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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/libvcflib">Debian Med / libvcflib</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/libvcflib/commit/a99be0fdb5ec1303d15203f44898a5716f8541d8">a99be0fd</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-09-04T03:57:23Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix spelling typos
</pre>
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<h4>2 changed files:</h4>
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<a href="#e4c19aed51618bf0c7ebd03189c67e422f84d4eb">
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+
debian/patches/spelling
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</a>
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<h4>Changes:</h4>
<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/libvcflib/commit/a99be0fdb5ec1303d15203f44898a5716f8541d8#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,3 +13,4 @@ fix_installation.patch</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">dont_link_pthread</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">override_version</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">hardening-flags</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">spelling</span></pre>
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<li id="e4c19aed51618bf0c7ebd03189c67e422f84d4eb">
<a href="https://salsa.debian.org/med-team/libvcflib/commit/a99be0fdb5ec1303d15203f44898a5716f8541d8#e4c19aed51618bf0c7ebd03189c67e422f84d4eb"><strong>debian/patches/spelling</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Subject: lintian-inspired spelling fixes</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- libvcflib.orig/src/abba-baba.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ libvcflib/src/abba-baba.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -47,7 +47,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> cerr << "INFO: usage: abba-baba --tree 0,1,2,3 --file my.vcf --type PL" << endl;</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> cerr << endl;</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cerr << "INFO: required: t,tree -- a zero based comma seperated list of target individuals corrisponding to VCF columns" << endl;</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cerr << "INFO: required: t,tree -- a zero based comma separated list of target individuals corrisponding to VCF columns" << endl;</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> cerr << "INFO: required: f,file -- a properly formatted VCF. " << endl;</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> cerr << "INFO: required: y,type -- genotype likelihood format ; genotypes: GP,GL or PL; " << endl;</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> cerr << endl;</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- libvcflib.orig/src/gl-XPEHH.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ libvcflib/src/gl-XPEHH.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="p">@@ -488,8 +488,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> cerr << "INFO: gl-XPEHH --target 0,1,2,3,4,5,6,7 --background 11,12,13,16,17,19,22 --file my.vcf --deltaaf 0.1 --ancestral 0 " << endl;</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> cerr << endl;</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> cerr << "INFO: required: r,region -- a genomice range to calculate gl-XPEHH on in the format : \"seqid:start-end]\" or \"seqid\" " << endl;</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cerr << "INFO: required: t,target -- a zero base comma seperated list of target individuals corrisponding to VCF columns " << endl;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="21" 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">
21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cerr << "INFO: required: b,background -- a zero base comma seperated list of background individuals corrisponding to VCF columns " << endl;</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cerr << "INFO: required: t,target -- a zero base comma separated list of target individuals corrisponding to VCF columns " << endl;</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cerr << "INFO: required: b,background -- a zero base comma separated list of background individuals corrisponding to VCF columns " << endl;</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> cerr << "INFO: required: f,file a -- proper formatted VCF. the FORMAT field MUST contain \"PL\" if option phased == 0 " << endl; </span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> cerr << "INFO: optional: m,mutation -- which state is derived in vcf [0,1] default is 1 " << endl;</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> cerr << "INFO: optional: p,phased -- phasing flag [0,1] 0 = phase vcf, 1 = vcf is already phased " << endl;</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- libvcflib.orig/src/hapLrt.cpp</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ libvcflib/src/hapLrt.cpp</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="p">@@ -24,7 +24,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> cerr << endl << endl;</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> cerr << "INFO: help" << endl;</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> cerr << "INFO: description:" << endl;</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cerr << " HapLRT is a likelihood ratio test for haplotype lengths. The lengths are modeled with an exponential distribtuion. " << endl;</span></span>
</pre>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cerr << " HapLRT is a likelihood ratio test for haplotype lengths. The lengths are modeled with an exponential distribution. " << endl;</span></span>
</pre>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> cerr << " The sign denotes if the target has longer haplotypes (1) or the background (-1). " << endl << endl;</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> </span>
</pre>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> cerr << "Output : 4 columns : " << endl;</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="p">@@ -38,8 +38,8 @@</span></span>
</pre>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> cerr << "INFO: hapLRT --target 0,1,2,3,4,5,6,7 --background 11,12,13,16,17,19,22 --type GP --file my.vcf " << endl;</span>
</pre>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> cerr << endl;</span>
</pre>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> </span>
</pre>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cerr << "INFO: required: t,target -- argument: a zero base comma seperated list of target individuals corrisponding to VCF columns " << endl;</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cerr << "INFO: required: b,background -- argument: a zero base comma seperated list of background individuals corrisponding to VCF columns " << endl;</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cerr << "INFO: required: t,target -- argument: a zero base comma separated list of target individuals corrisponding to VCF columns " << endl;</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cerr << "INFO: required: b,background -- argument: a zero base comma separated list of background individuals corrisponding to VCF columns " << endl;</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> cerr << "INFO: required: f,file -- argument: a properly formatted phased VCF file " << endl;</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> cerr << "INFO: required: y,type -- argument: type of genotype likelihood: PL, GL or GP " << endl;</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> cerr << "INFO: optional: r,region -- argument: a genomice range to calculate hapLrt on in the format : \"seqid:start-end\" or \"seqid\" " << endl;</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- libvcflib.orig/src/vcfld.cpp</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ libvcflib/src/vcfld.cpp</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="p">@@ -26,8 +26,8 @@</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> cerr << "INFO: LD --target 0,1,2,3,4,5,6,7 --background 11,12,13,16,17,19,22 --file my.vcf -e -d -r " << endl;</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> cerr << endl;</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> </span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cerr << "INFO: required: t,target -- argument: a zero base comma seperated list of target individuals corrisponding to VCF columns " << endl;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="56" 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">
56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cerr << "INFO: required: b,background -- argument: a zero base comma seperated list of background individuals corrisponding to VCF columns " << endl;</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cerr << "INFO: required: t,target -- argument: a zero base comma separated list of target individuals corrisponding to VCF columns " << endl;</span></span>
</pre>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cerr << "INFO: required: b,background -- argument: a zero base comma separated list of background individuals corrisponding to VCF columns " << endl;</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> cerr << "INFO: required: f,file -- argument: a properly formatted phased VCF file " << endl;</span>
</pre>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> cerr << "INFO: required: y,type -- argument: type of genotype likelihood: PL, GL or GP " << endl;</span>
</pre>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> cerr << "INFO: optional: w,window -- argument: window size to average LD; default is 1000 " << endl;</span>
</pre>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- libvcflib.orig/src/genotypeSummary.cpp</span></span>
</pre>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ libvcflib/src/genotypeSummary.cpp</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="p">@@ -356,7 +356,7 @@</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"> }</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> else{</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- std::cerr << "FATAL: unkown genotype index" << std::endl;</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ std::cerr << "FATAL: unknown genotype index" << std::endl;</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> cerr << populationTarget->genoIndex[i] << endl;</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> cerr << var << endl;</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> exit(1);</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- libvcflib.orig/src/permuteGPAT++.cpp</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ libvcflib/src/permuteGPAT++.cpp</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="p">@@ -169,7 +169,7 @@</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> }</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> }</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> else{</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cerr << "FATAL: coult not open file: " << globalOpts.file << endl;</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cerr << "FATAL: could not open file: " << globalOpts.file << endl;</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> exit(1);</span>
</pre>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> }</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> </span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="p">@@ -214,7 +214,7 @@</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> </span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> }</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> else{</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cerr << "FATAL: coult not open file: " << globalOpts.file << endl;</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cerr << "FATAL: could not open file: " << globalOpts.file << endl;</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> exit(1);</span>
</pre>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> }</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> </span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- libvcflib.orig/src/permuteGPATsmoother.cpp</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ libvcflib/src/permuteGPATsmoother.cpp</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="p">@@ -170,7 +170,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> }</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> }</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> else{</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cerr << "FATAL: coult not open file: " << globalOpts.file << endl;</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cerr << "FATAL: could not open file: " << globalOpts.file << endl;</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> exit(1);</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"> </span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="p">@@ -214,7 +214,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> } </span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> }</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> else{</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cerr << "FATAL: coult not open file: " << globalOpts.file << endl;</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cerr << "FATAL: could not open file: " << globalOpts.file << endl;</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> exit(1);</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"> </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;">--- libvcflib.orig/src/permuteRegions.cpp</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;">+++ libvcflib/src/permuteRegions.cpp</span></span>
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<td class="diff-line-num new new_line" data-linenumber="115" 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">
115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="p">@@ -340,7 +340,7 @@</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"> }</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"> }</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> else{</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cerr << "FATAL: coult not open file: " << globalOpts.file << endl;</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cerr << "FATAL: could not open file: " << globalOpts.file << endl;</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"> exit(1);</span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"> }</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"> </span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- libvcflib.orig/src/permuteSmooth.cpp</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ libvcflib/src/permuteSmooth.cpp</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="p">@@ -356,7 +356,7 @@</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"> }</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"> else{</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cerr << "FATAL: coult not open file: " << globalOpts.file << endl;</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cerr << "FATAL: could not open file: " << globalOpts.file << endl;</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> exit(1);</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"> }</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"> </span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- libvcflib.orig/src/plotHaps.cpp</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ libvcflib/src/plotHaps.cpp</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"><span class="p">@@ -281,7 +281,7 @@</span></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>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"> else{</span>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cerr << "FATAL: must specifiy a region" << endl;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="142" 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">
142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cerr << "FATAL: must specify a region" << endl;</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"> printHelp();</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"> return 1;</span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"> }</span></pre>
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