1 #ifndef OLIGOFAR_CSAM__HPP 2 #define OLIGOFAR_CSAM__HPP 3 4 #include "defs.hpp" 5 6 BEGIN_OLIGOFAR_SCOPES 7 8 class CSamBase 9 { 10 public: 11 enum ESamColumns { 12 eCol_qname = 0, 13 eCol_flags = 1, 14 eCol_rname = 2, 15 eCol_pos = 3, 16 eCol_mapq = 4, 17 eCol_cigar = 5, 18 eCol_mrnm = 6, 19 eCol_mpos = 7, 20 eCol_isize = 8, 21 eCol_seq = 9, 22 eCol_qual = 10, 23 eCol_tags = 11 24 }; 25 enum FSamFlags { 26 fPairedQuery = 0x0001, 27 fPairedHit = 0x0002, 28 fSeqUnmapped = 0x0004, 29 fMateUnmapped = 0x0008, 30 fSeqReverse = 0x0010, 31 fMateReverse = 0x0020, 32 fSeqIsFirst = 0x0040, 33 fSeqIsSecond = 0x0080, 34 fHitSuboptimal = 0x0100, 35 fReadFailedQC = 0x0200, 36 fReadDuplicate = 0x0400 37 }; 38 enum ESamTagType { 39 eTag_int = 'i', 40 eTag_char = 'A', 41 eTag_float = 'f', 42 eTag_string = 'Z', 43 eTag_hex = 'H', 44 eTag_none = 0 45 }; 46 }; 47 48 49 END_OLIGOFAR_SCOPES 50 51 #endif 52