network-aware-bwa/main.h at master · mpieva/network-aware-bwa · GitHub

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#ifndef BWA_MAIN_H
#define BWA_MAIN_H

#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.5.10-evan.6.3"
#endif

#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 bwa_bam_to_bam(int argc, char *argv[], char* vn);
    int bwa_worker(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