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2 | 2 | <!-- NewPage --> |
3 | 3 | <html lang="en"> |
4 | 4 | <head> |
5 | | -<!-- Generated by javadoc (1.8.0_181) on Mon Aug 27 15:49:10 GMT 2018 --> |
6 | | -<title>Index (ReadTools 1.5.1 API)</title> |
7 | | -<meta name="date" content="2018-08-27"> |
| 5 | +<!-- Generated by javadoc (1.8.0_181) on Thu Aug 30 12:57:47 GMT 2018 --> |
| 6 | +<title>Index (ReadTools 1.5.2 API)</title> |
| 7 | +<meta name="date" content="2018-08-30"> |
8 | 8 | <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style"> |
9 | 9 | <script type="text/javascript" src="script.js"></script> |
10 | 10 | </head> |
11 | 11 | <body> |
12 | 12 | <script type="text/javascript"><!-- |
13 | 13 | try { |
14 | 14 | if (location.href.indexOf('is-external=true') == -1) { |
15 | | - parent.document.title="Index (ReadTools 1.5.1 API)"; |
| 15 | + parent.document.title="Index (ReadTools 1.5.2 API)"; |
16 | 16 | } |
17 | 17 | } |
18 | 18 | catch(err) { |
@@ -479,6 +479,14 @@ <h2 class="title">D</h2> |
479 | 479 | <dd> |
480 | 480 | <div class="block">Decodes a single-end Distmap String.</div> |
481 | 481 | </dd> |
| 482 | +<dt><span class="memberNameLink"><a href="org/magicdgs/readtools/utils/read/RTReadUtils.html#DEFAULT_BARCODE_INDEX_SPLIT">DEFAULT_BARCODE_INDEX_SPLIT</a></span> - Static variable in class org.magicdgs.readtools.utils.read.<a href="org/magicdgs/readtools/utils/read/RTReadUtils.html" title="class in org.magicdgs.readtools.utils.read">RTReadUtils</a></dt> |
| 483 | +<dd> |
| 484 | +<div class="block">Default regular expression to split barcodes.</div> |
| 485 | +</dd> |
| 486 | +<dt><span class="memberNameLink"><a href="org/magicdgs/readtools/utils/read/RTReadUtils.html#DEFAULT_BARCODE_QUALITY_SPLIT">DEFAULT_BARCODE_QUALITY_SPLIT</a></span> - Static variable in class org.magicdgs.readtools.utils.read.<a href="org/magicdgs/readtools/utils/read/RTReadUtils.html" title="class in org.magicdgs.readtools.utils.read">RTReadUtils</a></dt> |
| 487 | +<dd> |
| 488 | +<div class="block">Default regular expression to split barcode qualities.</div> |
| 489 | +</dd> |
482 | 490 | <dt><span class="memberNameLink"><a href="org/magicdgs/readtools/utils/read/writer/ReadToolsIOFormat.html#DEFAULT_METRICS_EXTENSION">DEFAULT_METRICS_EXTENSION</a></span> - Static variable in interface org.magicdgs.readtools.utils.read.writer.<a href="org/magicdgs/readtools/utils/read/writer/ReadToolsIOFormat.html" title="interface in org.magicdgs.readtools.utils.read.writer">ReadToolsIOFormat</a></dt> |
483 | 491 | <dd> |
484 | 492 | <div class="block">Output extension for metric files.</div> |
@@ -667,7 +675,7 @@ <h2 class="title">E</h2> |
667 | 675 | <dt><span class="memberNameLink"><a href="org/magicdgs/readtools/utils/read/RTReadUtils.html#extractBarcodesFromReadName-org.broadinstitute.hellbender.utils.read.GATKRead-">extractBarcodesFromReadName(GATKRead)</a></span> - Static method in class org.magicdgs.readtools.utils.read.<a href="org/magicdgs/readtools/utils/read/RTReadUtils.html" title="class in org.magicdgs.readtools.utils.read">RTReadUtils</a></dt> |
668 | 676 | <dd> |
669 | 677 | <div class="block">Extract and remove the barcode from the read name, splitting the barcodes in the read name |
670 | | - using <a href="org/magicdgs/readtools/RTDefaults.html#BARCODE_INDEX_DELIMITER"><code>RTDefaults.BARCODE_INDEX_DELIMITER</code></a>.</div> |
| 678 | + using <a href="org/magicdgs/readtools/utils/read/RTReadUtils.html#DEFAULT_BARCODE_INDEX_SPLIT"><code>RTReadUtils.DEFAULT_BARCODE_INDEX_SPLIT</code></a>.</div> |
671 | 679 | </dd> |
672 | 680 | </dl> |
673 | 681 | <a name="I:F"> |
@@ -930,7 +938,7 @@ <h2 class="title">G</h2> |
930 | 938 | <dd> </dd> |
931 | 939 | <dt><span class="memberNameLink"><a href="org/magicdgs/readtools/utils/fastq/FastqReadNameEncoding.html#getBarcodes-java.lang.String-">getBarcodes(String)</a></span> - Method in enum org.magicdgs.readtools.utils.fastq.<a href="org/magicdgs/readtools/utils/fastq/FastqReadNameEncoding.html" title="enum in org.magicdgs.readtools.utils.fastq">FastqReadNameEncoding</a></dt> |
932 | 940 | <dd> |
933 | | -<div class="block">Returns the barcodes in the read name (splitted by <a href="org/magicdgs/readtools/RTDefaults.html#BARCODE_INDEX_DELIMITER"><code>RTDefaults.BARCODE_INDEX_DELIMITER</code></a>).</div> |
| 941 | +<div class="block">Returns the barcodes in the read name (splitted by <a href="org/magicdgs/readtools/utils/read/RTReadUtils.html#DEFAULT_BARCODE_INDEX_SPLIT"><code>RTReadUtils.DEFAULT_BARCODE_INDEX_SPLIT</code></a>).</div> |
934 | 942 | </dd> |
935 | 943 | <dt><span class="memberNameLink"><a href="org/magicdgs/readtools/utils/read/RTReadUtils.html#getBarcodesAndQualitiesFromTags-org.broadinstitute.hellbender.utils.read.GATKRead-java.util.List-java.util.List-">getBarcodesAndQualitiesFromTags(GATKRead, List<String>, List<String>)</a></span> - Static method in class org.magicdgs.readtools.utils.read.<a href="org/magicdgs/readtools/utils/read/RTReadUtils.html" title="class in org.magicdgs.readtools.utils.read">RTReadUtils</a></dt> |
936 | 944 | <dd> |
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