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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.Alignment;
import ngs.Pileup;
import ngs.PileupIterator;
import ngs.PileupEvent;
import ngs.PileupEventIterator;
public class PileupTest
{
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 count = stop - start + 1;
PileupIterator it = ref.getPileupSlice ( start - 1, count );
// walk all primary alignments within range
long i;
for ( i = 0; it.nextPileup (); ++ i )
{
String qual = "";
String base = "";
System.out.print ( it.getReferenceSpec ()
+'\t'+ ( it.getReferencePosition () + 1 )
+'\t'+ it.getReferenceBase ()
+'\t'+ it.getPileupDepth ()
);
while ( it . nextPileupEvent () )
{
int e = it.getEventType ();
if ( ( e & PileupEvent.alignment_start ) != 0 )
{
base += '^';
base += ( char ) ( it.getMappingQuality () + 33 );
}
if ( ( e & PileupEvent.insertion ) != 0 )
{
base += '+';
String ibases= it.getInsertionBases();
int c = ibases.length();
base += Integer.toString(c);
if( (e & PileupEvent.alignment_minus_strand ) != 0)
base += ibases.toLowerCase ();
else
base += ibases;
}
int evt = e & 7;
if ( ( e & PileupEvent.alignment_minus_strand ) != 0 )
{
if ( evt == PileupEvent.deletion )
base += '<';
else if ( evt == PileupEvent.match )
base += ',';
else if ( evt == PileupEvent.mismatch )
base += Character.toLowerCase ( it.getAlignmentBase () );
}
else
{
if ( evt == PileupEvent.deletion )
base += '>';
else if ( evt == PileupEvent.match )
base += '.';
else if ( evt == PileupEvent.mismatch )
base += Character.toUpperCase (it.getAlignmentBase () );
}
if ( ( e & PileupEvent.alignment_stop ) != 0 )
base +='$';
qual += it . getAlignmentQuality ();
}
System.out.println ( '\t' + base
+ '\t' + qual
);
}
// report to stderr
System.err.println ( "Read " + i + " pileups for " + run_name );
}
public static void main ( String [] args )
{
if ( args.length != 4 )
{
System.out.print ( "Usage: PileupTest 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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