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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.AlignmentIterator;
import ngs.Alignment;
public class AlignTest
{
static void run ( String acc, int splitNum, int splitNo )
throws ErrorMsg, Exception
{
// open requested accession using SRA implementation of the API
ReadCollection run = gov.nih.nlm.ncbi.ngs.NGS.openReadCollection ( acc );
String run_name = run.getName ();
// compute window to iterate through
long MAX_ROW = run.getAlignmentCount ();
double chunk = ( double ) MAX_ROW / splitNum;
long first = ( long ) Math.round ( chunk * ( splitNo-1 ) );
long next_first = ( long ) Math.round ( chunk * ( splitNo ) );
if ( next_first > MAX_ROW )
next_first = MAX_ROW;
// start iterator on primary alignments
long count = next_first - first;
AlignmentIterator it = run.getAlignmentRange ( first+1, count, Alignment.primaryAlignment );
long i;
for (i = 0; it.nextAlignment (); ++ i )
{
System.out.println ( it.getReadId ()
+'\t'+ it.getReferenceSpec ()
+'\t'+ it.getAlignmentPosition()
+'\t'+ it.getShortCigar ( false ) // unclipped
+'\t'+ it.getFragmentBases ()
);
}
System.err.println ( "Read " + i + " alignments for " + run_name );
}
public static void main ( String [] args )
{
if ( args.length != 3 )
{
System.out.print ( "Usage: AlignTest accession NumChunks ChunkNo\n" );
}
else try
{
run ( args[0], Integer.parseInt ( args[1] ), Integer.parseInt ( args[2] ) );
}
catch ( ErrorMsg x )
{
System.err.println ( x.toString () );
x.printStackTrace ();
}
catch ( Exception x )
{
System.err.println ( x.toString () );
x.printStackTrace ();
}
}
}
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