Mercurial > repos > lz_hust > gatktools

comparison gatk-tools @ 6:a4e5c90cf6cb draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author lz_hust
date Sat, 01 Jun 2019 07:03:27 -0400
parents
children
comparison
equal deleted inserted replaced
5:e0a6b2ba8bd3 6:a4e5c90cf6cb
1
2
3
4
5
6
7 <!DOCTYPE html>
8 <html lang="en">
9 <head>
10 <meta charset="utf-8">
11 <link rel="dns-prefetch" href="https://github.githubassets.com">
12 <link rel="dns-prefetch" href="https://avatars0.githubusercontent.com">
13 <link rel="dns-prefetch" href="https://avatars1.githubusercontent.com">
14 <link rel="dns-prefetch" href="https://avatars2.githubusercontent.com">
15 <link rel="dns-prefetch" href="https://avatars3.githubusercontent.com">
16 <link rel="dns-prefetch" href="https://github-cloud.s3.amazonaws.com">
17 <link rel="dns-prefetch" href="https://user-images.githubusercontent.com/">
18
19
20
21 <link crossorigin="anonymous" media="all" integrity="sha512-3+HOqCwtQal5hOJQ+mdxiq5zmGOTjF6RhjDsPLxbKDYgGlLFeCwzoIanb7j5IiCuXKUqyC2q8FdkC4nmx2P2rA==" rel="stylesheet" href="https://github.githubassets.com/assets/frameworks-a2fba223d5af91496cac70d4ec3624df.css" />
22 <link crossorigin="anonymous" media="all" integrity="sha512-MRlTIqIyb8caK5+o8llXVntXovciHyAM4qE3kWU2S7SIjAPDxYp4mE0jQp4kP5UYegy+lG9y1I6VlsdzEjb5Qw==" rel="stylesheet" href="https://github.githubassets.com/assets/site-294181adec18ed639e160b96b45d17ac.css" />
23 <link crossorigin="anonymous" media="all" integrity="sha512-e2cd11Gwm/SnNMk4avW8Pegf5TL3BOHKEDRrRx/u2dt3vZ/V1jI3ckZPooFM9/nY6QPCmoa7QpyUEho4JqtJIg==" rel="stylesheet" href="https://github.githubassets.com/assets/github-7d88b16c450c546e1d642f3e2215a89c.css" />
24
25
26
27
28
29 <meta name="viewport" content="width=device-width">
30
31 <title>GitHub - huster16/gatk-tools</title>
32 <meta name="description" content="Contribute to huster16/gatk-tools development by creating an account on GitHub.">
33 <link rel="search" type="application/opensearchdescription+xml" href="/opensearch.xml" title="GitHub">
34 <link rel="fluid-icon" href="https://github.com/fluidicon.png" title="GitHub">
35 <meta property="fb:app_id" content="1401488693436528">
36
37 <meta name="twitter:image:src" content="https://avatars3.githubusercontent.com/u/50308301?s=400&amp;v=4" /><meta name="twitter:site" content="@github" /><meta name="twitter:card" content="summary" /><meta name="twitter:title" content="huster16/gatk-tools" /><meta name="twitter:description" content="Contribute to huster16/gatk-tools development by creating an account on GitHub." />
38 <meta property="og:image" content="https://avatars3.githubusercontent.com/u/50308301?s=400&amp;v=4" /><meta property="og:site_name" content="GitHub" /><meta property="og:type" content="object" /><meta property="og:title" content="huster16/gatk-tools" /><meta property="og:url" content="https://github.com/huster16/gatk-tools" /><meta property="og:description" content="Contribute to huster16/gatk-tools development by creating an account on GitHub." />
39
40 <link rel="assets" href="https://github.githubassets.com/">
41
42 <meta name="pjax-timeout" content="1000">
43
44 <meta name="request-id" content="9296:3F63:B1FBFC:1321364:5CF25B7F" data-pjax-transient>
45
46
47
48
49 <meta name="selected-link" value="repo_source" data-pjax-transient>
50
51 <meta name="google-site-verification" content="KT5gs8h0wvaagLKAVWq8bbeNwnZZK1r1XQysX3xurLU">
52 <meta name="google-site-verification" content="ZzhVyEFwb7w3e0-uOTltm8Jsck2F5StVihD0exw2fsA">
53 <meta name="google-site-verification" content="GXs5KoUUkNCoaAZn7wPN-t01Pywp9M3sEjnt_3_ZWPc">
54
55 <meta name="octolytics-host" content="collector.githubapp.com" /><meta name="octolytics-app-id" content="github" /><meta name="octolytics-event-url" content="https://collector.githubapp.com/github-external/browser_event" /><meta name="octolytics-dimension-request_id" content="9296:3F63:B1FBFC:1321364:5CF25B7F" /><meta name="octolytics-dimension-region_edge" content="iad" /><meta name="octolytics-dimension-region_render" content="iad" />
56 <meta name="analytics-location" content="/&lt;user-name&gt;/&lt;repo-name&gt;" data-pjax-transient="true" />
57
58
59
60 <meta name="google-analytics" content="UA-3769691-2">
61
62
63 <meta class="js-ga-set" name="dimension1" content="Logged Out">
64
65
66
67
68
69 <meta name="hostname" content="github.com">
70 <meta name="user-login" content="">
71
72 <meta name="expected-hostname" content="github.com">
73 <meta name="js-proxy-site-detection-payload" content="MGQzNzE0OTI3ZTEzMTA1M2M2MDcwOGU2OGEyY2E0MjYzMzhhNzAzMmU2ZmYyZWIwMjk2YmU4Y2QyZmQ0OTYyYnx7InJlbW90ZV9hZGRyZXNzIjoiMTI4LjExOC4yNTAuNSIsInJlcXVlc3RfaWQiOiI5Mjk2OjNGNjM6QjFGQkZDOjEzMjEzNjQ6NUNGMjVCN0YiLCJ0aW1lc3RhbXAiOjE1NTkzODcwMDcsImhvc3QiOiJnaXRodWIuY29tIn0=">
74
75 <meta name="enabled-features" content="UNIVERSE_BANNER,MARKETPLACE_INVOICED_BILLING,MARKETPLACE_SOCIAL_PROOF_CUSTOMERS,MARKETPLACE_TRENDING_SOCIAL_PROOF,MARKETPLACE_RECOMMENDATIONS">
76
77 <meta name="html-safe-nonce" content="af84c43ce04aafde5136153012f871e50304f037">
78
79 <meta http-equiv="x-pjax-version" content="3adbd63ea2ad294c944dc0fffcb8e5b8">
80
81
82 <link href="https://github.com/huster16/gatk-tools/commits/master.atom" rel="alternate" title="Recent Commits to gatk-tools:master" type="application/atom+xml">
83
84 <meta name="go-import" content="github.com/huster16/gatk-tools git https://github.com/huster16/gatk-tools.git">
85
86 <meta name="octolytics-dimension-user_id" content="50308301" /><meta name="octolytics-dimension-user_login" content="huster16" /><meta name="octolytics-dimension-repository_id" content="189599350" /><meta name="octolytics-dimension-repository_nwo" content="huster16/gatk-tools" /><meta name="octolytics-dimension-repository_public" content="true" /><meta name="octolytics-dimension-repository_is_fork" content="false" /><meta name="octolytics-dimension-repository_network_root_id" content="189599350" /><meta name="octolytics-dimension-repository_network_root_nwo" content="huster16/gatk-tools" /><meta name="octolytics-dimension-repository_explore_github_marketplace_ci_cta_shown" content="false" />
87
88
89 <link rel="canonical" href="https://github.com/huster16/gatk-tools" data-pjax-transient>
90
91
92 <meta name="browser-stats-url" content="https://api.github.com/_private/browser/stats">
93
94 <meta name="browser-errors-url" content="https://api.github.com/_private/browser/errors">
95
96 <link rel="mask-icon" href="https://github.githubassets.com/pinned-octocat.svg" color="#000000">
97 <link rel="icon" type="image/x-icon" class="js-site-favicon" href="https://github.githubassets.com/favicon.ico">
98
99 <meta name="theme-color" content="#1e2327">
100
101
102
103
104
105 <link rel="manifest" href="/manifest.json" crossOrigin="use-credentials">
106
107 </head>
108
109 <body class="logged-out env-production min-width-lg">
110
111
112 <div class="position-relative js-header-wrapper ">
113 <a href="#start-of-content" tabindex="1" class="px-2 py-4 bg-blue text-white show-on-focus js-skip-to-content">Skip to content</a>
114 <div id="js-pjax-loader-bar" class="pjax-loader-bar"><div class="progress"></div></div>
115
116
117
118
119
120
121 <header class="Header-old header-logged-out position-relative f4 py-2" role="banner">
122 <div class="container-lg d-flex px-3">
123 <div class="d-flex flex-justify-between flex-items-center">
124 <a class="mr-4" href="https://github.com/" aria-label="Homepage" data-ga-click="(Logged out) Header, go to homepage, icon:logo-wordmark">
125 <svg height="32" class="octicon octicon-mark-github text-white" viewBox="0 0 16 16" version="1.1" width="32" aria-hidden="true"><path fill-rule="evenodd" d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29 6.53 5.47 7.59.4.07.55-.17.55-.38 0-.19-.01-.82-.01-1.49-2.01.37-2.53-.49-2.69-.94-.09-.23-.48-.94-.82-1.13-.28-.15-.68-.52-.01-.53.63-.01 1.08.58 1.23.82.72 1.21 1.87.87 2.33.66.07-.52.28-.87.51-1.07-1.78-.2-3.64-.89-3.64-3.95 0-.87.31-1.59.82-2.15-.08-.2-.36-1.02.08-2.12 0 0 .67-.21 2.2.82.64-.18 1.32-.27 2-.27.68 0 1.36.09 2 .27 1.53-1.04 2.2-.82 2.2-.82.44 1.1.16 1.92.08 2.12.51.56.82 1.27.82 2.15 0 3.07-1.87 3.75-3.65 3.95.29.25.54.73.54 1.48 0 1.07-.01 1.93-.01 2.2 0 .21.15.46.55.38A8.013 8.013 0 0 0 16 8c0-4.42-3.58-8-8-8z"/></svg>
126 </a>
127 </div>
128
129 <div class="HeaderMenu HeaderMenu--logged-out d-flex flex-justify-between flex-items-center flex-auto">
130 <div class="d-none">
131 <button class="btn-link js-details-target" type="button" aria-label="Toggle navigation" aria-expanded="false">
132 <svg height="24" class="octicon octicon-x text-gray" viewBox="0 0 12 16" version="1.1" width="18" aria-hidden="true"><path fill-rule="evenodd" d="M7.48 8l3.75 3.75-1.48 1.48L6 9.48l-3.75 3.75-1.48-1.48L4.52 8 .77 4.25l1.48-1.48L6 6.52l3.75-3.75 1.48 1.48L7.48 8z"/></svg>
133 </button>
134 </div>
135
136 <nav class="mt-0" aria-label="Global">
137 <ul class="d-flex list-style-none">
138 <li class=" mr-3 mr-lg-3 edge-item-fix position-relative flex-wrap flex-justify-between d-flex flex-items-center ">
139 <details class="HeaderMenu-details details-overlay details-reset width-full">
140 <summary class="HeaderMenu-summary HeaderMenu-link px-0 py-3 border-0 no-wrap d-inline-block">
141 Why GitHub?
142 <svg x="0px" y="0px" viewBox="0 0 14 8" xml:space="preserve" fill="none" class="icon-chevon-down-mktg position-relative">
143 <path d="M1,1l6.2,6L13,1"></path>
144 </svg>
145 </summary>
146 <div class="dropdown-menu flex-auto rounded-1 bg-white px-0 mt-0 p-4 left-n4 position-absolute">
147 <a href="/features" class="py-2 lh-condensed-ultra d-block link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Features">Features <span class="Bump-link-symbol float-right text-normal text-gray-light">&rarr;</span></a>
148 <ul class="list-style-none f5 pb-3">
149 <li class="edge-item-fix"><a href="/features/code-review/" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Code review">Code review</a></li>
150 <li class="edge-item-fix"><a href="/features/project-management/" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Project management">Project management</a></li>
151 <li class="edge-item-fix"><a href="/features/integrations" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Integrations">Integrations</a></li>
152 <li class="edge-item-fix"><a href="/features/actions" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Actions">Actions</a>
153 <li class="edge-item-fix"><a href="/features/package-registry" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Package Registry">Package registry</a>
154 <li class="edge-item-fix"><a href="/features#team-management" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Team management">Team management</a></li>
155 <li class="edge-item-fix"><a href="/features#social-coding" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Social coding">Social coding</a></li>
156 <li class="edge-item-fix"><a href="/features#documentation" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Documentation">Documentation</a></li>
157 <li class="edge-item-fix"><a href="/features#code-hosting" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Code hosting">Code hosting</a></li>
158 </ul>
159
160 <ul class="list-style-none mb-0 border-lg-top pt-lg-3">
161 <li class="edge-item-fix"><a href="/customer-stories" class="py-2 lh-condensed-ultra d-block no-underline link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Customer stories">Customer stories <span class="Bump-link-symbol float-right text-normal text-gray-light">&rarr;</span></a></li>
162 <li class="edge-item-fix"><a href="/security" class="py-2 lh-condensed-ultra d-block no-underline link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Security">Security <span class="Bump-link-symbol float-right text-normal text-gray-light">&rarr;</span></a></li>
163 </ul>
164 </div>
165 </details>
166 </li>
167 <li class=" mr-3 mr-lg-3">
168 <a href="/enterprise" class="HeaderMenu-link no-underline py-3 d-block d-lg-inline-block" data-ga-click="(Logged out) Header, go to Enterprise">Enterprise</a>
169 </li>
170
171 <li class=" mr-3 mr-lg-3 edge-item-fix position-relative flex-wrap flex-justify-between d-flex flex-items-center ">
172 <details class="HeaderMenu-details details-overlay details-reset width-full">
173 <summary class="HeaderMenu-summary HeaderMenu-link px-0 py-3 border-0 no-wrap d-inline-block">
174 Explore
175 <svg x="0px" y="0px" viewBox="0 0 14 8" xml:space="preserve" fill="none" class="icon-chevon-down-mktg position-relative">
176 <path d="M1,1l6.2,6L13,1"></path>
177 </svg>
178 </summary>
179
180 <div class="dropdown-menu flex-auto rounded-1 bg-white px-0 pt-2 pb-0 mt-0 p-4 left-n4 position-absolute">
181 <ul class="list-style-none mb-3">
182 <li class="edge-item-fix"><a href="/explore" class="py-2 lh-condensed-ultra d-block link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Explore">Explore GitHub <span class="Bump-link-symbol float-right text-normal text-gray-light">&rarr;</span></a></li>
183 </ul>
184
185 <h4 class="text-gray-light text-normal text-mono f5 mb-2 border-top pt-3">Learn &amp; contribute</h4>
186 <ul class="list-style-none mb-3">
187 <li class="edge-item-fix"><a href="/topics" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Topics">Topics</a></li>
188 <li class="edge-item-fix"><a href="/collections" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Collections">Collections</a></li>
189 <li class="edge-item-fix"><a href="/trending" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Trending">Trending</a></li>
190 <li class="edge-item-fix"><a href="https://lab.github.com/" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Learning lab">Learning Lab</a></li>
191 <li class="edge-item-fix"><a href="https://opensource.guide" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Open source guides">Open source guides</a></li>
192 </ul>
193
194 <h4 class="text-gray-light text-normal text-mono f5 mb-2 border-top pt-3">Connect with others</h4>
195 <ul class="list-style-none mb-0">
196 <li class="edge-item-fix"><a href="https://github.com/events" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Events">Events</a></li>
197 <li class="edge-item-fix"><a href="https://github.community" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Community forum">Community forum</a></li>
198 <li class="edge-item-fix"><a href="https://education.github.com" class="py-2 pb-0 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to GitHub Education">GitHub Education</a></li>
199 </ul>
200 </div>
201 </details>
202 </li>
203
204 <li class=" mr-3 mr-lg-3">
205 <a href="/marketplace" class="HeaderMenu-link no-underline py-3 d-block d-lg-inline-block" data-ga-click="(Logged out) Header, go to Marketplace">Marketplace</a>
206 </li>
207
208 <li class=" mr-3 mr-lg-3 edge-item-fix position-relative flex-wrap flex-justify-between d-flex flex-items-center ">
209 <details class="HeaderMenu-details details-overlay details-reset width-full">
210 <summary class="HeaderMenu-summary HeaderMenu-link px-0 py-3 border-0 no-wrap d-inline-block">
211 Pricing
212 <svg x="0px" y="0px" viewBox="0 0 14 8" xml:space="preserve" fill="none" class="icon-chevon-down-mktg position-relative">
213 <path d="M1,1l6.2,6L13,1"></path>
214 </svg>
215 </summary>
216
217 <div class="dropdown-menu flex-auto rounded-1 bg-white px-0 pt-2 pb-4 mt-0 p-4 left-n4 position-absolute">
218 <a href="/pricing" class="pb-2 lh-condensed-ultra d-block link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Pricing">Plans <span class="Bump-link-symbol float-right text-normal text-gray-light">&rarr;</span></a>
219
220 <ul class="list-style-none mb-3">
221 <li class="edge-item-fix"><a href="/pricing#feature-comparison" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Compare plans">Compare plans</a></li>
222 <li class="edge-item-fix"><a href="https://enterprise.github.com/contact" class="py-2 lh-condensed-ultra d-block link-gray no-underline f5" data-ga-click="(Logged out) Header, go to Contact Sales">Contact Sales</a></li>
223 </ul>
224
225 <ul class="list-style-none mb-0 border-top pt-3">
226 <li class="edge-item-fix"><a href="/nonprofit" class="py-2 lh-condensed-ultra d-block no-underline link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Nonprofits">Nonprofit <span class="Bump-link-symbol float-right text-normal text-gray-light">&rarr;</span></a></li>
227 <li class="edge-item-fix"><a href="https://education.github.com" class="py-2 pb-0 lh-condensed-ultra d-block no-underline link-gray-dark no-underline h5 Bump-link--hover" data-ga-click="(Logged out) Header, go to Education">Education <span class="Bump-link-symbol float-right text-normal text-gray-light">&rarr;</span></a></li>
228 </ul>
229 </div>
230 </details>
231 </li>
232 </ul>
233 </nav>
234
235 <div class="d-flex flex-items-center px-0 text-center text-left">
236 <div class="d-lg-flex ">
237 <div class="header-search mr-3 scoped-search site-scoped-search js-site-search position-relative js-jump-to"
238 role="combobox"
239 aria-owns="jump-to-results"
240 aria-label="Search or jump to"
241 aria-haspopup="listbox"
242 aria-expanded="false"
243 >
244 <div class="position-relative">
245 <!-- '"` --><!-- </textarea></xmp> --></option></form><form class="js-site-search-form" role="search" aria-label="Site" data-scope-type="Repository" data-scope-id="189599350" data-scoped-search-url="/huster16/gatk-tools/search" data-unscoped-search-url="/search" action="/huster16/gatk-tools/search" accept-charset="UTF-8" method="get"><input name="utf8" type="hidden" value="&#x2713;" />
246 <label class="form-control input-sm header-search-wrapper p-0 header-search-wrapper-jump-to position-relative d-flex flex-justify-between flex-items-center js-chromeless-input-container">
247 <input type="text"
248 class="form-control input-sm header-search-input jump-to-field js-jump-to-field js-site-search-focus js-site-search-field is-clearable"
249 data-hotkey="s,/"
250 name="q"
251 value=""
252 placeholder="Search"
253 data-unscoped-placeholder="Search GitHub"
254 data-scoped-placeholder="Search"
255 autocapitalize="off"
256 aria-autocomplete="list"
257 aria-controls="jump-to-results"
258 aria-label="Search"
259 data-jump-to-suggestions-path="/_graphql/GetSuggestedNavigationDestinations#csrf-token=MYscG5aOEWK5QO1LxVWdiStZpn47ml0TjWb+9OnZkh1iOu3q2lfu85ssA/51V0P5USivs11k4JXi80LyFvS0Hw=="
260 spellcheck="false"
261 autocomplete="off"
262 >
263 <input type="hidden" class="js-site-search-type-field" name="type" >
264 <img src="https://github.githubassets.com/images/search-key-slash.svg" alt="" class="mr-2 header-search-key-slash">
265
266 <div class="Box position-absolute overflow-hidden d-none jump-to-suggestions js-jump-to-suggestions-container">
267
268 <ul class="d-none js-jump-to-suggestions-template-container">
269
270
271 <li class="d-flex flex-justify-start flex-items-center p-0 f5 navigation-item js-navigation-item js-jump-to-suggestion" role="option">
272 <a tabindex="-1" class="no-underline d-flex flex-auto flex-items-center jump-to-suggestions-path js-jump-to-suggestion-path js-navigation-open p-2" href="">
273 <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none">
274 <svg height="16" width="16" class="octicon octicon-repo flex-shrink-0 js-jump-to-octicon-repo d-none" title="Repository" aria-label="Repository" viewBox="0 0 12 16" version="1.1" role="img"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg>
275 <svg height="16" width="16" class="octicon octicon-project flex-shrink-0 js-jump-to-octicon-project d-none" title="Project" aria-label="Project" viewBox="0 0 15 16" version="1.1" role="img"><path fill-rule="evenodd" d="M10 12h3V2h-3v10zm-4-2h3V2H6v8zm-4 4h3V2H2v12zm-1 1h13V1H1v14zM14 0H1a1 1 0 0 0-1 1v14a1 1 0 0 0 1 1h13a1 1 0 0 0 1-1V1a1 1 0 0 0-1-1z"/></svg>
276 <svg height="16" width="16" class="octicon octicon-search flex-shrink-0 js-jump-to-octicon-search d-none" title="Search" aria-label="Search" viewBox="0 0 16 16" version="1.1" role="img"><path fill-rule="evenodd" d="M15.7 13.3l-3.81-3.83A5.93 5.93 0 0 0 13 6c0-3.31-2.69-6-6-6S1 2.69 1 6s2.69 6 6 6c1.3 0 2.48-.41 3.47-1.11l3.83 3.81c.19.2.45.3.7.3.25 0 .52-.09.7-.3a.996.996 0 0 0 0-1.41v.01zM7 10.7c-2.59 0-4.7-2.11-4.7-4.7 0-2.59 2.11-4.7 4.7-4.7 2.59 0 4.7 2.11 4.7 4.7 0 2.59-2.11 4.7-4.7 4.7z"/></svg>
277 </div>
278
279 <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28">
280
281 <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target">
282 </div>
283
284 <div class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none js-jump-to-badge-search">
285 <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository">
286 In this repository
287 </span>
288 <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub">
289 All GitHub
290 </span>
291 <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span>
292 </div>
293
294 <div aria-hidden="true" class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump">
295 Jump to
296 <span class="d-inline-block ml-1 v-align-middle">↵</span>
297 </div>
298 </a>
299 </li>
300
301 </ul>
302
303 <ul class="d-none js-jump-to-no-results-template-container">
304 <li class="d-flex flex-justify-center flex-items-center f5 d-none js-jump-to-suggestion p-2">
305 <span class="text-gray">No suggested jump to results</span>
306 </li>
307 </ul>
308
309 <ul id="jump-to-results" role="listbox" class="p-0 m-0 js-navigation-container jump-to-suggestions-results-container js-jump-to-suggestions-results-container">
310
311
312 <li class="d-flex flex-justify-start flex-items-center p-0 f5 navigation-item js-navigation-item js-jump-to-scoped-search d-none" role="option">
313 <a tabindex="-1" class="no-underline d-flex flex-auto flex-items-center jump-to-suggestions-path js-jump-to-suggestion-path js-navigation-open p-2" href="">
314 <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none">
315 <svg height="16" width="16" class="octicon octicon-repo flex-shrink-0 js-jump-to-octicon-repo d-none" title="Repository" aria-label="Repository" viewBox="0 0 12 16" version="1.1" role="img"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg>
316 <svg height="16" width="16" class="octicon octicon-project flex-shrink-0 js-jump-to-octicon-project d-none" title="Project" aria-label="Project" viewBox="0 0 15 16" version="1.1" role="img"><path fill-rule="evenodd" d="M10 12h3V2h-3v10zm-4-2h3V2H6v8zm-4 4h3V2H2v12zm-1 1h13V1H1v14zM14 0H1a1 1 0 0 0-1 1v14a1 1 0 0 0 1 1h13a1 1 0 0 0 1-1V1a1 1 0 0 0-1-1z"/></svg>
317 <svg height="16" width="16" class="octicon octicon-search flex-shrink-0 js-jump-to-octicon-search d-none" title="Search" aria-label="Search" viewBox="0 0 16 16" version="1.1" role="img"><path fill-rule="evenodd" d="M15.7 13.3l-3.81-3.83A5.93 5.93 0 0 0 13 6c0-3.31-2.69-6-6-6S1 2.69 1 6s2.69 6 6 6c1.3 0 2.48-.41 3.47-1.11l3.83 3.81c.19.2.45.3.7.3.25 0 .52-.09.7-.3a.996.996 0 0 0 0-1.41v.01zM7 10.7c-2.59 0-4.7-2.11-4.7-4.7 0-2.59 2.11-4.7 4.7-4.7 2.59 0 4.7 2.11 4.7 4.7 0 2.59-2.11 4.7-4.7 4.7z"/></svg>
318 </div>
319
320 <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28">
321
322 <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target">
323 </div>
324
325 <div class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none js-jump-to-badge-search">
326 <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository">
327 In this repository
328 </span>
329 <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub">
330 All GitHub
331 </span>
332 <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span>
333 </div>
334
335 <div aria-hidden="true" class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump">
336 Jump to
337 <span class="d-inline-block ml-1 v-align-middle">↵</span>
338 </div>
339 </a>
340 </li>
341
342
343
344 <li class="d-flex flex-justify-start flex-items-center p-0 f5 navigation-item js-navigation-item js-jump-to-global-search d-none" role="option">
345 <a tabindex="-1" class="no-underline d-flex flex-auto flex-items-center jump-to-suggestions-path js-jump-to-suggestion-path js-navigation-open p-2" href="">
346 <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none">
347 <svg height="16" width="16" class="octicon octicon-repo flex-shrink-0 js-jump-to-octicon-repo d-none" title="Repository" aria-label="Repository" viewBox="0 0 12 16" version="1.1" role="img"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg>
348 <svg height="16" width="16" class="octicon octicon-project flex-shrink-0 js-jump-to-octicon-project d-none" title="Project" aria-label="Project" viewBox="0 0 15 16" version="1.1" role="img"><path fill-rule="evenodd" d="M10 12h3V2h-3v10zm-4-2h3V2H6v8zm-4 4h3V2H2v12zm-1 1h13V1H1v14zM14 0H1a1 1 0 0 0-1 1v14a1 1 0 0 0 1 1h13a1 1 0 0 0 1-1V1a1 1 0 0 0-1-1z"/></svg>
349 <svg height="16" width="16" class="octicon octicon-search flex-shrink-0 js-jump-to-octicon-search d-none" title="Search" aria-label="Search" viewBox="0 0 16 16" version="1.1" role="img"><path fill-rule="evenodd" d="M15.7 13.3l-3.81-3.83A5.93 5.93 0 0 0 13 6c0-3.31-2.69-6-6-6S1 2.69 1 6s2.69 6 6 6c1.3 0 2.48-.41 3.47-1.11l3.83 3.81c.19.2.45.3.7.3.25 0 .52-.09.7-.3a.996.996 0 0 0 0-1.41v.01zM7 10.7c-2.59 0-4.7-2.11-4.7-4.7 0-2.59 2.11-4.7 4.7-4.7 2.59 0 4.7 2.11 4.7 4.7 0 2.59-2.11 4.7-4.7 4.7z"/></svg>
350 </div>
351
352 <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28">
353
354 <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target">
355 </div>
356
357 <div class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none js-jump-to-badge-search">
358 <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository">
359 In this repository
360 </span>
361 <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub">
362 All GitHub
363 </span>
364 <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span>
365 </div>
366
367 <div aria-hidden="true" class="border rounded-1 flex-shrink-0 bg-gray px-1 text-gray-light ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump">
368 Jump to
369 <span class="d-inline-block ml-1 v-align-middle">↵</span>
370 </div>
371 </a>
372 </li>
373
374
375 </ul>
376
377 </div>
378 </label>
379 </form> </div>
380 </div>
381
382 </div>
383
384 <a class="HeaderMenu-link no-underline mr-3" data-hydro-click="{&quot;event_type&quot;:&quot;authentication.click&quot;,&quot;payload&quot;:{&quot;location_in_page&quot;:&quot;site header menu&quot;,&quot;repository_id&quot;:null,&quot;auth_type&quot;:&quot;LOG_IN&quot;,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;9296:3F63:B1FBFC:1321364:5CF25B7F&quot;,&quot;originating_url&quot;:&quot;https://github.com/huster16/gatk-tools&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="fd39d520055d8446e558ee9e8a4559fcf3c2707ff08aa36af3730909059570dd" data-ga-click="(Logged out) Header, clicked Sign in, text:sign-in" href="/login?return_to=%2Fhuster16%2Fgatk-tools">
385 Sign&nbsp;in
386 </a> <a class="HeaderMenu-link d-inline-block no-underline border border-gray-dark rounded-1 px-2 py-1" data-hydro-click="{&quot;event_type&quot;:&quot;authentication.click&quot;,&quot;payload&quot;:{&quot;location_in_page&quot;:&quot;site header menu&quot;,&quot;repository_id&quot;:null,&quot;auth_type&quot;:&quot;SIGN_UP&quot;,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;9296:3F63:B1FBFC:1321364:5CF25B7F&quot;,&quot;originating_url&quot;:&quot;https://github.com/huster16/gatk-tools&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="64c8aa9f44411d6847c02cf39127ae3a325a4d3950eccd853bc3d3d21f56be63" data-ga-click="(Logged out) Header, clicked Sign up, text:sign-up" href="/join">
387 Sign&nbsp;up
388 </a> </div>
389 </div>
390 </div>
391 </header>
392
393 </div>
394
395 <div id="start-of-content" class="show-on-focus"></div>
396
397
398 <div id="js-flash-container">
399
400 </div>
401
402
403
404 <div class="application-main " data-commit-hovercards-enabled>
405 <div itemscope itemtype="http://schema.org/SoftwareSourceCode" class="">
406 <main id="js-repo-pjax-container" data-pjax-container >
407
408
409
410
411
412
413
414
415 <div class="pagehead repohead instapaper_ignore readability-menu experiment-repo-nav ">
416 <div class="repohead-details-container clearfix container">
417
418 <ul class="pagehead-actions">
419
420
421
422
423 <li>
424
425 <a class="tooltipped tooltipped-s btn btn-sm btn-with-count" aria-label="You must be signed in to watch a repository" rel="nofollow" data-hydro-click="{&quot;event_type&quot;:&quot;authentication.click&quot;,&quot;payload&quot;:{&quot;location_in_page&quot;:&quot;notification subscription menu watch&quot;,&quot;repository_id&quot;:null,&quot;auth_type&quot;:&quot;LOG_IN&quot;,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;9296:3F63:B1FBFC:1321364:5CF25B7F&quot;,&quot;originating_url&quot;:&quot;https://github.com/huster16/gatk-tools&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="dbd991e234ce46fc4f62b3bc77da0c3873ee09a32e84f05236c983f8ec38e576" href="/login?return_to=%2Fhuster16%2Fgatk-tools">
426 <svg class="octicon octicon-eye v-align-text-bottom" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8.06 2C3 2 0 8 0 8s3 6 8.06 6C13 14 16 8 16 8s-3-6-7.94-6zM8 12c-2.2 0-4-1.78-4-4 0-2.2 1.8-4 4-4 2.22 0 4 1.8 4 4 0 2.22-1.78 4-4 4zm2-4c0 1.11-.89 2-2 2-1.11 0-2-.89-2-2 0-1.11.89-2 2-2 1.11 0 2 .89 2 2z"/></svg>
427 Watch
428 </a> <a class="social-count" href="/huster16/gatk-tools/watchers"
429 aria-label="0 users are watching this repository">
430 0
431 </a>
432
433 </li>
434
435 <li>
436 <a class="btn btn-sm btn-with-count tooltipped tooltipped-s" aria-label="You must be signed in to star a repository" rel="nofollow" data-hydro-click="{&quot;event_type&quot;:&quot;authentication.click&quot;,&quot;payload&quot;:{&quot;location_in_page&quot;:&quot;star button&quot;,&quot;repository_id&quot;:189599350,&quot;auth_type&quot;:&quot;LOG_IN&quot;,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;9296:3F63:B1FBFC:1321364:5CF25B7F&quot;,&quot;originating_url&quot;:&quot;https://github.com/huster16/gatk-tools&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="7bed868485937510b69e0bc19d11023a5a1cc70d3d2d2036be837e66372ba7a0" href="/login?return_to=%2Fhuster16%2Fgatk-tools">
437 <svg class="octicon octicon-star v-align-text-bottom" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M14 6l-4.9-.64L7 1 4.9 5.36 0 6l3.6 3.26L2.67 14 7 11.67 11.33 14l-.93-4.74L14 6z"/></svg>
438 Star
439 </a>
440 <a class="social-count js-social-count" href="/huster16/gatk-tools/stargazers"
441 aria-label="0 users starred this repository">
442 0
443 </a>
444
445 </li>
446
447 <li>
448 <a class="btn btn-sm btn-with-count tooltipped tooltipped-s" aria-label="You must be signed in to fork a repository" rel="nofollow" data-hydro-click="{&quot;event_type&quot;:&quot;authentication.click&quot;,&quot;payload&quot;:{&quot;location_in_page&quot;:&quot;repo details fork button&quot;,&quot;repository_id&quot;:189599350,&quot;auth_type&quot;:&quot;LOG_IN&quot;,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;9296:3F63:B1FBFC:1321364:5CF25B7F&quot;,&quot;originating_url&quot;:&quot;https://github.com/huster16/gatk-tools&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="b471484d807715f3d9e3791444007693482a90517d741978272abdc02d7df366" href="/login?return_to=%2Fhuster16%2Fgatk-tools">
449 <svg class="octicon octicon-repo-forked v-align-text-bottom" viewBox="0 0 10 16" version="1.1" width="10" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8 1a1.993 1.993 0 0 0-1 3.72V6L5 8 3 6V4.72A1.993 1.993 0 0 0 2 1a1.993 1.993 0 0 0-1 3.72V6.5l3 3v1.78A1.993 1.993 0 0 0 5 15a1.993 1.993 0 0 0 1-3.72V9.5l3-3V4.72A1.993 1.993 0 0 0 8 1zM2 4.2C1.34 4.2.8 3.65.8 3c0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2zm3 10c-.66 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2zm3-10c-.66 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2z"/></svg>
450 Fork
451 </a>
452 <a href="/huster16/gatk-tools/network/members" class="social-count"
453 aria-label="0 users forked this repository">
454 0
455 </a>
456 </li>
457 </ul>
458
459 <h1 class="public ">
460 <svg class="octicon octicon-repo" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M4 9H3V8h1v1zm0-3H3v1h1V6zm0-2H3v1h1V4zm0-2H3v1h1V2zm8-1v12c0 .55-.45 1-1 1H6v2l-1.5-1.5L3 16v-2H1c-.55 0-1-.45-1-1V1c0-.55.45-1 1-1h10c.55 0 1 .45 1 1zm-1 10H1v2h2v-1h3v1h5v-2zm0-10H2v9h9V1z"/></svg>
461 <span class="author" itemprop="author"><a class="url fn" rel="author" data-hovercard-type="user" data-hovercard-url="/hovercards?user_id=50308301" data-octo-click="hovercard-link-click" data-octo-dimensions="link_type:self" href="/huster16">huster16</a></span><!--
462 --><span class="path-divider">/</span><!--
463 --><strong itemprop="name"><a data-pjax="#js-repo-pjax-container" href="/huster16/gatk-tools">gatk-tools</a></strong>
464
465
466 </h1>
467
468 </div>
469
470 <nav class="hx_reponav reponav js-repo-nav js-sidenav-container-pjax container"
471 itemscope
472 itemtype="http://schema.org/BreadcrumbList"
473 aria-label="Repository"
474 data-pjax="#js-repo-pjax-container">
475
476 <span itemscope itemtype="http://schema.org/ListItem" itemprop="itemListElement">
477 <a class="js-selected-navigation-item selected reponav-item" itemprop="url" data-hotkey="g c" aria-current="page" data-selected-links="repo_source repo_downloads repo_commits repo_releases repo_tags repo_branches repo_packages /huster16/gatk-tools" href="/huster16/gatk-tools">
478 <svg class="octicon octicon-code" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M9.5 3L8 4.5 11.5 8 8 11.5 9.5 13 14 8 9.5 3zm-5 0L0 8l4.5 5L6 11.5 2.5 8 6 4.5 4.5 3z"/></svg>
479 <span itemprop="name">Code</span>
480 <meta itemprop="position" content="1">
481 </a> </span>
482
483 <span itemscope itemtype="http://schema.org/ListItem" itemprop="itemListElement">
484 <a itemprop="url" data-hotkey="g i" class="js-selected-navigation-item reponav-item" data-selected-links="repo_issues repo_labels repo_milestones /huster16/gatk-tools/issues" href="/huster16/gatk-tools/issues">
485 <svg class="octicon octicon-issue-opened" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M7 2.3c3.14 0 5.7 2.56 5.7 5.7s-2.56 5.7-5.7 5.7A5.71 5.71 0 0 1 1.3 8c0-3.14 2.56-5.7 5.7-5.7zM7 1C3.14 1 0 4.14 0 8s3.14 7 7 7 7-3.14 7-7-3.14-7-7-7zm1 3H6v5h2V4zm0 6H6v2h2v-2z"/></svg>
486 <span itemprop="name">Issues</span>
487 <span class="Counter">0</span>
488 <meta itemprop="position" content="2">
489 </a> </span>
490
491 <span itemscope itemtype="http://schema.org/ListItem" itemprop="itemListElement">
492 <a data-hotkey="g p" itemprop="url" class="js-selected-navigation-item reponav-item" data-selected-links="repo_pulls checks /huster16/gatk-tools/pulls" href="/huster16/gatk-tools/pulls">
493 <svg class="octicon octicon-git-pull-request" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M11 11.28V5c-.03-.78-.34-1.47-.94-2.06C9.46 2.35 8.78 2.03 8 2H7V0L4 3l3 3V4h1c.27.02.48.11.69.31.21.2.3.42.31.69v6.28A1.993 1.993 0 0 0 10 15a1.993 1.993 0 0 0 1-3.72zm-1 2.92c-.66 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2zM4 3c0-1.11-.89-2-2-2a1.993 1.993 0 0 0-1 3.72v6.56A1.993 1.993 0 0 0 2 15a1.993 1.993 0 0 0 1-3.72V4.72c.59-.34 1-.98 1-1.72zm-.8 10c0 .66-.55 1.2-1.2 1.2-.65 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2zM2 4.2C1.34 4.2.8 3.65.8 3c0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2z"/></svg>
494 <span itemprop="name">Pull requests</span>
495 <span class="Counter">0</span>
496 <meta itemprop="position" content="3">
497 </a> </span>
498
499
500 <a data-hotkey="g b" class="js-selected-navigation-item reponav-item" data-selected-links="repo_projects new_repo_project repo_project /huster16/gatk-tools/projects" href="/huster16/gatk-tools/projects">
501 <svg class="octicon octicon-project" viewBox="0 0 15 16" version="1.1" width="15" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M10 12h3V2h-3v10zm-4-2h3V2H6v8zm-4 4h3V2H2v12zm-1 1h13V1H1v14zM14 0H1a1 1 0 0 0-1 1v14a1 1 0 0 0 1 1h13a1 1 0 0 0 1-1V1a1 1 0 0 0-1-1z"/></svg>
502 Projects
503 <span class="Counter" >0</span>
504 </a>
505
506
507 <a data-skip-pjax="true" class="js-selected-navigation-item reponav-item" data-selected-links="security alerts policy /huster16/gatk-tools/security/advisories" href="/huster16/gatk-tools/security/advisories">
508 <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 16 16" class="octicon" height="16px" width="16px">
509 <path fill-rule="evenodd" clip-rule="evenodd" d="M1 2l7-2 7 2v6.02C15 12.69 9.69 16 8 16c-1.69 0-7-3.31-7-7.98V2zm1 .75L8 1l6 1.75v5.268C14 12.104 9.45 15 8 15c-1.45 0-6-2.896-6-6.982V2.75z"></path>
510 <path d="M3 3.5L8 2v12c-1.207 0-5-2.482-5-5.985V3.5z"></path>
511 </svg>
512
513 Security
514 </a>
515 <a class="js-selected-navigation-item reponav-item" data-selected-links="repo_graphs repo_contributors dependency_graph pulse people /huster16/gatk-tools/pulse" href="/huster16/gatk-tools/pulse">
516 <svg class="octicon octicon-graph" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M16 14v1H0V0h1v14h15zM5 13H3V8h2v5zm4 0H7V3h2v10zm4 0h-2V6h2v7z"/></svg>
517 Insights
518 </a>
519
520 </nav>
521
522
523 </div>
524 <div class="container new-discussion-timeline experiment-repo-nav ">
525 <div class="repository-content ">
526
527
528
529 <div class="signup-prompt-bg rounded-1">
530 <div class="signup-prompt p-4 text-center mb-4 rounded-1">
531 <div class="position-relative">
532 <!-- '"` --><!-- </textarea></xmp> --></option></form><form action="/prompt_dismissals/signup" accept-charset="UTF-8" method="post"><input name="utf8" type="hidden" value="&#x2713;" /><input type="hidden" name="_method" value="put" /><input type="hidden" name="authenticity_token" value="C347xA/wfN9S1Brf3jkG7GCKplNmZoFerGeOImNxa8PZNsinckqKBCSoP2KYkwLIig6M6En5RG5kpxHsZ8OJYQ==" />
533 <button type="submit" class="position-absolute top-0 right-0 btn-link link-gray" data-ga-click="(Logged out) Sign up prompt, clicked Dismiss, text:dismiss">
534 Dismiss
535 </button>
536 </form> <h3 class="pt-2">Join GitHub today</h3>
537 <p class="col-6 mx-auto">GitHub is home to over 36 million developers working together to host and review code, manage projects, and build software together.</p>
538 <a class="btn btn-primary" data-hydro-click="{&quot;event_type&quot;:&quot;authentication.click&quot;,&quot;payload&quot;:{&quot;location_in_page&quot;:&quot;files signup prompt&quot;,&quot;repository_id&quot;:null,&quot;auth_type&quot;:&quot;SIGN_UP&quot;,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;9296:3F63:B1FBFC:1321364:5CF25B7F&quot;,&quot;originating_url&quot;:&quot;https://github.com/huster16/gatk-tools&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="eeb4f110f9edd5a734bf991fd9dfa730510b25158f8871a8f3270dc219a0e7bc" data-ga-click="(Logged out) Sign up prompt, clicked Sign up, text:sign-up" href="/join?source=prompt-code">Sign up</a>
539 </div>
540 </div>
541 </div>
542
543
544
545 <div class="d-flex flex-items-start">
546 <div class="flex-auto mb-3"> <div class="f4">
547 <em class="d-block text-gray">
548 No description, website, or topics provided.
549 </em>
550 </div>
551 </div>
552 </div>
553
554
555
556
557 <div class="overall-summary overall-summary-bottomless">
558 <div class="stats-switcher-viewport js-stats-switcher-viewport">
559 <div class="stats-switcher-wrapper">
560 <ul class="numbers-summary">
561 <li class="commits">
562 <a data-pjax href="/huster16/gatk-tools/commits/master">
563 <svg class="octicon octicon-history" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8 13H6V6h5v2H8v5zM7 1C4.81 1 2.87 2.02 1.59 3.59L0 2v4h4L2.5 4.5C3.55 3.17 5.17 2.3 7 2.3c3.14 0 5.7 2.56 5.7 5.7s-2.56 5.7-5.7 5.7A5.71 5.71 0 0 1 1.3 8c0-.34.03-.67.09-1H.08C.03 7.33 0 7.66 0 8c0 3.86 3.14 7 7 7s7-3.14 7-7-3.14-7-7-7z"/></svg>
564 <span class="num text-emphasized">
565 4
566 </span>
567 commits
568 </a>
569 </li>
570 <li>
571 <a data-pjax href="/huster16/gatk-tools/branches">
572 <svg class="octicon octicon-git-branch" viewBox="0 0 10 16" version="1.1" width="10" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M10 5c0-1.11-.89-2-2-2a1.993 1.993 0 0 0-1 3.72v.3c-.02.52-.23.98-.63 1.38-.4.4-.86.61-1.38.63-.83.02-1.48.16-2 .45V4.72a1.993 1.993 0 0 0-1-3.72C.88 1 0 1.89 0 3a2 2 0 0 0 1 1.72v6.56c-.59.35-1 .99-1 1.72 0 1.11.89 2 2 2 1.11 0 2-.89 2-2 0-.53-.2-1-.53-1.36.09-.06.48-.41.59-.47.25-.11.56-.17.94-.17 1.05-.05 1.95-.45 2.75-1.25S8.95 7.77 9 6.73h-.02C9.59 6.37 10 5.73 10 5zM2 1.8c.66 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2C1.35 4.2.8 3.65.8 3c0-.65.55-1.2 1.2-1.2zm0 12.41c-.66 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2zm6-8c-.66 0-1.2-.55-1.2-1.2 0-.65.55-1.2 1.2-1.2.65 0 1.2.55 1.2 1.2 0 .65-.55 1.2-1.2 1.2z"/></svg>
573 <span class="num text-emphasized">
574 1
575 </span>
576 branch
577 </a>
578 </li>
579
580 <li>
581 <a href="/huster16/gatk-tools/releases">
582 <svg class="octicon octicon-tag" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M7.73 1.73C7.26 1.26 6.62 1 5.96 1H3.5C2.13 1 1 2.13 1 3.5v2.47c0 .66.27 1.3.73 1.77l6.06 6.06c.39.39 1.02.39 1.41 0l4.59-4.59a.996.996 0 0 0 0-1.41L7.73 1.73zM2.38 7.09c-.31-.3-.47-.7-.47-1.13V3.5c0-.88.72-1.59 1.59-1.59h2.47c.42 0 .83.16 1.13.47l6.14 6.13-4.73 4.73-6.13-6.15zM3.01 3h2v2H3V3h.01z"/></svg>
583 <span class="num text-emphasized">
584 0
585 </span>
586 releases
587 </a>
588 </li>
589
590
591 <li >
592 <include-fragment src="/huster16/gatk-tools/contributors_size">
593 <a href="/huster16/gatk-tools/graphs/contributors">
594 <svg class="octicon octicon-organization" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M16 12.999c0 .439-.45 1-1 1H7.995c-.539 0-.994-.447-.995-.999H1c-.54 0-1-.561-1-1 0-2.634 3-4 3-4s.229-.409 0-1c-.841-.621-1.058-.59-1-3 .058-2.419 1.367-3 2.5-3s2.442.58 2.5 3c.058 2.41-.159 2.379-1 3-.229.59 0 1 0 1s1.549.711 2.42 2.088C9.196 9.369 10 8.999 10 8.999s.229-.409 0-1c-.841-.62-1.058-.59-1-3 .058-2.419 1.367-3 2.5-3s2.437.581 2.495 3c.059 2.41-.158 2.38-1 3-.229.59 0 1 0 1s3.005 1.366 3.005 4z"/></svg>
595 <span class="num text-emphasized"></span>
596 Fetching contributors
597 </a>
598 </include-fragment> </li>
599
600 <li>
601 <a href="/huster16/gatk-tools/blob/master/LICENSE">
602 <svg class="octicon octicon-law" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M7 4c-.83 0-1.5-.67-1.5-1.5S6.17 1 7 1s1.5.67 1.5 1.5S7.83 4 7 4zm7 6c0 1.11-.89 2-2 2h-1c-1.11 0-2-.89-2-2l2-4h-1c-.55 0-1-.45-1-1H8v8c.42 0 1 .45 1 1h1c.42 0 1 .45 1 1H3c0-.55.58-1 1-1h1c0-.55.58-1 1-1h.03L6 5H5c0 .55-.45 1-1 1H3l2 4c0 1.11-.89 2-2 2H2c-1.11 0-2-.89-2-2l2-4H1V5h3c0-.55.45-1 1-1h4c.55 0 1 .45 1 1h3v1h-1l2 4zM2.5 7L1 10h3L2.5 7zM13 10l-1.5-3-1.5 3h3z"/></svg>
603 Apache-2.0
604 </a>
605 </li>
606 </ul>
607
608 <div class="repository-lang-stats">
609 <ol class="repository-lang-stats-numbers">
610 <li>
611 <a href="/huster16/gatk-tools/search?l=xslt" data-ga-click="Repository, language stats search click, location:repo overview">
612 <span class="color-block language-color" style="background-color:#EB8CEB;"></span>
613 <span class="lang">XSLT</span>
614 <span class="percent">75.2%</span>
615 </a>
616 </li>
617 <li>
618 <a href="/huster16/gatk-tools/search?l=python" data-ga-click="Repository, language stats search click, location:repo overview">
619 <span class="color-block language-color" style="background-color:#3572A5;"></span>
620 <span class="lang">Python</span>
621 <span class="percent">24.8%</span>
622 </a>
623 </li>
624 </ol>
625 </div>
626 </div>
627 </div>
628 </div>
629
630 <button type="button" class="d-flex p-0 repository-lang-stats-graph js-toggle-lang-stats" title="Click for language details" data-ga-click="Repository, language bar stats toggle, location:repo overview">
631 <span class="language-color" aria-label="XSLT 75.2%" style="width:75.2%; background-color:#EB8CEB;" itemprop="keywords">XSLT</span>
632 <span class="language-color" aria-label="Python 24.8%" style="width:24.8%; background-color:#3572A5;" itemprop="keywords">Python</span>
633 </button>
634
635
636
637
638
639
640 <div class="file-navigation in-mid-page d-flex flex-items-start">
641
642 <details class="details-reset details-overlay select-menu branch-select-menu hx_rsm" id="branch-select-menu">
643 <summary class="btn btn-sm select-menu-button css-truncate"
644 data-hotkey="w"
645
646 title="Switch branches or tags">
647 <i>Branch:</i>
648 <span class="css-truncate-target">master</span>
649 </summary>
650
651 <details-menu class="select-menu-modal hx_rsm-modal position-absolute" style="z-index: 99;" src="/huster16/gatk-tools/ref-list/master?source_action=disambiguate&amp;source_controller=files" preload>
652 <include-fragment class="select-menu-loading-overlay anim-pulse">
653 <svg height="32" class="octicon octicon-octoface" viewBox="0 0 16 16" version="1.1" width="32" aria-hidden="true"><path fill-rule="evenodd" d="M14.7 5.34c.13-.32.55-1.59-.13-3.31 0 0-1.05-.33-3.44 1.3-1-.28-2.07-.32-3.13-.32s-2.13.04-3.13.32c-2.39-1.64-3.44-1.3-3.44-1.3-.68 1.72-.26 2.99-.13 3.31C.49 6.21 0 7.33 0 8.69 0 13.84 3.33 15 7.98 15S16 13.84 16 8.69c0-1.36-.49-2.48-1.3-3.35zM8 14.02c-3.3 0-5.98-.15-5.98-3.35 0-.76.38-1.48 1.02-2.07 1.07-.98 2.9-.46 4.96-.46 2.07 0 3.88-.52 4.96.46.65.59 1.02 1.3 1.02 2.07 0 3.19-2.68 3.35-5.98 3.35zM5.49 9.01c-.66 0-1.2.8-1.2 1.78s.54 1.79 1.2 1.79c.66 0 1.2-.8 1.2-1.79s-.54-1.78-1.2-1.78zm5.02 0c-.66 0-1.2.79-1.2 1.78s.54 1.79 1.2 1.79c.66 0 1.2-.8 1.2-1.79s-.53-1.78-1.2-1.78z"/></svg>
654 </include-fragment>
655 </details-menu>
656 </details>
657
658
659 <button type="button" class="btn btn-sm disabled tooltipped tooltipped-n new-pull-request-btn" aria-label="You must be signed in to create a pull request">
660 New pull request
661 </button>
662
663 <div class="breadcrumb flex-auto">
664
665 </div>
666
667 <div class="BtnGroup">
668
669 <a class="btn btn-sm empty-icon float-right BtnGroup-item" data-hydro-click="{&quot;event_type&quot;:&quot;repository.click&quot;,&quot;payload&quot;:{&quot;target&quot;:&quot;FIND_FILE_BUTTON&quot;,&quot;repository_id&quot;:189599350,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;9296:3F63:B1FBFC:1321364:5CF25B7F&quot;,&quot;originating_url&quot;:&quot;https://github.com/huster16/gatk-tools&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="2202b3ffe5544f8163f8b93af3713fc7029c4f471879a84fe8f338309f52faab" data-ga-click="Repository, find file, location:repo overview" data-hotkey="t" data-pjax="true" href="/huster16/gatk-tools/find/master">Find File</a>
670 </div>
671
672
673
674
675 <details class="get-repo-select-menu js-get-repo-select-menu js-anon-get-repo-select-menu position-relative details-overlay details-reset">
676 <summary class="btn btn-sm ml-2 btn-primary" data-hydro-click="{&quot;event_type&quot;:&quot;repository.click&quot;,&quot;payload&quot;:{&quot;repository_id&quot;:189599350,&quot;target&quot;:&quot;CLONE_OR_DOWNLOAD_BUTTON&quot;,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;9296:3F63:B1FBFC:1321364:5CF25B7F&quot;,&quot;originating_url&quot;:&quot;https://github.com/huster16/gatk-tools&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="4525d521fa4701080dc4256fee3f654f20406206ba9f433f0e4d0b3ce8e26964">
677 Clone or download
678 <span class="dropdown-caret"></span>
679 </summary> <div class="position-relative">
680 <div class="get-repo-modal dropdown-menu dropdown-menu-sw pb-0 js-toggler-container js-get-repo-modal">
681
682 <div class="get-repo-modal-options">
683 <div class="clone-options https-clone-options">
684
685 <h4 class="mb-1">
686 Clone with HTTPS
687 <a class="muted-link" href="https://help.github.com/articles/which-remote-url-should-i-use" target="_blank" title="Which remote URL should I use?">
688 <svg class="octicon octicon-question" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M6 10h2v2H6v-2zm4-3.5C10 8.64 8 9 8 9H6c0-.55.45-1 1-1h.5c.28 0 .5-.22.5-.5v-1c0-.28-.22-.5-.5-.5h-1c-.28 0-.5.22-.5.5V7H4c0-1.5 1.5-3 3-3s3 1 3 2.5zM7 2.3c3.14 0 5.7 2.56 5.7 5.7s-2.56 5.7-5.7 5.7A5.71 5.71 0 0 1 1.3 8c0-3.14 2.56-5.7 5.7-5.7zM7 1C3.14 1 0 4.14 0 8s3.14 7 7 7 7-3.14 7-7-3.14-7-7-7z"/></svg>
689 </a>
690 </h4>
691 <p class="mb-2 get-repo-decription-text">
692 Use Git or checkout with SVN using the web URL.
693 </p>
694
695 <div class="input-group">
696 <input type="text" class="form-control input-monospace input-sm" data-autoselect value="https://github.com/huster16/gatk-tools.git" aria-label="Clone this repository at https://github.com/huster16/gatk-tools.git" readonly>
697 <div class="input-group-button">
698 <clipboard-copy value="https://github.com/huster16/gatk-tools.git" aria-label="Copy to clipboard" class="btn btn-sm" data-hydro-click="{&quot;event_type&quot;:&quot;clone_or_download.click&quot;,&quot;payload&quot;:{&quot;feature_clicked&quot;:&quot;COPY_URL&quot;,&quot;git_repository_type&quot;:&quot;REPOSITORY&quot;,&quot;repository_id&quot;:189599350,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;9296:3F63:B1FBFC:1321364:5CF25B7F&quot;,&quot;originating_url&quot;:&quot;https://github.com/huster16/gatk-tools&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="11678c39c42eee5608601cea62776722ddc19e672194910a3f7e339e0c1dd6e6"><svg class="octicon octicon-clippy" viewBox="0 0 14 16" version="1.1" width="14" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M2 13h4v1H2v-1zm5-6H2v1h5V7zm2 3V8l-3 3 3 3v-2h5v-2H9zM4.5 9H2v1h2.5V9zM2 12h2.5v-1H2v1zm9 1h1v2c-.02.28-.11.52-.3.7-.19.18-.42.28-.7.3H1c-.55 0-1-.45-1-1V4c0-.55.45-1 1-1h3c0-1.11.89-2 2-2 1.11 0 2 .89 2 2h3c.55 0 1 .45 1 1v5h-1V6H1v9h10v-2zM2 5h8c0-.55-.45-1-1-1H8c-.55 0-1-.45-1-1s-.45-1-1-1-1 .45-1 1-.45 1-1 1H3c-.55 0-1 .45-1 1z"/></svg></clipboard-copy>
699 </div>
700 </div>
701
702 </div>
703
704 <div class="mt-2">
705
706 <a class="btn btn-outline get-repo-btn js-anon-download-zip-link " rel="nofollow" data-hydro-click="{&quot;event_type&quot;:&quot;clone_or_download.click&quot;,&quot;payload&quot;:{&quot;feature_clicked&quot;:&quot;DOWNLOAD_ZIP&quot;,&quot;git_repository_type&quot;:&quot;REPOSITORY&quot;,&quot;repository_id&quot;:189599350,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;9296:3F63:B1FBFC:1321364:5CF25B7F&quot;,&quot;originating_url&quot;:&quot;https://github.com/huster16/gatk-tools&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="f38afae5eed2525a512560364e73cf9629a62f093e6936acc841e643eb1f6dc8" data-ga-click="Repository, download zip, location:repo overview" href="/huster16/gatk-tools/archive/master.zip">Download ZIP</a>
707
708 </div>
709 </div>
710
711 <div class="js-modal-downloading" hidden>
712 <div class="py-2 px-3">
713 <h4 class="lh-condensed mb-3">Downloading<span class="animated-ellipsis-container"><span class="animated-ellipsis">...</span></span></h4>
714 <p class="text-gray">
715 Want to be notified of new releases in
716 <span class="text-bold">huster16/gatk-tools</span>?
717 </p>
718 </div>
719 <div class="width-full d-flex">
720 <a rel="nofollow" class="get-repo-btn btn btn-outline" style="width: 50%" data-hydro-click="{&quot;event_type&quot;:&quot;authentication.click&quot;,&quot;payload&quot;:{&quot;location_in_page&quot;:&quot;download popover&quot;,&quot;repository_id&quot;:189599350,&quot;auth_type&quot;:&quot;LOG_IN&quot;,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;9296:3F63:B1FBFC:1321364:5CF25B7F&quot;,&quot;originating_url&quot;:&quot;https://github.com/huster16/gatk-tools&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="cb61463cc7655c64c1c248161ce77d7b3d3c314ea70146f402f8c7d75b0680e3" href="/login?return_to=https%3A%2F%2Fgithub.com%2Fhuster16%2Fgatk-tools">Sign in</a>
721 <a rel="nofollow" class="get-repo-btn btn btn-primary" style="width: 50%" data-hydro-click="{&quot;event_type&quot;:&quot;authentication.click&quot;,&quot;payload&quot;:{&quot;location_in_page&quot;:&quot;download popover&quot;,&quot;repository_id&quot;:189599350,&quot;auth_type&quot;:&quot;SIGN_UP&quot;,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;9296:3F63:B1FBFC:1321364:5CF25B7F&quot;,&quot;originating_url&quot;:&quot;https://github.com/huster16/gatk-tools&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="4de2cd77e5bd2d2867a7b2d5a861644713963b0a7cf6f57303dd2946291b114e" href="/join?return_to=%2Fhuster16%2Fgatk-tools">Sign up</a>
722 </div>
723 </div>
724
725 <div class="js-modal-download-mac py-2 px-3 d-none">
726 <h4 class="lh-condensed mb-3">Launching GitHub Desktop<span class="animated-ellipsis-container"><span class="animated-ellipsis">...</span></span></h4>
727 <p class="text-gray">If nothing happens, <a href="https://desktop.github.com/">download GitHub Desktop</a> and try again.</p>
728 <p><button class="btn-link js-get-repo-modal-download-back">Go back</button></p>
729 </div>
730
731 <div class="js-modal-download-windows py-2 px-3 d-none">
732 <h4 class="lh-condensed mb-3">Launching GitHub Desktop<span class="animated-ellipsis-container"><span class="animated-ellipsis">...</span></span></h4>
733 <p class="text-gray">If nothing happens, <a href="https://desktop.github.com/">download GitHub Desktop</a> and try again.</p>
734 <p><button class="btn-link js-get-repo-modal-download-back">Go back</button></p>
735 </div>
736
737 <div class="js-modal-download-xcode py-2 px-3 d-none">
738 <h4 class="lh-condensed mb-3">Launching Xcode<span class="animated-ellipsis-container"><span class="animated-ellipsis">...</span></span></h4>
739 <p class="text-gray">If nothing happens, <a href="https://developer.apple.com/xcode/">download Xcode</a> and try again.</p>
740 <p><button class="btn-link js-get-repo-modal-download-back">Go back</button></p>
741 </div>
742
743 <div class="js-modal-download-visual-studio py-2 px-3 d-none">
744 <h4 class="lh-condensed mb-3">Launching Visual Studio<span class="animated-ellipsis-container"><span class="animated-ellipsis">...</span></span></h4>
745 <p class="text-gray">If nothing happens, <a href="https://visualstudio.github.com/">download the GitHub extension for Visual Studio</a> and try again.</p>
746 <p><button class="btn-link js-get-repo-modal-download-back">Go back</button></p>
747 </div>
748
749 </div>
750 </div>
751 </details>
752
753 </div>
754
755
756
757
758 <include-fragment src="/huster16/gatk-tools/tree-commit/8396208ba320ef1f0cd4b6b02607a2d2aae5f760" class="commit-tease commit-loader">
759 <div class="blank loader-loading">
760 <img alt="" class="loader" src="https://github.githubassets.com/images/spinners/octocat-spinner-32-EAF2F5.gif" width="16" height="16" />
761 Fetching latest commit…
762 </div>
763 <div class="loader-error">
764 Cannot retrieve the latest commit at this time.
765 </div>
766 </include-fragment>
767
768
769 <include-fragment class="file-wrap" src="/huster16/gatk-tools/file-list/master">
770 <a class="d-none js-permalink-shortcut" data-hotkey="y" href="/huster16/gatk-tools/tree/8396208ba320ef1f0cd4b6b02607a2d2aae5f760">Permalink</a>
771
772 <table class="files js-navigation-container js-active-navigation-container" data-pjax>
773 <thead>
774 <tr>
775 <th><span class="sr-only">Type</span></th>
776 <th><span class="sr-only">Name</span></th>
777 <th><span class="sr-only">Latest commit message</span></th>
778 <th><span class="sr-only">Commit time</span></th>
779 </tr>
780 </thead>
781
782
783 <tbody>
784 <tr class="warning include-fragment-error">
785 <td class="icon"><svg class="octicon octicon-alert" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8.893 1.5c-.183-.31-.52-.5-.887-.5s-.703.19-.886.5L.138 13.499a.98.98 0 0 0 0 1.001c.193.31.53.501.886.501h13.964c.367 0 .704-.19.877-.5a1.03 1.03 0 0 0 .01-1.002L8.893 1.5zm.133 11.497H6.987v-2.003h2.039v2.003zm0-3.004H6.987V5.987h2.039v4.006z"/></svg></td>
786 <td class="content" colspan="3">Failed to load latest commit information.</td>
787 </tr>
788
789 <tr class="js-navigation-item">
790 <td class="icon">
791 <svg aria-label="directory" class="octicon octicon-file-directory" viewBox="0 0 14 16" version="1.1" width="14" height="16" role="img"><path fill-rule="evenodd" d="M13 4H7V3c0-.66-.31-1-1-1H1c-.55 0-1 .45-1 1v10c0 .55.45 1 1 1h12c.55 0 1-.45 1-1V5c0-.55-.45-1-1-1zM6 4H1V3h5v1z"/></svg>
792 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
793 </td>
794 <td class="content">
795 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="generation" id="9cb9ce5bd9e807867d42a740c9633fc7-3625a25873af83c0541afd8f95fc07be91aabe3a" href="/huster16/gatk-tools/tree/master/generation">generation</a></span>
796 </td>
797 <td class="message">
798 <span class="css-truncate css-truncate-target">
799 </span>
800 </td>
801 <td class="age">
802 <span class="css-truncate css-truncate-target"></span>
803 </td>
804 </tr>
805 <tr class="js-navigation-item">
806 <td class="icon">
807 <svg aria-label="directory" class="octicon octicon-file-directory" viewBox="0 0 14 16" version="1.1" width="14" height="16" role="img"><path fill-rule="evenodd" d="M13 4H7V3c0-.66-.31-1-1-1H1c-.55 0-1 .45-1 1v10c0 .55.45 1 1 1h12c.55 0 1-.45 1-1V5c0-.55-.45-1-1-1zM6 4H1V3h5v1z"/></svg>
808 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
809 </td>
810 <td class="content">
811 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="tool-data" id="cacc76c3f8e5d46af3e9a108d7a64298-a54d24bc89b721726d1816c1d84b612e87530b2c" href="/huster16/gatk-tools/tree/master/tool-data">tool-data</a></span>
812 </td>
813 <td class="message">
814 <span class="css-truncate css-truncate-target">
815 </span>
816 </td>
817 <td class="age">
818 <span class="css-truncate css-truncate-target"></span>
819 </td>
820 </tr>
821 <tr class="js-navigation-item">
822 <td class="icon">
823 <svg aria-label="file" class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" role="img"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg>
824 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
825 </td>
826 <td class="content">
827 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title=".shed.yml" id="cdcc89357908fc034bde629890b000b5-2325e6cb39480ba78f39c79f6c003dbd1e31d57f" href="/huster16/gatk-tools/blob/master/.shed.yml">.shed.yml</a></span>
828 </td>
829 <td class="message">
830 <span class="css-truncate css-truncate-target">
831 </span>
832 </td>
833 <td class="age">
834 <span class="css-truncate css-truncate-target"></span>
835 </td>
836 </tr>
837 <tr class="js-navigation-item">
838 <td class="icon">
839 <svg aria-label="file" class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" role="img"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg>
840 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
841 </td>
842 <td class="content">
843 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="LICENSE" id="9879d6db96fd29134fc802214163b95a-261eeb9e9f8b2b4b0d119366dda99c6fd7d35c64" itemprop="license" href="/huster16/gatk-tools/blob/master/LICENSE">LICENSE</a></span>
844 </td>
845 <td class="message">
846 <span class="css-truncate css-truncate-target">
847 </span>
848 </td>
849 <td class="age">
850 <span class="css-truncate css-truncate-target"></span>
851 </td>
852 </tr>
853 <tr class="js-navigation-item">
854 <td class="icon">
855 <svg aria-label="file" class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" role="img"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg>
856 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
857 </td>
858 <td class="content">
859 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="README" id="c47c7c7383225ab55ff591cb59c41e6b-a8addefe468edbe7d68593ece5e8aa412b4899ff" href="/huster16/gatk-tools/blob/master/README">README</a></span>
860 </td>
861 <td class="message">
862 <span class="css-truncate css-truncate-target">
863 </span>
864 </td>
865 <td class="age">
866 <span class="css-truncate css-truncate-target"></span>
867 </td>
868 </tr>
869 <tr class="js-navigation-item">
870 <td class="icon">
871 <svg aria-label="file" class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" role="img"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg>
872 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
873 </td>
874 <td class="content">
875 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="analyze_covariates.xml" id="59610722be95a0212262688dcbf7c239-2e2bbaf59e3a3ca897dbc81ce2bd795b9d42325f" href="/huster16/gatk-tools/blob/master/analyze_covariates.xml">analyze_covariates.xml</a></span>
876 </td>
877 <td class="message">
878 <span class="css-truncate css-truncate-target">
879 </span>
880 </td>
881 <td class="age">
882 <span class="css-truncate css-truncate-target"></span>
883 </td>
884 </tr>
885 <tr class="js-navigation-item">
886 <td class="icon">
887 <svg aria-label="file" class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" role="img"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg>
888 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
889 </td>
890 <td class="content">
891 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="base_recalibrator.xml" id="48bdf74141faebe19e0066be8cd87dd5-7317df4b6cf2302f9127fd576bc4ae33f4492009" href="/huster16/gatk-tools/blob/master/base_recalibrator.xml">base_recalibrator.xml</a></span>
892 </td>
893 <td class="message">
894 <span class="css-truncate css-truncate-target">
895 </span>
896 </td>
897 <td class="age">
898 <span class="css-truncate css-truncate-target"></span>
899 </td>
900 </tr>
901 <tr class="js-navigation-item">
902 <td class="icon">
903 <svg aria-label="file" class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" role="img"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg>
904 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
905 </td>
906 <td class="content">
907 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="combine_gvcfs.xml" id="5a42bf8ebd8f0473dfab105bce4454bd-8f5dab6ecfcf6eecdc49559973a0f517c7ce51fe" href="/huster16/gatk-tools/blob/master/combine_gvcfs.xml">combine_gvcfs.xml</a></span>
908 </td>
909 <td class="message">
910 <span class="css-truncate css-truncate-target">
911 </span>
912 </td>
913 <td class="age">
914 <span class="css-truncate css-truncate-target"></span>
915 </td>
916 </tr>
917 <tr class="js-navigation-item">
918 <td class="icon">
919 <svg aria-label="file" class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" role="img"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg>
920 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
921 </td>
922 <td class="content">
923 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="combine_variants.xml" id="27122924aa0d6acdcda3d1a0fdd0ca79-9f7532b3fd7b7bc45137cdb66ad4deadbf2637be" href="/huster16/gatk-tools/blob/master/combine_variants.xml">combine_variants.xml</a></span>
924 </td>
925 <td class="message">
926 <span class="css-truncate css-truncate-target">
927 </span>
928 </td>
929 <td class="age">
930 <span class="css-truncate css-truncate-target"></span>
931 </td>
932 </tr>
933 <tr class="js-navigation-item">
934 <td class="icon">
935 <svg aria-label="file" class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" role="img"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg>
936 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
937 </td>
938 <td class="content">
939 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="gatk.xml" id="6aeaf5662a51985b4f74c250a5ccefa2-715530fdb731605326741b7f0e5da00bfaea2c70" href="/huster16/gatk-tools/blob/master/gatk.xml">gatk.xml</a></span>
940 </td>
941 <td class="message">
942 <span class="css-truncate css-truncate-target">
943 </span>
944 </td>
945 <td class="age">
946 <span class="css-truncate css-truncate-target"></span>
947 </td>
948 </tr>
949 <tr class="js-navigation-item">
950 <td class="icon">
951 <svg aria-label="file" class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" role="img"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg>
952 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
953 </td>
954 <td class="content">
955 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="gatk_macros.xml" id="e86fbc71297931c373dc3c1ebbc5aa9b-0edfc715939f63ad66fd7e4555ecac6bc3623748" href="/huster16/gatk-tools/blob/master/gatk_macros.xml">gatk_macros.xml</a></span>
956 </td>
957 <td class="message">
958 <span class="css-truncate css-truncate-target">
959 </span>
960 </td>
961 <td class="age">
962 <span class="css-truncate css-truncate-target"></span>
963 </td>
964 </tr>
965 <tr class="js-navigation-item">
966 <td class="icon">
967 <svg aria-label="file" class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" role="img"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg>
968 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
969 </td>
970 <td class="content">
971 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="genotype_gvcfs.xml" id="0372ebae7a90c232ee5e7536d5fc3d71-18e615ecb169da998a8246b66159d1c6819ef222" href="/huster16/gatk-tools/blob/master/genotype_gvcfs.xml">genotype_gvcfs.xml</a></span>
972 </td>
973 <td class="message">
974 <span class="css-truncate css-truncate-target">
975 </span>
976 </td>
977 <td class="age">
978 <span class="css-truncate css-truncate-target"></span>
979 </td>
980 </tr>
981 <tr class="js-navigation-item">
982 <td class="icon">
983 <svg aria-label="file" class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" role="img"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg>
984 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
985 </td>
986 <td class="content">
987 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="haplotype_caller.xml" id="3ba21ca32b06283a30eaa19f3d2aacb7-0fddf817930f1bfbd2c286514af781a06edf1fe0" href="/huster16/gatk-tools/blob/master/haplotype_caller.xml">haplotype_caller.xml</a></span>
988 </td>
989 <td class="message">
990 <span class="css-truncate css-truncate-target">
991 </span>
992 </td>
993 <td class="age">
994 <span class="css-truncate css-truncate-target"></span>
995 </td>
996 </tr>
997 <tr class="js-navigation-item">
998 <td class="icon">
999 <svg aria-label="file" class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" role="img"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg>
1000 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
1001 </td>
1002 <td class="content">
1003 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="indel_realigner.xml" id="e7b986d614bb6b302bf2fc4aa93817d0-6c46b5cf10b2b57e641689d5474b80f538bc11bc" href="/huster16/gatk-tools/blob/master/indel_realigner.xml">indel_realigner.xml</a></span>
1004 </td>
1005 <td class="message">
1006 <span class="css-truncate css-truncate-target">
1007 </span>
1008 </td>
1009 <td class="age">
1010 <span class="css-truncate css-truncate-target"></span>
1011 </td>
1012 </tr>
1013 <tr class="js-navigation-item">
1014 <td class="icon">
1015 <svg aria-label="file" class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" role="img"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg>
1016 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
1017 </td>
1018 <td class="content">
1019 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="print_reads.xml" id="084bb1c569888ece53345b6d80b919d7-19269244ac276c5ac4c3ea35d88a0faa1c63dbf1" href="/huster16/gatk-tools/blob/master/print_reads.xml">print_reads.xml</a></span>
1020 </td>
1021 <td class="message">
1022 <span class="css-truncate css-truncate-target">
1023 </span>
1024 </td>
1025 <td class="age">
1026 <span class="css-truncate css-truncate-target"></span>
1027 </td>
1028 </tr>
1029 <tr class="js-navigation-item">
1030 <td class="icon">
1031 <svg aria-label="file" class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" role="img"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg>
1032 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
1033 </td>
1034 <td class="content">
1035 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="realigner_target_creator.xml" id="00d1312b6f84e2192f19921c8e5e53d7-86621b8b4cbbf521fa5741f6fecc16f87c810c1d" href="/huster16/gatk-tools/blob/master/realigner_target_creator.xml">realigner_target_creator.xml</a></span>
1036 </td>
1037 <td class="message">
1038 <span class="css-truncate css-truncate-target">
1039 </span>
1040 </td>
1041 <td class="age">
1042 <span class="css-truncate css-truncate-target"></span>
1043 </td>
1044 </tr>
1045 <tr class="js-navigation-item">
1046 <td class="icon">
1047 <svg aria-label="file" class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" role="img"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg>
1048 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
1049 </td>
1050 <td class="content">
1051 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="tool_data_table_conf.xml.sample" id="60160a6e4efd651b475bcbf960abcc2d-b0e4b46b92ceb44e50c9abf01cf31db95628ac93" href="/huster16/gatk-tools/blob/master/tool_data_table_conf.xml.sample">tool_data_table_conf.xml.sample</a></span>
1052 </td>
1053 <td class="message">
1054 <span class="css-truncate css-truncate-target">
1055 </span>
1056 </td>
1057 <td class="age">
1058 <span class="css-truncate css-truncate-target"></span>
1059 </td>
1060 </tr>
1061 <tr class="js-navigation-item">
1062 <td class="icon">
1063 <svg aria-label="file" class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" role="img"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg>
1064 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
1065 </td>
1066 <td class="content">
1067 <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="tool_dependencies.xml" id="1f1e2fcbf1ddc07a88bc59ca246c9a90-3ac9ffc6df38d4633e8022ed0b78e3c95e586b10" href="/huster16/gatk-tools/blob/master/tool_dependencies.xml">tool_dependencies.xml</a></span>
1068 </td>
1069 <td class="message">
1070 <span class="css-truncate css-truncate-target">
1071 </span>
1072 </td>
1073 <td class="age">
1074 <span class="css-truncate css-truncate-target"></span>
1075 </td>
1076 </tr>
1077 </tbody>
1078 </table>
1079
1080 </include-fragment>
1081
1082
1083
1084 <div id="readme" class="Box Box--condensed instapaper_body js-code-block-container">
1085 <div class="Box-header d-flex flex-items-center flex-justify-between px-2">
1086 <h3 class="Box-title pr-3">
1087 <svg class="octicon octicon-book" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M3 5h4v1H3V5zm0 3h4V7H3v1zm0 2h4V9H3v1zm11-5h-4v1h4V5zm0 2h-4v1h4V7zm0 2h-4v1h4V9zm2-6v9c0 .55-.45 1-1 1H9.5l-1 1-1-1H2c-.55 0-1-.45-1-1V3c0-.55.45-1 1-1h5.5l1 1 1-1H15c.55 0 1 .45 1 1zm-8 .5L7.5 3H2v9h6V3.5zm7-.5H9.5l-.5.5V12h6V3z"/></svg>
1088 README
1089 </h3>
1090 </div>
1091 <div class="Box-body">
1092 <div class="plain"><pre style="white-space: pre-wrap">Installation note:
1093 A GATK license needs to be obtained separately from the Broad Institute (<a href="https://www.broadinstitute.org/gatk/" rel="nofollow">https://www.broadinstitute.org/gatk/</a>)
1094 to be able to use this tool. Once the license is obtained, the GATK Jar file must then be downloaded and moved
1095 to /mnt/galaxy/tools/GATK/x.x-x on the server. Substitute the appropriate version number in the file path.
1096 Be sure to download the correct version of the Jar file for the toolshed version installed.
1097 </pre></div>
1098 </div>
1099 </div>
1100
1101
1102
1103 </div>
1104 <div class="modal-backdrop js-touch-events"></div>
1105 </div>
1106
1107 </main>
1108 </div>
1109
1110
1111 </div>
1112
1113
1114 <div class="footer container-lg width-full px-3" role="contentinfo">
1115 <div class="position-relative d-flex flex-justify-between pt-6 pb-2 mt-6 f6 text-gray border-top border-gray-light ">
1116 <ul class="list-style-none d-flex flex-wrap ">
1117 <li class="mr-3">&copy; 2019 <span title="0.27328s from unicorn-68fcf5fc59-q8f8h">GitHub</span>, Inc.</li>
1118 <li class="mr-3"><a data-ga-click="Footer, go to terms, text:terms" href="https://github.com/site/terms">Terms</a></li>
1119 <li class="mr-3"><a data-ga-click="Footer, go to privacy, text:privacy" href="https://github.com/site/privacy">Privacy</a></li>
1120 <li class="mr-3"><a data-ga-click="Footer, go to security, text:security" href="https://github.com/security">Security</a></li>
1121 <li class="mr-3"><a href="https://githubstatus.com/" data-ga-click="Footer, go to status, text:status">Status</a></li>
1122 <li><a data-ga-click="Footer, go to help, text:help" href="https://help.github.com">Help</a></li>
1123 </ul>
1124
1125 <a aria-label="Homepage" title="GitHub" class="footer-octicon d-none d-lg-block mx-lg-4" href="https://github.com">
1126 <svg height="24" class="octicon octicon-mark-github" viewBox="0 0 16 16" version="1.1" width="24" aria-hidden="true"><path fill-rule="evenodd" d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29 6.53 5.47 7.59.4.07.55-.17.55-.38 0-.19-.01-.82-.01-1.49-2.01.37-2.53-.49-2.69-.94-.09-.23-.48-.94-.82-1.13-.28-.15-.68-.52-.01-.53.63-.01 1.08.58 1.23.82.72 1.21 1.87.87 2.33.66.07-.52.28-.87.51-1.07-1.78-.2-3.64-.89-3.64-3.95 0-.87.31-1.59.82-2.15-.08-.2-.36-1.02.08-2.12 0 0 .67-.21 2.2.82.64-.18 1.32-.27 2-.27.68 0 1.36.09 2 .27 1.53-1.04 2.2-.82 2.2-.82.44 1.1.16 1.92.08 2.12.51.56.82 1.27.82 2.15 0 3.07-1.87 3.75-3.65 3.95.29.25.54.73.54 1.48 0 1.07-.01 1.93-.01 2.2 0 .21.15.46.55.38A8.013 8.013 0 0 0 16 8c0-4.42-3.58-8-8-8z"/></svg>
1127 </a>
1128 <ul class="list-style-none d-flex flex-wrap ">
1129 <li class="mr-3"><a data-ga-click="Footer, go to contact, text:contact" href="https://github.com/contact">Contact GitHub</a></li>
1130 <li class="mr-3"><a href="https://github.com/pricing" data-ga-click="Footer, go to Pricing, text:Pricing">Pricing</a></li>
1131 <li class="mr-3"><a href="https://developer.github.com" data-ga-click="Footer, go to api, text:api">API</a></li>
1132 <li class="mr-3"><a href="https://training.github.com" data-ga-click="Footer, go to training, text:training">Training</a></li>
1133 <li class="mr-3"><a href="https://github.blog" data-ga-click="Footer, go to blog, text:blog">Blog</a></li>
1134 <li><a data-ga-click="Footer, go to about, text:about" href="https://github.com/about">About</a></li>
1135
1136 </ul>
1137 </div>
1138 <div class="d-flex flex-justify-center pb-6">
1139 <span class="f6 text-gray-light"></span>
1140 </div>
1141 </div>
1142
1143
1144
1145 <div id="ajax-error-message" class="ajax-error-message flash flash-error">
1146 <svg class="octicon octicon-alert" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8.893 1.5c-.183-.31-.52-.5-.887-.5s-.703.19-.886.5L.138 13.499a.98.98 0 0 0 0 1.001c.193.31.53.501.886.501h13.964c.367 0 .704-.19.877-.5a1.03 1.03 0 0 0 .01-1.002L8.893 1.5zm.133 11.497H6.987v-2.003h2.039v2.003zm0-3.004H6.987V5.987h2.039v4.006z"/></svg>
1147 <button type="button" class="flash-close js-ajax-error-dismiss" aria-label="Dismiss error">
1148 <svg class="octicon octicon-x" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M7.48 8l3.75 3.75-1.48 1.48L6 9.48l-3.75 3.75-1.48-1.48L4.52 8 .77 4.25l1.48-1.48L6 6.52l3.75-3.75 1.48 1.48L7.48 8z"/></svg>
1149 </button>
1150 You can’t perform that action at this time.
1151 </div>
1152
1153
1154 <script crossorigin="anonymous" integrity="sha512-EPrD+nddbyhpiLL8l3M8VfJpZr4J2EWQLaPXZ+6A3VDJKzS5HeZ3dkMVieHSdvIPHsMbWPyVlY42SWKoS4XTfA==" type="application/javascript" src="https://github.githubassets.com/assets/compat-bootstrap-831f12d4.js"></script>
1155 <script crossorigin="anonymous" integrity="sha512-P6rRiDq0lrIYgYfVPJ4Is2goJODXsywx7ozNssJbEOAwc5cBChqaUFZ+puemlu3KAI/q5XfkOBaSNjXExBE3ag==" type="application/javascript" src="https://github.githubassets.com/assets/frameworks-15d12409.js"></script>
1156
1157 <script crossorigin="anonymous" async="async" integrity="sha512-sD5UHbq6I3rl+U+HEPeL+7sTZmew8P0O2uOtuHlXNJjtex4uLuwjFRTEKF/F1KbqXw52uf1B2lIwVE5ZNUqxqg==" type="application/javascript" src="https://github.githubassets.com/assets/github-bootstrap-857b0672.js"></script>
1158
1159
1160
1161 <div class="js-stale-session-flash stale-session-flash flash flash-warn flash-banner" hidden
1162 >
1163 <svg class="octicon octicon-alert" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8.893 1.5c-.183-.31-.52-.5-.887-.5s-.703.19-.886.5L.138 13.499a.98.98 0 0 0 0 1.001c.193.31.53.501.886.501h13.964c.367 0 .704-.19.877-.5a1.03 1.03 0 0 0 .01-1.002L8.893 1.5zm.133 11.497H6.987v-2.003h2.039v2.003zm0-3.004H6.987V5.987h2.039v4.006z"/></svg>
1164 <span class="signed-in-tab-flash">You signed in with another tab or window. <a href="">Reload</a> to refresh your session.</span>
1165 <span class="signed-out-tab-flash">You signed out in another tab or window. <a href="">Reload</a> to refresh your session.</span>
1166 </div>
1167 <template id="site-details-dialog">
1168 <details class="details-reset details-overlay details-overlay-dark lh-default text-gray-dark hx_rsm" open>
1169 <summary role="button" aria-label="Close dialog"></summary>
1170 <details-dialog class="Box Box--overlay d-flex flex-column anim-fade-in fast hx_rsm-dialog hx_rsm-modal">
1171 <button class="Box-btn-octicon m-0 btn-octicon position-absolute right-0 top-0" type="button" aria-label="Close dialog" data-close-dialog>
1172 <svg class="octicon octicon-x" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M7.48 8l3.75 3.75-1.48 1.48L6 9.48l-3.75 3.75-1.48-1.48L4.52 8 .77 4.25l1.48-1.48L6 6.52l3.75-3.75 1.48 1.48L7.48 8z"/></svg>
1173 </button>
1174 <div class="octocat-spinner my-6 js-details-dialog-spinner"></div>
1175 </details-dialog>
1176 </details>
1177 </template>
1178
1179 <div class="Popover js-hovercard-content position-absolute" style="display: none; outline: none;" tabindex="0">
1180 <div class="Popover-message Popover-message--bottom-left Popover-message--large Box box-shadow-large" style="width:360px;">
1181 </div>
1182 </div>
1183
1184 <div aria-live="polite" class="js-global-screen-reader-notice sr-only"></div>
1185
1186 </body>
1187 </html>
1188