1 #ifndef theplu_yat_utility_cigar 2 #define theplu_yat_utility_cigar 31 #ifdef YAT_HAVE_LIBBAM 32 #include "yat/omic/config_bam.h" 33 #include YAT_SAM_HEADER 34 #else // if sam.h is not available #define CIGAR 35 #define BAM_CIGAR_SHIFT 4 37 #define BAM_CIGAR_MASK ((1 << BAM_CIGAR_SHIFT) - 1) 45 #define BAM_CREF_SKIP 3 47 #define BAM_CSOFT_CLIP 4 50 #define BAM_CHARD_CLIP 5 58 #endif // end of YAT_HAVE_LIBBAM 67 #define BAM_CIGAR_STR "MIDNSHP=XB" 69 #define BAM_CIGAR_TYPE 0x3C1A7 72 #define bam_cigar_op(c) ((c)&BAM_CIGAR_MASK) 74 #define bam_cigar_oplen(c) ((c)>>BAM_CIGAR_SHIFT) 76 #define bam_cigar_opchr(c) (BAM_CIGAR_STR[bam_cigar_op(c)]) 78 #define bam_cigar_gen(l, o) ((l)<<BAM_CIGAR_SHIFT|(o)) 84 #define bam_cigar_type(o) (BAM_CIGAR_TYPE>>((o)<<1)&3) 85 #endif // end of backport
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