/usr/share/doc/libbamtools-dev/html/class_bam_tools_1_1_bam_writer.html is in libbamtools-doc 2.4.1+dfsg-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 | <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
<meta http-equiv="X-UA-Compatible" content="IE=9"/>
<meta name="generator" content="Doxygen 1.8.13"/>
<meta name="viewport" content="width=device-width, initial-scale=1"/>
<title>BamTools: BamTools::BamWriter Class Reference</title>
<link href="tabs.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="jquery.js"></script>
<script type="text/javascript" src="dynsections.js"></script>
<link href="search/search.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="search/searchdata.js"></script>
<script type="text/javascript" src="search/search.js"></script>
<link href="doxygen.css" rel="stylesheet" type="text/css" />
</head>
<body>
<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
<div id="titlearea">
<table cellspacing="0" cellpadding="0">
<tbody>
<tr style="height: 56px;">
<td id="projectalign" style="padding-left: 0.5em;">
<div id="projectname">BamTools
 <span id="projectnumber">2.4.1</span>
</div>
</td>
</tr>
</tbody>
</table>
</div>
<!-- end header part -->
<!-- Generated by Doxygen 1.8.13 -->
<script type="text/javascript">
var searchBox = new SearchBox("searchBox", "search",false,'Search');
</script>
<script type="text/javascript" src="menudata.js"></script>
<script type="text/javascript" src="menu.js"></script>
<script type="text/javascript">
$(function() {
initMenu('',true,false,'search.php','Search');
$(document).ready(function() { init_search(); });
});
</script>
<div id="main-nav"></div>
<!-- window showing the filter options -->
<div id="MSearchSelectWindow"
onmouseover="return searchBox.OnSearchSelectShow()"
onmouseout="return searchBox.OnSearchSelectHide()"
onkeydown="return searchBox.OnSearchSelectKey(event)">
</div>
<!-- iframe showing the search results (closed by default) -->
<div id="MSearchResultsWindow">
<iframe src="javascript:void(0)" frameborder="0"
name="MSearchResults" id="MSearchResults">
</iframe>
</div>
<div id="nav-path" class="navpath">
<ul>
<li class="navelem"><a class="el" href="namespace_bam_tools.html">BamTools</a></li><li class="navelem"><a class="el" href="class_bam_tools_1_1_bam_writer.html">BamWriter</a></li> </ul>
</div>
</div><!-- top -->
<div class="header">
<div class="summary">
<a href="#pub-types">Public Types</a> |
<a href="#pub-methods">Public Member Functions</a> |
<a href="class_bam_tools_1_1_bam_writer-members.html">List of all members</a> </div>
<div class="headertitle">
<div class="title">BamTools::BamWriter Class Reference</div> </div>
</div><!--header-->
<div class="contents">
<p>Provides write access for generating BAM files.
<a href="class_bam_tools_1_1_bam_writer.html#details">More...</a></p>
<p><code>#include <<a class="el" href="_bam_writer_8h_source.html">BamWriter.h</a>></code></p>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-types"></a>
Public Types</h2></td></tr>
<tr class="memitem:af602e9ed717a9fb8288c46a55a6cff8a"><td class="memItemLeft" align="right" valign="top">enum  </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_writer.html#af602e9ed717a9fb8288c46a55a6cff8a">CompressionMode</a> { <a class="el" href="class_bam_tools_1_1_bam_writer.html#af602e9ed717a9fb8288c46a55a6cff8aa09f4d73eb4763388e9f1e3e223afb921">Compressed</a> = 0,
<a class="el" href="class_bam_tools_1_1_bam_writer.html#af602e9ed717a9fb8288c46a55a6cff8aab0b9d5faf2962cfa82f7b97a9884192a">Uncompressed</a>
}<tr class="memdesc:af602e9ed717a9fb8288c46a55a6cff8a"><td class="mdescLeft"> </td><td class="mdescRight">This enum describes the compression behaviors for output BAM files. <a href="class_bam_tools_1_1_bam_writer.html#af602e9ed717a9fb8288c46a55a6cff8a">More...</a><br /></td></tr>
</td></tr>
<tr class="separator:af602e9ed717a9fb8288c46a55a6cff8a"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:a1aed3afd373875e3b26dd14a0a3fb488"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_writer.html#a1aed3afd373875e3b26dd14a0a3fb488">BamWriter</a> (void)</td></tr>
<tr class="memdesc:a1aed3afd373875e3b26dd14a0a3fb488"><td class="mdescLeft"> </td><td class="mdescRight">constructor <a href="#a1aed3afd373875e3b26dd14a0a3fb488">More...</a><br /></td></tr>
<tr class="separator:a1aed3afd373875e3b26dd14a0a3fb488"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a6d16ab6622a12d03e76f06f9f80c4535"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_writer.html#a6d16ab6622a12d03e76f06f9f80c4535">~BamWriter</a> (void)</td></tr>
<tr class="memdesc:a6d16ab6622a12d03e76f06f9f80c4535"><td class="mdescLeft"> </td><td class="mdescRight">destructor <a href="#a6d16ab6622a12d03e76f06f9f80c4535">More...</a><br /></td></tr>
<tr class="separator:a6d16ab6622a12d03e76f06f9f80c4535"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:acf06b57f75e03de0096640adcdfe0ad5"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_writer.html#acf06b57f75e03de0096640adcdfe0ad5">Close</a> (void)</td></tr>
<tr class="memdesc:acf06b57f75e03de0096640adcdfe0ad5"><td class="mdescLeft"> </td><td class="mdescRight">Closes the current BAM file. <a href="#acf06b57f75e03de0096640adcdfe0ad5">More...</a><br /></td></tr>
<tr class="separator:acf06b57f75e03de0096640adcdfe0ad5"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a4a9515d5f11cf9cfdf42c4360fac7cff"><td class="memItemLeft" align="right" valign="top">std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_writer.html#a4a9515d5f11cf9cfdf42c4360fac7cff">GetErrorString</a> (void) const</td></tr>
<tr class="memdesc:a4a9515d5f11cf9cfdf42c4360fac7cff"><td class="mdescLeft"> </td><td class="mdescRight">Returns a human-readable description of the last error that occurred. <a href="#a4a9515d5f11cf9cfdf42c4360fac7cff">More...</a><br /></td></tr>
<tr class="separator:a4a9515d5f11cf9cfdf42c4360fac7cff"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae7ad70e11236f0fd443c510e1c5b0ff8"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_writer.html#ae7ad70e11236f0fd443c510e1c5b0ff8">IsOpen</a> (void) const</td></tr>
<tr class="memdesc:ae7ad70e11236f0fd443c510e1c5b0ff8"><td class="mdescLeft"> </td><td class="mdescRight">Returns <code>true</code> if BAM file is open for writing. <a href="#ae7ad70e11236f0fd443c510e1c5b0ff8">More...</a><br /></td></tr>
<tr class="separator:ae7ad70e11236f0fd443c510e1c5b0ff8"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:afb0f6e04c32f60a92210be99ba1219a7"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_writer.html#afb0f6e04c32f60a92210be99ba1219a7">Open</a> (const std::string &filename, const std::string &samHeaderText, const <a class="el" href="namespace_bam_tools.html#abf3564b867a24092bf6575fdda87d573">RefVector</a> &referenceSequences)</td></tr>
<tr class="memdesc:afb0f6e04c32f60a92210be99ba1219a7"><td class="mdescLeft"> </td><td class="mdescRight">Opens a BAM file for writing. <a href="#afb0f6e04c32f60a92210be99ba1219a7">More...</a><br /></td></tr>
<tr class="separator:afb0f6e04c32f60a92210be99ba1219a7"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a6106772d6ff8c66e8703cbb55060fb09"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_writer.html#a6106772d6ff8c66e8703cbb55060fb09">Open</a> (const std::string &filename, const <a class="el" href="struct_bam_tools_1_1_sam_header.html">SamHeader</a> &samHeader, const <a class="el" href="namespace_bam_tools.html#abf3564b867a24092bf6575fdda87d573">RefVector</a> &referenceSequences)</td></tr>
<tr class="memdesc:a6106772d6ff8c66e8703cbb55060fb09"><td class="mdescLeft"> </td><td class="mdescRight">Opens a BAM file for writing. <a href="#a6106772d6ff8c66e8703cbb55060fb09">More...</a><br /></td></tr>
<tr class="separator:a6106772d6ff8c66e8703cbb55060fb09"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af15602db0267ae7394afff0c1d74ea68"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_writer.html#af15602db0267ae7394afff0c1d74ea68">SaveAlignment</a> (const <a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamAlignment</a> &alignment)</td></tr>
<tr class="memdesc:af15602db0267ae7394afff0c1d74ea68"><td class="mdescLeft"> </td><td class="mdescRight">Saves an alignment to the BAM file. <a href="#af15602db0267ae7394afff0c1d74ea68">More...</a><br /></td></tr>
<tr class="separator:af15602db0267ae7394afff0c1d74ea68"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae2bb85258ab329a6d2ab9287e1c6b8ad"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_bam_writer.html#ae2bb85258ab329a6d2ab9287e1c6b8ad">SetCompressionMode</a> (const <a class="el" href="class_bam_tools_1_1_bam_writer.html#af602e9ed717a9fb8288c46a55a6cff8a">BamWriter::CompressionMode</a> &compressionMode)</td></tr>
<tr class="memdesc:ae2bb85258ab329a6d2ab9287e1c6b8ad"><td class="mdescLeft"> </td><td class="mdescRight">Sets the output compression mode. <a href="#ae2bb85258ab329a6d2ab9287e1c6b8ad">More...</a><br /></td></tr>
<tr class="separator:ae2bb85258ab329a6d2ab9287e1c6b8ad"><td class="memSeparator" colspan="2"> </td></tr>
</table>
<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>Provides write access for generating BAM files. </p>
</div><h2 class="groupheader">Member Enumeration Documentation</h2>
<a id="af602e9ed717a9fb8288c46a55a6cff8a"></a>
<h2 class="memtitle"><span class="permalink"><a href="#af602e9ed717a9fb8288c46a55a6cff8a">◆ </a></span>CompressionMode</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">enum <a class="el" href="class_bam_tools_1_1_bam_writer.html#af602e9ed717a9fb8288c46a55a6cff8a">BamTools::BamWriter::CompressionMode</a></td>
</tr>
</table>
</div><div class="memdoc">
<p>This enum describes the compression behaviors for output BAM files. </p>
<table class="fieldtable">
<tr><th colspan="2">Enumerator</th></tr><tr><td class="fieldname"><a id="af602e9ed717a9fb8288c46a55a6cff8aa09f4d73eb4763388e9f1e3e223afb921"></a>Compressed </td><td class="fielddoc"><p>Use normal BAM compression. </p>
</td></tr>
<tr><td class="fieldname"><a id="af602e9ed717a9fb8288c46a55a6cff8aab0b9d5faf2962cfa82f7b97a9884192a"></a>Uncompressed </td><td class="fielddoc"><p>Disable BAM compression. </p>
<p>Useful in situations where the BAM data is streamed (e.g. piping). It would be wasteful to compress, and then immediately decompress the data. </p>
</td></tr>
</table>
</div>
</div>
<h2 class="groupheader">Constructor & Destructor Documentation</h2>
<a id="a1aed3afd373875e3b26dd14a0a3fb488"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a1aed3afd373875e3b26dd14a0a3fb488">◆ </a></span>BamWriter()</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">BamWriter::BamWriter </td>
<td>(</td>
<td class="paramtype">void </td>
<td class="paramname"></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>constructor </p>
</div>
</div>
<a id="a6d16ab6622a12d03e76f06f9f80c4535"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a6d16ab6622a12d03e76f06f9f80c4535">◆ </a></span>~BamWriter()</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">BamWriter::~BamWriter </td>
<td>(</td>
<td class="paramtype">void </td>
<td class="paramname"></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>destructor </p>
</div>
</div>
<h2 class="groupheader">Member Function Documentation</h2>
<a id="acf06b57f75e03de0096640adcdfe0ad5"></a>
<h2 class="memtitle"><span class="permalink"><a href="#acf06b57f75e03de0096640adcdfe0ad5">◆ </a></span>Close()</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">void BamWriter::Close </td>
<td>(</td>
<td class="paramtype">void </td>
<td class="paramname"></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Closes the current BAM file. </p>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_bam_writer.html#afb0f6e04c32f60a92210be99ba1219a7" title="Opens a BAM file for writing. ">Open()</a> </dd></dl>
</div>
</div>
<a id="a4a9515d5f11cf9cfdf42c4360fac7cff"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a4a9515d5f11cf9cfdf42c4360fac7cff">◆ </a></span>GetErrorString()</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">std::string BamWriter::GetErrorString </td>
<td>(</td>
<td class="paramtype">void </td>
<td class="paramname"></td><td>)</td>
<td> const</td>
</tr>
</table>
</div><div class="memdoc">
<p>Returns a human-readable description of the last error that occurred. </p>
<p>This method allows elimination of STDERR pollution. Developers of client code may choose how the messages are displayed to the user, if at all.</p>
<dl class="section return"><dt>Returns</dt><dd>error description </dd></dl>
</div>
</div>
<a id="ae7ad70e11236f0fd443c510e1c5b0ff8"></a>
<h2 class="memtitle"><span class="permalink"><a href="#ae7ad70e11236f0fd443c510e1c5b0ff8">◆ </a></span>IsOpen()</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">bool BamWriter::IsOpen </td>
<td>(</td>
<td class="paramtype">void </td>
<td class="paramname"></td><td>)</td>
<td> const</td>
</tr>
</table>
</div><div class="memdoc">
<p>Returns <code>true</code> if BAM file is open for writing. </p>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_bam_writer.html#afb0f6e04c32f60a92210be99ba1219a7" title="Opens a BAM file for writing. ">Open()</a> </dd></dl>
</div>
</div>
<a id="afb0f6e04c32f60a92210be99ba1219a7"></a>
<h2 class="memtitle"><span class="permalink"><a href="#afb0f6e04c32f60a92210be99ba1219a7">◆ </a></span>Open() <span class="overload">[1/2]</span></h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">bool BamWriter::Open </td>
<td>(</td>
<td class="paramtype">const std::string & </td>
<td class="paramname"><em>filename</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const std::string & </td>
<td class="paramname"><em>samHeaderText</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const <a class="el" href="namespace_bam_tools.html#abf3564b867a24092bf6575fdda87d573">RefVector</a> & </td>
<td class="paramname"><em>referenceSequences</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Opens a BAM file for writing. </p>
<p>Will overwrite the BAM file if it already exists.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramdir">[in]</td><td class="paramname">filename</td><td>name of output BAM file </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">samHeaderText</td><td>header data, as SAM-formatted string </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">referenceSequences</td><td>list of reference entries</td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd><code>true</code> if opened successfully </dd></dl>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_bam_writer.html#acf06b57f75e03de0096640adcdfe0ad5" title="Closes the current BAM file. ">Close()</a>, <a class="el" href="class_bam_tools_1_1_bam_writer.html#ae7ad70e11236f0fd443c510e1c5b0ff8" title="Returns true if BAM file is open for writing. ">IsOpen()</a>, <a class="el" href="class_bam_tools_1_1_bam_reader.html#ab22109b6db2999ea99fc4511b963d705" title="Returns SAM header data, as SAM-formatted text. ">BamReader::GetHeaderText()</a>, <a class="el" href="class_bam_tools_1_1_bam_reader.html#aec1ff34f2718cb7a6f3d17861c58620b" title="Returns all reference sequence entries. ">BamReader::GetReferenceData()</a> </dd></dl>
</div>
</div>
<a id="a6106772d6ff8c66e8703cbb55060fb09"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a6106772d6ff8c66e8703cbb55060fb09">◆ </a></span>Open() <span class="overload">[2/2]</span></h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">bool BamWriter::Open </td>
<td>(</td>
<td class="paramtype">const std::string & </td>
<td class="paramname"><em>filename</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const <a class="el" href="struct_bam_tools_1_1_sam_header.html">SamHeader</a> & </td>
<td class="paramname"><em>samHeader</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const <a class="el" href="namespace_bam_tools.html#abf3564b867a24092bf6575fdda87d573">RefVector</a> & </td>
<td class="paramname"><em>referenceSequences</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Opens a BAM file for writing. </p>
<p>This is an overloaded function.</p>
<p>Will overwrite the BAM file if it already exists.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramdir">[in]</td><td class="paramname">filename</td><td>name of output BAM file </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">samHeader</td><td>header data, wrapped in <a class="el" href="struct_bam_tools_1_1_sam_header.html" title="Represents the SAM-formatted text header that is part of the BAM file header. ">SamHeader</a> object </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">referenceSequences</td><td>list of reference entries</td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd><code>true</code> if opened successfully </dd></dl>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_bam_writer.html#acf06b57f75e03de0096640adcdfe0ad5" title="Closes the current BAM file. ">Close()</a>, <a class="el" href="class_bam_tools_1_1_bam_writer.html#ae7ad70e11236f0fd443c510e1c5b0ff8" title="Returns true if BAM file is open for writing. ">IsOpen()</a>, <a class="el" href="class_bam_tools_1_1_bam_reader.html#aa12c15ad26839fd2daa4d5fa1d483810" title="Returns SAM header data. ">BamReader::GetHeader()</a>, <a class="el" href="class_bam_tools_1_1_bam_reader.html#aec1ff34f2718cb7a6f3d17861c58620b" title="Returns all reference sequence entries. ">BamReader::GetReferenceData()</a> </dd></dl>
</div>
</div>
<a id="af15602db0267ae7394afff0c1d74ea68"></a>
<h2 class="memtitle"><span class="permalink"><a href="#af15602db0267ae7394afff0c1d74ea68">◆ </a></span>SaveAlignment()</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">bool BamWriter::SaveAlignment </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="class_bam_tools_1_1_bam_alignment.html">BamAlignment</a> & </td>
<td class="paramname"><em>alignment</em></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Saves an alignment to the BAM file. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramdir">[in]</td><td class="paramname">alignment</td><td><a class="el" href="class_bam_tools_1_1_bam_alignment.html" title="The main BAM alignment data structure. ">BamAlignment</a> record to save </td></tr>
</table>
</dd>
</dl>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_bam_reader.html#aa19d6b5effb5b840946a611b7ae039ae" title="Retrieves next available alignment. ">BamReader::GetNextAlignment()</a>, <a class="el" href="class_bam_tools_1_1_bam_reader.html#ac95d20470a02a104990f5a8cf9868f95" title="Retrieves next available alignment, without populating the alignment's string data fields...">BamReader::GetNextAlignmentCore()</a> </dd></dl>
</div>
</div>
<a id="ae2bb85258ab329a6d2ab9287e1c6b8ad"></a>
<h2 class="memtitle"><span class="permalink"><a href="#ae2bb85258ab329a6d2ab9287e1c6b8ad">◆ </a></span>SetCompressionMode()</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">void BamWriter::SetCompressionMode </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="class_bam_tools_1_1_bam_writer.html#af602e9ed717a9fb8288c46a55a6cff8a">BamWriter::CompressionMode</a> & </td>
<td class="paramname"><em>compressionMode</em></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Sets the output compression mode. </p>
<p>Default mode is <a class="el" href="class_bam_tools_1_1_bam_writer.html#af602e9ed717a9fb8288c46a55a6cff8aa09f4d73eb4763388e9f1e3e223afb921" title="Use normal BAM compression. ">BamWriter::Compressed</a>.</p>
<dl class="section note"><dt>Note</dt><dd>Changing the compression mode is disabled on open files (i.e. the request will be ignored). Be sure to call this function before opening the BAM file.</dd></dl>
<div class="fragment"><div class="line"><a class="code" href="class_bam_tools_1_1_bam_writer.html#a1aed3afd373875e3b26dd14a0a3fb488">BamWriter</a> writer;</div><div class="line">writer.SetCompressionMode(<a class="code" href="class_bam_tools_1_1_bam_writer.html#af602e9ed717a9fb8288c46a55a6cff8aab0b9d5faf2962cfa82f7b97a9884192a">BamWriter::Uncompressed</a>);</div><div class="line">writer.Open( ... );</div><div class="line"><span class="comment">// ...</span></div></div><!-- fragment --><dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramdir">[in]</td><td class="paramname">compressionMode</td><td>desired output compression behavior </td></tr>
</table>
</dd>
</dl>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_bam_writer.html#ae7ad70e11236f0fd443c510e1c5b0ff8" title="Returns true if BAM file is open for writing. ">IsOpen()</a>, <a class="el" href="class_bam_tools_1_1_bam_writer.html#afb0f6e04c32f60a92210be99ba1219a7" title="Opens a BAM file for writing. ">Open()</a> </dd></dl>
</div>
</div>
<hr/>The documentation for this class was generated from the following files:<ul>
<li><a class="el" href="_bam_writer_8h_source.html">BamWriter.h</a></li>
<li><a class="el" href="_bam_writer_8cpp.html">BamWriter.cpp</a></li>
</ul>
</div><!-- contents -->
<!-- start footer part -->
<hr class="footer"/><address class="footer"><small>
Generated by  <a href="http://www.doxygen.org/index.html">
<img class="footer" src="doxygen.png" alt="doxygen"/>
</a> 1.8.13
</small></address>
</body>
</html>
|