{"id":775,"date":"2014-01-30T10:23:13","date_gmt":"2014-01-30T08:23:13","guid":{"rendered":"http:\/\/oldblogs.uct.ac.za\/blog\/big-bytes\/2014\/01\/30\/v-phaser2-error-when-compiling"},"modified":"2015-08-14T11:34:46","modified_gmt":"2015-08-14T09:34:46","slug":"v-phaser2-error-when-compiling","status":"publish","type":"post","link":"https:\/\/ucthpc.uct.ac.za\/index.php\/2014\/01\/30\/v-phaser2-error-when-compiling\/","title":{"rendered":"V-Phaser2 error when compiling"},"content":{"rendered":"<a title=\"VPhaser2\" href=\"http:\/\/www.broadinstitute.org\/scientific-community\/science\/projects\/viral-genomics\/v-phaser-2\"><strong>V-Phaser 2<\/strong><\/a>\u00a0is a tool to call variants in genetically heterogeneous populations from ultra-deep sequence data. Compiling the \" variant_caller \" binary will result in the following.\r\n\r\n&nbsp;\r\n\r\n<strong>bam_manip.cpp: In function \u2018void sampling(int&amp;, int&amp;, int&amp;, int&amp;, int&amp;, const strvec_t&amp;, int)\u2019:\r\nbam_manip.cpp:184:9: error: \u2018INT_MAX\u2019 was not declared in this scope\r\nbam_manip.cpp:185:9: error: \u2018INT_MIN\u2019 was not declared in this scope\r\nmake: *** [all] Error 1<\/strong>\r\n\r\n&nbsp;\r\n\r\nAdd the \"#include &lt;climits&gt;\" to the <strong>\"bam_manip.h\" <\/strong>file. Rerun the compile with \" make -lz \". Once this is complete, change directory from src into ..\/bin. The \" variant_caller \" should be available and ready to use.","protected":false},"excerpt":{"rendered":"<p><a href=\"http:\/\/www.broadinstitute.org\/scientific-community\/science\/projects\/viral-genomics\/v-phaser-2\" title=\"VPhaser2\"><strong>V-Phaser 2<\/strong><\/a>&nbsp;is a tool to call variants in genetically heterogeneous populations from ultra-deep sequence data. Compiling the &#8221; variant_caller &#8221; binary will result in the following.<\/p>\n<p>&nbsp;<\/p>\n<p><strong>bam_manip.cpp: In function &lsquo;void sampling(int&amp;, int&amp;, int&amp;, int&amp;, int&amp;, const strvec_t&amp;, int)&rsquo;:<br \/>bam_manip.cpp:184:9: error: &lsquo;INT_MAX&rsquo; was not declared in this scope<br \/>bam_manip.cpp:185:9: error: &lsquo;INT_MIN&rsquo; was not declared in this scope<br \/>make: *** [all] Error 1<\/strong><\/p>\n<p>&nbsp;<\/p>\n<p>Add the &#8220;#include &lt;climits&gt;&#8221; to the <strong>&#8220;bam_manip.h&#8221; <\/strong>file. Rerun the compile with &#8221; make -lz &#8220;. Once this is complete, change directory from src into ..\/bin. The &#8221; variant_caller &#8221; should be available and ready to use. <\/p>\n","protected":false},"author":3,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":[],"categories":[9],"tags":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v21.4 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>V-Phaser2 error when compiling - UCT HPC<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/ucthpc.uct.ac.za\/index.php\/2014\/01\/30\/v-phaser2-error-when-compiling\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"V-Phaser2 error when compiling - UCT HPC\" \/>\n<meta property=\"og:description\" content=\"V-Phaser 2&nbsp;is a tool to call variants in genetically heterogeneous populations from ultra-deep sequence data. Compiling the &quot; variant_caller &quot; binary will result in the following.&nbsp;bam_manip.cpp: In function &lsquo;void sampling(int&amp;, int&amp;, int&amp;, int&amp;, int&amp;, const strvec_t&amp;, int)&rsquo;:bam_manip.cpp:184:9: error: &lsquo;INT_MAX&rsquo; was not declared in this scopebam_manip.cpp:185:9: error: &lsquo;INT_MIN&rsquo; was not declared in this scopemake: *** [all] Error 1&nbsp;Add the &quot;#include &lt;climits&gt;&quot; to the &quot;bam_manip.h&quot; file. Rerun the compile with &quot; make -lz &quot;. Once this is complete, change directory from src into ..\/bin. The &quot; variant_caller &quot; should be available and ready to use.\" \/>\n<meta property=\"og:url\" content=\"https:\/\/ucthpc.uct.ac.za\/index.php\/2014\/01\/30\/v-phaser2-error-when-compiling\/\" \/>\n<meta property=\"og:site_name\" content=\"UCT HPC\" \/>\n<meta property=\"article:published_time\" content=\"2014-01-30T08:23:13+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2015-08-14T09:34:46+00:00\" \/>\n<meta name=\"author\" content=\"Timothy Carr\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Timothy Carr\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"1 minute\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"Article\",\"@id\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2014\/01\/30\/v-phaser2-error-when-compiling\/#article\",\"isPartOf\":{\"@id\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2014\/01\/30\/v-phaser2-error-when-compiling\/\"},\"author\":{\"name\":\"Timothy Carr\",\"@id\":\"https:\/\/ucthpc.uct.ac.za\/#\/schema\/person\/41f6cd039836d7741f2b82a7b7cfe8d0\"},\"headline\":\"V-Phaser2 error when compiling\",\"datePublished\":\"2014-01-30T08:23:13+00:00\",\"dateModified\":\"2015-08-14T09:34:46+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2014\/01\/30\/v-phaser2-error-when-compiling\/\"},\"wordCount\":118,\"publisher\":{\"@id\":\"https:\/\/ucthpc.uct.ac.za\/#organization\"},\"articleSection\":[\"application\"],\"inLanguage\":\"en-ZA\"},{\"@type\":\"WebPage\",\"@id\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2014\/01\/30\/v-phaser2-error-when-compiling\/\",\"url\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2014\/01\/30\/v-phaser2-error-when-compiling\/\",\"name\":\"V-Phaser2 error when compiling - 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UCT HPC","robots":{"index":"index","follow":"follow","max-snippet":"max-snippet:-1","max-image-preview":"max-image-preview:large","max-video-preview":"max-video-preview:-1"},"canonical":"https:\/\/ucthpc.uct.ac.za\/index.php\/2014\/01\/30\/v-phaser2-error-when-compiling\/","og_locale":"en_US","og_type":"article","og_title":"V-Phaser2 error when compiling - UCT HPC","og_description":"V-Phaser 2&nbsp;is a tool to call variants in genetically heterogeneous populations from ultra-deep sequence data. Compiling the \" variant_caller \" binary will result in the following.&nbsp;bam_manip.cpp: In function &lsquo;void sampling(int&amp;, int&amp;, int&amp;, int&amp;, int&amp;, const strvec_t&amp;, int)&rsquo;:bam_manip.cpp:184:9: error: &lsquo;INT_MAX&rsquo; was not declared in this scopebam_manip.cpp:185:9: error: &lsquo;INT_MIN&rsquo; was not declared in this scopemake: *** [all] Error 1&nbsp;Add the \"#include &lt;climits&gt;\" to the \"bam_manip.h\" file. Rerun the compile with \" make -lz \". Once this is complete, change directory from src into ..\/bin. 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