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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.Reference;
import ngs.AlignmentIterator;
import ngs.Alignment;
public class AlignSliceTest
{
static void run ( String acc, String refname, int start, int stop )
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 ();
// get requested reference
Reference ref = run.getReference ( refname );
// start iterator on requested range of primary alignments
long length = stop - start + 1;
AlignmentIterator it = ref.getAlignmentSlice ( start, length, Alignment.primaryAlignment );
// walk all primary alignments within range
long i;
for ( i = 0; it.nextAlignment (); ++ i )
{
System.out.println ( it.getReadId ()
+'\t'+ it.getReferenceSpec ()
+'\t'+ it.getAlignmentPosition ()
+'\t'+ it.getLongCigar ( false ) // unclipped
+'\t'+ it.getAlignedFragmentBases ()
);
}
// report to stderr
System.err.println ( "Read " + i + " alignments for " + run_name );
}
public static void main ( String [] args )
{
if ( args.length != 4 )
{
System.out.print ( "Usage: AlignSliceTest accession reference start stop\n" );
}
else try
{
run ( args[0], args[1], Integer.parseInt ( args[2] ), Integer.parseInt ( args[3] ) );
}
catch ( ErrorMsg x )
{
System.err.println ( x.toString () );
x.printStackTrace ();
}
catch ( Exception x )
{
System.err.println ( x.toString () );
x.printStackTrace ();
}
}
}
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