SamFlag.h

00001 /*
00002  *  Copyright (C) 2010  Regents of the University of Michigan
00003  *
00004  *   This program is free software: you can redistribute it and/or modify
00005  *   it under the terms of the GNU General Public License as published by
00006  *   the Free Software Foundation, either version 3 of the License, or
00007  *   (at your option) any later version.
00008  *
00009  *   This program is distributed in the hope that it will be useful,
00010  *   but WITHOUT ANY WARRANTY; without even the implied warranty of
00011  *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
00012  *   GNU General Public License for more details.
00013  *
00014  *   You should have received a copy of the GNU General Public License
00015  *   along with this program.  If not, see <http://www.gnu.org/licenses/>.
00016  */
00017 
00018 #ifndef __SAM_FLAG_H__
00019 #define __SAM_FLAG_H__
00020 
00021 #include <stdint.h>
00022 
00023 
00024 class SamFlag
00025 {
00026 public:
00027     /// Constants for parsing a flag.
00028     static const int16_t PAIRED              = 0x0001;
00029     static const int16_t PROPER_PAIR         = 0x0002;
00030     static const int16_t UNMAPPED            = 0x0004;
00031     static const int16_t MATE_UNMAPPED       = 0x0008;
00032     static const int16_t REVERSE             = 0x0010;
00033     static const int16_t MATE_REVERSED       = 0x0020;
00034     static const int16_t FIRST_READ          = 0x0040;
00035     static const int16_t SECOND_READ         = 0x0080;
00036     static const int16_t SECONDARY_ALIGNMENT = 0x0100;
00037     static const int16_t FAILED_QUALITY      = 0x0200;
00038     static const int16_t DUPLICATE           = 0x0400;
00039 
00040     static const int16_t FRAGMENT_INFO       = 0x00C0;
00041     static const int16_t FRAGMENT_SHIFT      = 6;
00042 
00043     static inline bool isMapped(uint16_t flag) {return(!(flag & UNMAPPED));}
00044     static inline bool isPaired(uint16_t flag) {return(flag & PAIRED);}
00045     static inline bool isReverse(uint16_t flag) {return(flag & REVERSE);}
00046     static inline bool isProperPair(uint16_t flag) {return(flag & PROPER_PAIR);}
00047     static inline bool isDuplicate(uint16_t flag) {return(flag & DUPLICATE);}
00048     static inline bool isQCFailure(uint16_t flag) {return(flag & FAILED_QUALITY);}
00049     static inline bool isFirstFragment(uint16_t flag) 
00050     {
00051         // first fragment if FIRST_READ is set and SECOND_READ is not.
00052         return((flag & FIRST_READ) && !(flag & SECOND_READ));
00053     }
00054     static inline bool isLastFragment(uint16_t flag) 
00055     {
00056         // last fragment if FIRST_READ is not set and SECOND_READ is set.
00057         return(!(flag & FIRST_READ) && (flag & SECOND_READ));
00058     }
00059     static inline bool isMidFragment(uint16_t flag) 
00060     {
00061         // mid fragment if both FIRST_READ and SECOND_READ are set.
00062         return((flag & FIRST_READ) && (flag & SECOND_READ));
00063     }
00064     static inline bool isUnknownFragment(uint16_t flag) 
00065     {
00066         // unknown fragment index if neither FIRST_READ nor SECOND_READ are not.
00067         return(!(flag & FIRST_READ) && !(flag & SECOND_READ));
00068     }
00069 
00070     static inline uint8_t getFragmentType(uint16_t flag)
00071     {
00072         return((flag & FRAGMENT_INFO) >> FRAGMENT_SHIFT);
00073     }
00074 
00075     static inline void setUnmapped(uint16_t& flag) { flag |= UNMAPPED;}
00076 
00077 private:
00078     SamFlag();
00079 };
00080 
00081 
00082 #endif