1 /*=========================================================================== 2 * 3 * PUBLIC DOMAIN NOTICE 4 * National Center for Biotechnology Information 5 * 6 * This software/database is a "United States Government Work" under the 7 * terms of the United States Copyright Act. It was written as part of 8 * the author's official duties as a United States Government employee and 9 * thus cannot be copyrighted. This software/database is freely available 10 * to the public for use. The National Library of Medicine and the U.S. 11 * Government have not placed any restriction on its use or reproduction. 12 * 13 * Although all reasonable efforts have been taken to ensure the accuracy 14 * and reliability of the software and data, the NLM and the U.S. 15 * Government do not and cannot warrant the performance or results that 16 * may be obtained by using this software or data. The NLM and the U.S. 17 * Government disclaim all warranties, express or implied, including 18 * warranties of performance, merchantability or fitness for any particular 19 * purpose. 20 * 21 * Please cite the author in any work or product based on this material. 22 * 23 * =========================================================================== 24 * 25 */ 26 27 #ifndef _hpp_ngs_itf_pileup_eventitf_ 28 #define _hpp_ngs_itf_pileup_eventitf_ 29 30 #ifndef _hpp_ngs_itf_refcount_ 31 #include <ngs/itf/Refcount.hpp> 32 #endif 33 34 struct NGS_PileupEvent_v1; 35 36 namespace ngs 37 { 38 39 /*---------------------------------------------------------------------- 40 * forwards 41 */ 42 class StringItf; 43 44 /*---------------------------------------------------------------------- 45 * PileupEventItf 46 */ 47 class PileupEventItf : public Refcount < PileupEventItf, NGS_PileupEvent_v1 > 48 { 49 public: 50 51 int32_t getMappingQuality () const 52 NGS_THROWS ( ErrorMsg ); 53 StringItf * getAlignmentId () const 54 NGS_THROWS ( ErrorMsg ); 55 int64_t getAlignmentPosition () const 56 NGS_THROWS ( ErrorMsg ); 57 int64_t getFirstAlignmentPosition () const 58 NGS_THROWS ( ErrorMsg ); 59 int64_t getLastAlignmentPosition () const 60 NGS_THROWS ( ErrorMsg ); 61 uint32_t getEventType () const 62 NGS_THROWS ( ErrorMsg ); 63 char getAlignmentBase () const 64 NGS_THROWS ( ErrorMsg ); 65 char getAlignmentQuality () const 66 NGS_THROWS ( ErrorMsg ); 67 StringItf * getInsertionBases () const 68 NGS_THROWS ( ErrorMsg ); 69 StringItf * getInsertionQualities () const 70 NGS_THROWS ( ErrorMsg ); 71 uint32_t getEventRepeatCount () const 72 NGS_THROWS ( ErrorMsg ); 73 uint32_t getEventIndelType () const 74 NGS_THROWS ( ErrorMsg ); 75 bool nextPileupEvent () 76 NGS_THROWS ( ErrorMsg ); 77 void resetPileupEvent () 78 NGS_THROWS ( ErrorMsg ); 79 80 }; 81 82 } // namespace ngs 83 84 #endif // _hpp_ngs_itf_pileup_eventitf_ 85