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#ifndef BWA_MAIN_H
#define BWA_MAIN_H
#ifdef __cplusplus
extern "C" {
#endif
int bwa_fa2pac(int argc, char *argv[]);
int bwa_pac_rev(int argc, char *argv[]);
int bwa_pac2cspac(int argc, char *argv[]);
int bwa_pac2bwt(int argc, char *argv[]);
int bwa_bwtupdate(int argc, char *argv[]);
int bwa_bwt2sa(int argc, char *argv[]);
int bwa_index(int argc, char *argv[]);
int bwa_aln(int argc, char *argv[]);
int bwt_bwtgen_main(int argc, char *argv[]);
int bwa_sai2sam_se(int argc, char *argv[]);
int bwa_sai2sam_pe(int argc, char *argv[]);
int bwa_stdsw(int argc, char *argv[]);
int bwa_bwtsw2(int argc, char *argv[]);
#ifdef __cplusplus
}
#endif
#endif