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/*===========================================================================
* *
* * PUBLIC DOMAIN NOTICE
* * National Center for Biotechnology Information
* *
* * This software/database is a "United States Government Work" under the
* * terms of the United States Copyright Act. It was written as part of
* * the author's official duties as a United States Government employee and
* * thus cannot be copyrighted. This software/database is freely available
* * to the public for use. The National Library of Medicine and the U.S.
* * Government have not placed any restriction on its use or reproduction.
* *
* * Although all reasonable efforts have been taken to ensure the accuracy
* * and reliability of the software and data, the NLM and the U.S.
* * Government do not and cannot warrant the performance or results that
* * may be obtained by using this software or data. The NLM and the U.S.
* * Government disclaim all warranties, express or implied, including
* * warranties of performance, merchantability or fitness for any particular
* * purpose.
* *
* * Please cite the author in any work or product based on this material.
* *
* * ===========================================================================
* *
* */
package examples;
import ngs.ErrorMsg;
import ngs.ReadCollection;
import ngs.ReadGroup;
import ngs.ReadGroupIterator;
import ngs.Statistics;
public class ReadGroupTest
{
static void run (String acc)
throws ErrorMsg, Exception
{
long i;
//open requested accession using SRA implementation of the API
ReadCollection run = gov.nih.nlm.ncbi.ngs.NGS.openReadCollection(acc);
String run_name = run.getName();
//get requested reference
ReadGroupIterator it = run.getReadGroups();
for (i = 0; it . nextReadGroup (); ++ i )
{
Statistics s = it.getStatistics();
System.out.println("Statistics for group <" + it.getName() + ">");
for(String p=s.nextPath("");!p.equals("");p=s.nextPath(p)){
System.out.println("\t"+p+": "+s.getAsString(p));
}
}
System . err . println ( "Read " + i + " ReadGroups for " + run_name);
}
public static void main ( String [] args )
{
if ( args.length != 1 )
{
System.out.print("Usage: ReadGroupTest accession\n");
}
else try
{
run (args[0]);
}
catch ( ErrorMsg x )
{
System . err . println ( x . toString () );
x . printStackTrace ();
}
catch ( Exception x )
{
System . err . println ( x . toString () );
x . printStackTrace ();
}
}
}
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