// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 4 October 2010
+// Last modified: 17 November 2010
// ---------------------------------------------------------------------------
// Filters BAM file(s) according to some user-specified criteria.
// ***************************************************************************
}
// everything checks out, just iterate through specified region, filtering alignments
- while ( reader.GetNextAlignmentCore(al) )
+ while ( reader.GetNextAlignment(al) )
if ( CheckAlignment(al) )
writer.SaveAlignment(al);
}
// no index data available, we have to iterate through until we
// find overlapping alignments
else {
- while ( reader.GetNextAlignmentCore(al) ) {
+ while ( reader.GetNextAlignment(al) ) {
if ( (al.RefID >= region.LeftRefID) && ((al.Position + al.Length) >= region.LeftPosition) &&
(al.RefID <= region.RightRefID) && ( al.Position <= region.RightPosition) )
{