pdbA, CdsArray *baseA,</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> if (msa->seq[k][p] != '-') /* not a gap */</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncpy(cdsj->resName[n], pdbj->resName[m], 3);</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;">+ strcpy(cdsj->resName[n], pdbj->resName[m]); // possibly problematic</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> cdsj->chainID[n] = pdbj->chainID[m];</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> cdsj->resSeq[n] = pdbj->resSeq[m];</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> cdsj->x[n] = pdbj->x[m];</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -650,7 +650,7 @@ GetCdsFrAlignment(PDBCdsArray *pdbA, CdsArray *baseA,</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> }</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> else /* is a gap */</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncpy(cdsj->resName[n], "GAP", 3);</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ strcpy(cdsj->resName[n], "GAP");</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> cdsj->chainID[n] = pdbj->chainID[m];</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> cdsj->resSeq[n] = 0;</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> cdsj->x[n] = 0.0;</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -696,7 +696,7 @@ GetCdsFrAlignment(PDBCdsArray *pdbA, CdsArray *baseA,</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> for (q = n; q < vlen; ++q)</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncpy(cdsj->resName[q], "GAP", 3);</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ strcpy(cdsj->resName[q], "GAP");</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> cdsj->chainID[q] = pdbj->chainID[m-1];</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> cdsj->resSeq[q] = 0;</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> cdsj->x[q] = 0.0;</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -912,7 +912,7 @@ Align2MSA_singletons(PDBCdsArray *pdbA, CdsArray *baseA, MSA *msa)</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> </span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> for (i = 0; i < cnum; ++i)</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncpy(baseA->cds[i]->filename, pdbA->cds[i]->filename, FILENAME_MAX - 1);</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ snprintf(baseA->cds[i]->filename, FILENAME_MAX, "%s", pdbA->cds[i]->filename);</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> </span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> VerifyAlignmentVsPDBs(pdbA, baseA, msa, algo->atoms, pdbA->seq2pdb->map);</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> GetCdsFrAlignment(pdbA, baseA, pdbA->seq2pdb, msa, vlen, alnlen, pdbA->seq2pdb->singletons);</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -971,7 +971,7 @@ Align2MSA_crush(PDBCdsArray *pdbA, CdsArray *baseA, MSA *msa)</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> }</span>
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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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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> for (i = 0; i < cnum; ++i)</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;">- strncpy(baseA->cds[i]->filename, pdbA->cds[i]->filename, FILENAME_MAX - 1);</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;">+ snprintf(baseA->cds[i]->filename, FILENAME_MAX, "%s", pdbA->cds[i]->filename);</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> </span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> VerifyAlignmentVsPDBs(pdbA, baseA, msa, algo->atoms, pdbA->seq2pdb->map);</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> GetCdsFrAlignment(pdbA, baseA, pdbA->seq2pdb, msa, vlen, alnlen, pdbA->seq2pdb->singletons);</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1041,7 +1041,7 @@ Align2MSA(PDBCdsArray *pdbA, CdsArray *baseA, char *msafile_name, char *mapfile_</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> }</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> </span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> for (i = 0; i < cnum; ++i)</span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncpy(baseA->cds[i]->filename, pdbA->cds[i]->filename, FILENAME_MAX - 1);</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ snprintf(baseA->cds[i]->filename, FILENAME_MAX, "%s", pdbA->cds[i]->filename);</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> VerifyAlignmentVsPDBs(pdbA, baseA, msa, algo->atoms, pdbA->seq2pdb->map);</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> GetCdsFrAlignment(pdbA, baseA, pdbA->seq2pdb, msa, vlen, alnlen, pdbA->seq2pdb->singletons);</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1107,8 +1107,7 @@ pdb2fst(PDBCdsArray *pdbA)</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> for (i = 0; i < pdbA->cnum; ++i)</span>
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88
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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"> pdbi = (const PDBCds *) pdbA->cds[i];</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;">- strncpy(outfile, pdbi->filename, strlen(pdbi->filename)+1);</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;">- strncat(outfile, ".fst", 4);</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;">+ snprintf(outfile, FILENAME_MAX, "%.*s.fst", (int)FILENAME_MAX - 5, pdbi->filename);</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> fp = fopen(outfile, "w");</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/PCAstats.c b/PCAstats.c</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gh" style="color: #999;">index 41114ea..912574f 100644</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/PCAstats.c</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;">+++ b/PCAstats.c</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -428,7 +428,7 @@ WritePCAFile(PDBCdsArray *parray, CdsArray *cdsA, const char *outfile_root)</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> }</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> </span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> if (algo->cormat == 0)</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncpy(covcor_str, "covariance", 10);</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ memcpy(covcor_str, "covariance", 11);</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> </span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> fprintf(pdbfile, "REMARK ===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-=\n");</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"> fprintf(pdbfile, "REMARK + File made by Douglas Theobald's THESEUS program\n");</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -551,7 +551,7 @@ CalcFullCovMat(cdsA);</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> }</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> </span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> if (algo->cormat == 0)</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncpy(covcor_str, "covariance", 10);</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ memcpy(covcor_str, "covariance", 11);</span></span>
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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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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"> fprintf(pdbfile, "REMARK ===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-===-=\n");</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"> fprintf(pdbfile, "REMARK + File made by Douglas Theobald's THESEUS program \n");</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/RandCds.c b/RandCds.c</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="gh" style="color: #999;">index cb0bdac..3f77cb2 100644</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/RandCds.c</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/RandCds.c</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -735,14 +735,13 @@ PDBCdsArray</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"> PDBCdsArray *pdbA = NULL;</span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"> </span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"> if (getenv("PDBDIR"))</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncpy(pdbdir, getenv("PDBDIR"), FILENAME_MAX);</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ snprintf(pdbdir, FILENAME_MAX, "%.*s", (int)FILENAME_MAX - 1, getenv("PDBDIR"));</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"> </span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"> /* count atoms in first model and allocate */</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"> pdbfile = fopen(pdbfile_name, "r");</span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"> if (pdbfile == NULL)</span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncpy(dirpdbfile_name, pdbdir, FILENAME_MAX - 1);</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncat(dirpdbfile_name, pdbfile_name, FILENAME_MAX - strlen(pdbfile_name) - 1);</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ snprintf(dirpdbfile_name, FILENAME_MAX, "%s/%s", pdbdir, pdbfile_name);</span></span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"> </span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"> pdbfile = fopen(dirpdbfile_name, "r");</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="gu" style="color: #800080; font-weight: 600;">@@ -818,12 +817,12 @@ PDBCdsArray</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"> for (i = 0; i < vlen; ++i)</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"> {</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"> /* # COLs LEN DATA TYPE FIELD DEFINITION */</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;">- strncpy(cds->record[i], "ATOM ", 6); /* 1 0-5 6 Record name "ATOM " */</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;">+ strncpy(cds->record[i], "ATOM ", 7); /* 1 0-5 6 Record name "ATOM " */</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"> cds->serial[i] = i + 1; /* 2 6-10 5 Integer serial Atom serial number. */</span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncpy(cds->name[i], "CA ", 3); /* 4 13-15 4(3) Atom name Atom name. */</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;">+ strncpy(cds->name[i], "CA ", 4); /* 4 13-15 4(3) Atom name Atom name. */</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"> cds->Hnum[i] = ' '; /* 3 15 1 hydrogen number, (!official). */</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"> cds->altLoc[i] = ' '; /* 5 16 1 Character altLoc Alternate location indicator. */</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncpy(cds->resName[i], "ALA", 3); /* 6 17-19 3 Residue name resName Residue name. */</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;">+ strncpy(cds->resName[i], "ALA", 4); /* 6 17-19 3 Residue name resName Residue name. */</span></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"> cds->xchainID[i] = ' '; /* 7 20 1 Character xchainID Chain identifier (!official). */</span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"> cds->chainID[i] = 'A'; /* 8 21 1 Character chainID Chain identifier. */</span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"> cds->resSeq[i] = i + 1; /* 9 22-25 4 Integer resSeq Residue sequence number. */</span>
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/StructAlign.c b/StructAlign.c</span></span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"><span class="gh" style="color: #999;">index 7a32c12..9d4f234 100644</span></span>
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/StructAlign.c</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/StructAlign.c</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -378,7 +378,7 @@ StructAlign(PDBCdsArray *pdbA, int iCommon, CdsArray *cdsA, NWtable **nwTableA)</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"> jj -= 4; // To get rid of the filename extension</span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"> </span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"> fNamePt1[jj] = 0;</span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sprintf(fNamePt2, "%s_%s", fNamePt1, nwti->msa->name[1]);</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ snprintf(fNamePt2, FILENAME_MAX, "%s_%s", fNamePt1, nwti->msa->name[1]);</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"> jj = strlen(fNamePt2);</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"> </span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"> if (jj >= FILENAME_MAX)</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/libDLTutils/DLTutils.c b/libDLTutils/DLTutils.c</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"><span class="gh" style="color: #999;">index af51a61..f60c657 100644</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/libDLTutils/DLTutils.c</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/libDLTutils/DLTutils.c</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -156,7 +156,7 @@ char</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"> size_t len = strlen(s2); /* minimum allocated length of s2 */</span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"> len = MYMIN(n, len);</span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"> </span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncpy(s1, s2, len);</span></span>
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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;">+ memcpy(s1, s2, len);</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"> s1[len] = '\0';</span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"> </span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"> return(s1);</span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -170,7 +170,7 @@ char</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"> {</span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"> size_t len = strlen(s2);</span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"> </span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncpy(s1, s2, len);</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ memcpy(s1, s2, len);</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"> s1[len] = '\0';</span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"> </span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"> return(s1);</span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/libmsa/msa.c b/libmsa/msa.c</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"><span class="gh" style="color: #999;">index 867aa8a..3be8ad7 100644</span></span>
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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;">--- a/libmsa/msa.c</span></span>
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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;">+++ b/libmsa/msa.c</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;">@@ -953,10 +953,10 @@ MSAcombine2(MSAA *msaa, int msa1_i, int msa2_i, int seq1_i, int seq2_i, int msao</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"> </span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"> /* copy the names over */</span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"> for (m = 0; m < num1; ++m)</span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncpy(msao->name[m], msa1->name[m], strlen(msa1->name[m])+1);</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ strcpy(msao->name[m], msa1->name[m]);</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"> </span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"> for (m = 0; m < num2; ++m)</span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncpy(msao->name[m + num1], msa2->name[m], strlen(msa2->name[m])+1);</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ strcpy(msao->name[m + num1], msa2->name[m]);</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"> </span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"> i = j = k = 0;</span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="207" 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">
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;">@@ -1107,7 +1107,7 @@ reada2m(char *msafile_name, MSA *msa)</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"> exit(EXIT_FAILURE);</span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"> }</span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"> </span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncpy(msa->filename, msafile_name, strlen(msafile_name));</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ strcpy(msa->filename, msafile_name);</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff"> </span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff"> /* get the number of sequences in the a2m file */</span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"> msa->allocnum = 0;</span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1294,7 +1294,7 @@ readaln(char *msafile_name, MSA *msa)</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"> }</span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"> rewind(msafile);</span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncpy(msa->filename, msafile_name, strlen(msafile_name));</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ strcpy(msa->filename, msafile_name);</span></span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"> /* get the number of sequences in the aln file */</span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"> /* first skip "CLUSTAL" header line */</span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/make.inc b/make.inc</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"><span class="gh" style="color: #999;">index 54192dc..06bbfe9 100644</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/make.inc</span></span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/make.inc</span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -81,7 +81,7 @@ CC = /usr/bin/gcc</span></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"> OPT = -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer</span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"> ## OPT = -m64 -O3 -march=native -funroll-loops -ffast-math -mfpmath=sse</span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"> #OPT = -O0 -ggdb</span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-WARN = -Wall -Werror -pedantic -std=c99 -Wno-unused-result</span></span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+WARN = -Wall -Werror -pedantic -std=c99 -Wno-unused-result -Wformat-truncation=0</span></span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"> CFLAGS = $(WARN) -pthread</span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"> #CC = /usr/local/bin/gcc</span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"> </span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/pdbIO.c b/pdbIO.c</span></span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff"><span class="gh" style="color: #999;">index 7332f16..64f5ce9 100644</span></span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pdbIO.c</span></span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pdbIO.c</span></span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -370,7 +370,7 @@ ReadPDBCds(char *pdbfile_name, PDBCdsArray *pdbA, int cds_i, int modelnum, int a</span></span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"> char *buff = NULL;</span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff"> int i, j, pos;</span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"> FILE *pdbfile = NULL;</span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char pdbdir[FILENAME_MAX], dirpdbfile_name[FILENAME_MAX];</span></span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ char dirpdbfile_name[FILENAME_MAX];</span></span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="diff"> PDBCds **cds = pdbA->cds;</span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="diff"> PDBCds *cp = NULL;</span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -391,9 +391,7 @@ ReadPDBCds(char *pdbfile_name, PDBCdsArray *pdbA, int cds_i, int modelnum, int a</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"> if (getenv("PDBDIR"))</span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncpy(pdbdir, getenv("PDBDIR"), FILENAME_MAX);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="256" 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">
256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncpy(dirpdbfile_name, pdbdir, FILENAME_MAX - 1);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="257" 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">
257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncat(dirpdbfile_name, pdbfile_name, FILENAME_MAX - strlen(pdbfile_name) - 1);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="258" 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">
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;">+ snprintf(dirpdbfile_name, FILENAME_MAX, "%s/%s", getenv("PDBDIR"), pdbfile_name);</span></span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="diff"> </span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="diff"> pdbfile = fopen(dirpdbfile_name, "r");</span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="diff"> }</span>
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<td class="diff-line-num new new_line" data-linenumber="262" 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">
262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -476,12 +474,12 @@ ScanTPSLine(char *buff, PDBCds *cp, int j)</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="diff"> // if (endline) /* kill the newline, if there */</span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="diff"> // *endline = '\0';</span>
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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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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncpy(cp->record[j], "ATOM ", 6);</span></span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ strncpy(cp->record[j], "ATOM ", 7);</span></span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="diff"> cp->serial[j] = j;</span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="diff"> cp->Hnum[j] = ' ';</span>
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<td class="diff-line-num new new_line" data-linenumber="270" 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">
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;">- strncpy(cp->name[j], "CA ", 3);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="271" 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">
271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ strncpy(cp->name[j], "CA ", 4);</span></span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="diff"> cp->altLoc[j] = ' ';</span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncpy(cp->resName[j], "LM ", 3);</span></span>
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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;">+ strncpy(cp->resName[j], "LM ", 4);</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="diff"> cp->xchainID[j] = ' ';</span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="diff"> cp->chainID[j] = 'A';</span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="diff"> cp->resSeq[j] = j;</span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -489,9 +487,9 @@ ScanTPSLine(char *buff, PDBCds *cp, int j)</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="diff"> numret = sscanf(buff, "%lf%lf%lf", &cp->x[j], &cp->y[j], &cp->z[j]);</span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="diff"> cp->occupancy[j] = 1.0;</span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="diff"> cp->tempFactor[j] = 1.0;</span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncpy(cp->segID[j], " ", 4);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="283" 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">
283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncpy(cp->element[j], " ", 2);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="284" 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">
284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncpy(cp->charge[j], " ", 2);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="285" 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">
285
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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="LC285" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ strncpy(cp->segID[j], " ", 5);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="286" 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">
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;">+ strncpy(cp->element[j], " ", 3);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="287" 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">
287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ strncpy(cp->charge[j], " ", 3);</span></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="diff"> cp->nu[j] = 1;</span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="diff"> </span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="diff"> return(numret);</span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -506,7 +504,7 @@ ReadTPSCds(char *pdbfile_name, PDBCdsArray *pdbA, int cds_i, int modelnum)</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="diff"> char *buff = NULL;</span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="diff"> int i, j, pos, numret;</span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="diff"> FILE *pdbfile = NULL;</span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char pdbdir[FILENAME_MAX], dirpdbfile_name[FILENAME_MAX];</span></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ char dirpdbfile_name[FILENAME_MAX];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="297" 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">
297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="diff"> PDBCds **cds = pdbA->cds;</span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="diff"> PDBCds *cp = NULL;</span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="diff"> </span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -527,9 +525,7 @@ ReadTPSCds(char *pdbfile_name, PDBCdsArray *pdbA, int cds_i, int modelnum)</span></span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="diff"> {</span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="diff"> if (getenv("PDBDIR"))</span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="diff"> {</span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncpy(pdbdir, getenv("PDBDIR"), FILENAME_MAX);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="305" 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">
305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncpy(dirpdbfile_name, pdbdir, FILENAME_MAX - 1);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="306" 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">
306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncat(dirpdbfile_name, pdbfile_name, FILENAME_MAX - strlen(pdbfile_name) - 1);</span></span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ snprintf(dirpdbfile_name, FILENAME_MAX, "%s/%s", getenv("PDBDIR"), pdbfile_name);</span></span>
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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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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="diff"> pdbfile = fopen(dirpdbfile_name, "r");</span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="diff"> }</span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -619,7 +615,7 @@ PDBCdsArray</span></span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="diff"> PDBCdsArray *pdbA = NULL;</span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="diff"> </span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="diff"> if (getenv("PDBDIR"))</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;">- strncpy(pdbdir, getenv("PDBDIR"), FILENAME_MAX);</span></span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ snprintf(pdbdir, FILENAME_MAX, "%.*s", (int)FILENAME_MAX - 1, getenv("PDBDIR"));</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="diff"> </span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="diff"> vlen = last_vlen = 0;</span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="diff"> </span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -643,8 +639,7 @@ PDBCdsArray</span></span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="diff"> tpsfile = fopen(tpsfile_name, "r");</span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="diff"> if (tpsfile == NULL)</span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="diff"> {</span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncpy(dirtpsfile_name, pdbdir, FILENAME_MAX - 1);</span></span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncat(dirtpsfile_name, tpsfile_name, FILENAME_MAX - strlen(tpsfile_name) - 1);</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;">+ snprintf(dirtpsfile_name, FILENAME_MAX, "%s/%s", pdbdir, tpsfile_name);</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"> tpsfile = fopen(dirtpsfile_name, "r");</span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -991,11 +986,11 @@ GetCdsSelection(CdsArray *baseA, PDBCdsArray *pdbA)</span></span>
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="diff"> vlen = GetSlxnLen(pdbA, j, algo, chains, lower, upper, range_num, selection_index, 0);</span>
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="diff"> baseA->cds[j]->model = pdbA->cds[j]->model;</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;">- strncpy(baseA->cds[j]->filename, pdbA->cds[j]->filename, FILENAME_MAX - 1);</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;">+ snprintf(baseA->cds[j]->filename, FILENAME_MAX, "%.*s", (int)FILENAME_MAX - 1, pdbA->cds[j]->filename);</span></span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="diff"> for (i = 0; i < baseA->vlen; ++i)</span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncpy(baseA->cds[j]->resName[i], pdbA->cds[j]->resName[selection_index[i]], 3);</span></span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ strncpy(baseA->cds[j]->resName[i], pdbA->cds[j]->resName[selection_index[i]], 4);</span></span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="diff"> baseA->cds[j]->chainID[i] = pdbA->cds[j]->chainID[selection_index[i]];</span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="diff"> baseA->cds[j]->resSeq[i] = pdbA->cds[j]->resSeq[selection_index[i]];</span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="diff"> baseA->cds[j]->x[i] = pdbA->cds[j]->x[selection_index[i]];</span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1035,7 +1030,7 @@ PDBCdsArray</span></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="diff"> PDBCdsArray *pdbA = NULL;</span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="diff"> if (getenv("PDBDIR"))</span>
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncpy(pdbdir, getenv("PDBDIR"), FILENAME_MAX);</span></span>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ snprintf(pdbdir, FILENAME_MAX, "%.*s", (int)FILENAME_MAX - 1, getenv("PDBDIR"));</span></span>
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="diff"> vlen = last_vlen = 0;</span>
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1059,8 +1054,7 @@ PDBCdsArray</span></span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="diff"> pdbfile = fopen(pdbfile_name, "r");</span>
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="diff"> if (pdbfile == NULL)</span>
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="diff"> {</span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncpy(dirpdbfile_name, pdbdir, FILENAME_MAX - 1);</span></span>
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncat(dirpdbfile_name, pdbfile_name, FILENAME_MAX - strlen(pdbfile_name) - 1);</span></span>
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ snprintf(dirpdbfile_name, FILENAME_MAX, "%s/%s", pdbdir, pdbfile_name);</span></span>
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="diff"> pdbfile = fopen(dirpdbfile_name, "r");</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 class="gu" style="color: #800080; font-weight: 600;">@@ -1419,7 +1413,7 @@ char</span></span>
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="diff"> for (ii = 0; ii < myPDBs->cnum; ++ii)</span>
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="diff"> tmpLen = strlen(myPDBs->cds[ii]->filename);</span>
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncpy(tmpStr, myPDBs->cds[ii]->filename, (tmpLen + 1) * sizeof(char));</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;">+ memcpy(tmpStr, myPDBs->cds[ii]->filename, (tmpLen + 1) * sizeof(char));</span></span>
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="diff"> tmpLen--;</span>
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="diff"> while (tmpLen)</span>
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1715,9 +1709,7 @@ WriteTheseusPDBFiles(PDBCdsArray *pdbA, Algorithm *algo, Statistics *stats, char</span></span>
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="diff"> for (i = 0; i < pdbA->cnum; ++i)</span>
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncpy(outfile_name, fname, strlen(fname)+1);</span></span>
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strcat(outfile_name, "_");</span></span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncat(outfile_name, pdbA->cds[i]->filename, strlen(pdbA->cds[i]->filename)+1);</span></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ (void)snprintf(outfile_name, FILENAME_MAX, "%s_%s", fname, pdbA->cds[i]->filename);</span></span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="diff"> //strcpy(outfile_name, getroot(pdbA->cds[i]->filename));</span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="diff"> //strcat(outfile_name, "_ths.pdb");</span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="diff"> </span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/pdbMalloc.c b/pdbMalloc.c</span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="diff"><span class="gh" style="color: #999;">index d750d94..4d0ccbf 100644</span></span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pdbMalloc.c</span></span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pdbMalloc.c</span></span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -301,7 +301,7 @@ CdsArray</span></span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="diff"> exit(EXIT_FAILURE);</span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="diff"> }</span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="diff"> </span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncpy(cdsA->outfile_name, "theseus.pdb", 11);</span></span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ strncpy(cdsA->outfile_name, "theseus.pdb", 12);</span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="diff"> cdsA->anchorf_name = NULL;</span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="diff"> cdsA->mapfile_name = NULL;</span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="diff"> cdsA->msafile_name = NULL;</span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/pdbUtils.c b/pdbUtils.c</span></span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="diff"><span class="gh" style="color: #999;">index 781c77c..bf11b7f 100644</span></span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pdbUtils.c</span></span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pdbUtils.c</span></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -51,7 +51,7 @@ CdsCopyXYZ(Cds *cds1, const Cds *cds2) // DLT FIX MAT COORDS</span></span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="diff"> void</span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="diff"> CdsCopy(Cds *cds1, const Cds *cds2) // DLT FIX MAT COORDS</span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="diff"> {</span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncpy(cds1->filename, cds2->filename, FILENAME_MAX-1);</span></span>
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405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ memcpy(cds1->filename, cds2->filename, FILENAME_MAX);</span></span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="diff"> memcpy(cds1->resSeq, cds2->resSeq, cds2->vlen * sizeof(int));</span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="diff"> memcpy(cds1->x, cds2->x, cds2->vlen * sizeof(double));</span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="diff"> memcpy(cds1->y, cds2->y, cds2->vlen * sizeof(double));</span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -89,7 +89,7 @@ CdsCopyAll(Cds *cds1, const Cds *cds2) // DLT FIX MAT COORDS --- did it</span></span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="diff"> cds1->aalen = cds2->aalen;</span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="diff"> cds1->model = cds2->model;</span>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="diff"> </span>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncpy(cds1->filename, cds2->filename, FILENAME_MAX - 1);</span></span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ memcpy(cds1->filename, cds2->filename, FILENAME_MAX);</span></span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="diff"> </span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="diff"> memcpy(cds1->resName_space, cds2->resName_space, vlen * 4 * sizeof(char));</span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="diff"> memcpy(cds1->chainID, cds2->chainID, vlen * sizeof(char));</span>
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -122,7 +122,7 @@ PDBCdsCopyAll(PDBCds *cds1, const PDBCds *cds2)</span></span>
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="diff"> const int vlen = cds1->vlen = cds2->vlen;</span>
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="diff"> cds1->model = cds2->model;</span>
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncpy(cds1->filename, cds2->filename, FILENAME_MAX-1);</span></span>
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423
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ memcpy(cds1->filename, cds2->filename, FILENAME_MAX);</span></span>
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424
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="diff"> memcpy(cds1->record_space, cds2->record_space, vlen * 8 * sizeof(char));</span>
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="diff"> memcpy(cds1->name_space, cds2->name_space, vlen * 4 * sizeof(char));</span>
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -201,7 +201,6 @@ void</span></span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="diff"> FillSegIDWithResSeq(PDBCds *cds_to, const Cds *cds_from)</span>
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="diff"> int i, rn;</span>
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char resnum[5] ;</span></span>
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="diff"> for (i = 0; i < cds_to->vlen; ++i)</span>
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -209,8 +208,7 @@ FillSegIDWithResSeq(PDBCds *cds_to, const Cds *cds_from)</span></span>
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="diff"> if (rn != 0)</span>
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438
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sprintf(resnum, "%04d", rn);</span></span>
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncpy(cds_to->segID[i], resnum, 4);</span></span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sprintf(cds_to->segID[i], "%04d", rn);</span></span>
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -225,7 +223,7 @@ CopyCds2PDB(PDBCds *pdbcds, const Cds *cds)</span></span>
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="diff"> pdbcds->vlen = cds->vlen;</span>
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="diff"> pdbcds->model = cds->model;</span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncpy(pdbcds->filename, cds->filename, FILENAME_MAX-1);</span></span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ memcpy(pdbcds->filename, cds->filename, FILENAME_MAX);</span></span>
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="diff"> MatCpySqr(pdbcds->matrix, (const double **) cds->matrix, 3);</span>
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -273,9 +271,9 @@ CopyCds2PDB(PDBCds *pdbcds, const Cds *cds)</span></span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="diff"> pdbcds->z[i] = cds->z[i];</span>
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="diff"> pdbcds->occupancy[i] = cds->o[i];</span>
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="diff"> pdbcds->tempFactor[i] = cds->b[i];</span>
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458
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncpy(pdbcds->segID[i], " ", 4);</span></span>
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459
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncpy(pdbcds->element[i], " ", 2);</span></span>
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460
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncpy(pdbcds->charge[i], " ", 2);</span></span>
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ strncpy(pdbcds->segID[i], " ", 5);</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;">+ strncpy(pdbcds->element[i], " ", 3);</span></span>
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ strncpy(pdbcds->charge[i], " ", 3);</span></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"> }</span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/theseus.c b/theseus.c</span></span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="diff"><span class="gh" style="color: #999;">index 5d317ae..819ad43 100644</span></span>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/theseus.c</span></span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/theseus.c</span></span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -492,7 +492,7 @@ AlignPairsThenMultiple(PDBCdsArray *myPDBs, char *argv[])</span></span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="diff"> sprintf(fNameBuff, "AlignmentOf%d", cnum);</span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="diff"> //writealn(rtnMSA, 0, rtnMSA->seqlen, fNameBuff);</span>
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="diff"> writea2m(rtnMSA, 0, rtnMSA->seqlen, fNameBuff);</span>
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475
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncat(fNameBuff, ".a2m", 4);</span></span>
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476
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ strncat(fNameBuff, ".a2m", 5);</span></span>
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477
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="diff"> strcpy(rtnMSA->filename, fNameBuff);</span>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="diff"> //#endif</span>
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479
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="diff"> </span>
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480
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1537,7 +1537,6 @@ ParseCmdLine(int argc, char *argv[])</span></span>
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481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="diff"> int option_index = 0;</span>
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482
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="diff"> int i;</span>
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483
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="diff"> size_t cmdlinelen, argvlen;</span>
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484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- char space[] = " ";</span></span>
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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="diff"> </span>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="diff"> /* save the command line, both in parsed form and as a whole string */</span>
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487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="diff"> algo->argc = argc;</span>
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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1550,13 +1549,13 @@ ParseCmdLine(int argc, char *argv[])</span></span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="diff"> {</span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="diff"> algo->argv[i] = NULL;</span>
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="diff"> argvlen = strlen(argv[i]);</span>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cmdlinelen += argvlen + 1;</span></span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (cmdlinelen >= 1024)</span></span>
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494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (cmdlinelen + argvlen + 1 >= 1024)</span></span>
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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="diff"> break;</span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncat(algo->cmdline, argv[i], argvlen);</span></span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncat(algo->cmdline, space, 1);</span></span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- algo->argv[i] = calloc((argvlen+1), sizeof(char));</span></span>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- strncpy(algo->argv[i], argv[i], argvlen);</span></span>
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ // we now know that this fits</span></span>
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sprintf(algo->cmdline + cmdlinelen, "%s ", argv[i]);</span></span>
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cmdlinelen += argvlen + 1;</span></span>
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ algo->argv[i] = malloc(argvlen + 1); // strdup is unavailable</span></span>
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ memcpy(algo->argv[i], argv[i], argvlen + 1);</span></span>
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="diff"> char short_options[] = "a:A:b:B:cCd:D:e:EfFg:GhHi:Ij:JlLmM:n:No:Op:P:qQ:r:R:s:S:tT:uUvVWxXyYz:Z0123:4:69";</span></pre>
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<li id="200e4ccacc6026e14964a051d24712f4768fcf65">
<a href="https://salsa.debian.org/med-team/theseus/compare/fc973f3ea997f1857ddaec2e4001727b0b301a63...bbe22ea999b2d1933f45d8676876ecab9ffbae5a#200e4ccacc6026e14964a051d24712f4768fcf65"><strong>debian/patches/0004-create-lib-dir.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">From: =?utf-8?q?Fabian_Kl=C3=B6tzl?= <fabian@kloetzl.info></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Date: Mon, 10 Sep 2018 10:28:02 +0000</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Subject: create lib dir</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">---</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> Makefile | 5 ++++-</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> 1 file changed, 4 insertions(+), 1 deletion(-)</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/Makefile b/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gh" style="color: #999;">index cb1c708..a3ee651 100644</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -17,7 +17,10 @@ termcol.o theseuslib.o</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> all: libs ltheseus progs</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="17" 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">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-libs: ldistfit lDLTutils lmsa ldltmath ldssplite</span></span>
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<td class="diff-line-num new new_line" data-linenumber="18" 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">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+libs: makelibdir ldistfit lDLTutils lmsa ldltmath ldssplite</span></span>
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<pre style="margin: 0;">+<span id="LC19" 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="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+makelibdir:</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;">+ mkdir -p lib</span></span>
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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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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> progs: theseus libs</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/theseus/compare/fc973f3ea997f1857ddaec2e4001727b0b301a63...bbe22ea999b2d1933f45d8676876ecab9ffbae5a#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">30_fix_gcc_options.patch</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">gcc-7.patch</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">0003-fix-issues-uncovered-by-gcc8.patch</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">0004-create-lib-dir.patch</span></pre>
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