1 // ***************************************************************************
2 // bamtools_pileup.h (c) 2010 Derek Barnett, Erik Garrison
3 // Marth Lab, Department of Biology, Boston College
4 // All rights reserved.
5 // ---------------------------------------------------------------------------
6 // Last modified: 13 July 2010
7 // ---------------------------------------------------------------------------
8 // Provides pileup conversion functionality.
10 // The 'assembly' aspect of pileup makes this more complicated than the
11 // simpler one-to-one conversion methods for other formats.
12 // ***************************************************************************
14 #ifndef BAMTOOLS_PILEUP_H
15 #define BAMTOOLS_PILEUP_H
28 Pileup(BamMultiReader* reader, std::ostream* outStream);
33 void SetFastaFilename(const std::string& filename);
34 void SetIsPrintingMapQualities(bool ok);
35 void SetRegion(const BamRegion& region);
42 } // namespace BamTools
44 #endif // BAMTOOLS_PILEUP_H