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Devon Ryan
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How to read .bwt file .sa file?

In BWA project in bwt.c file I found bwt_dump_bwt method and bwt_dump_sa method. I want to use them to read .bwt file and .sa file. I wrote the following program:

int main(void)
{
  char *tmp, *prefix;
    bwt_t *bwt;
    prefix = bwa_idx_infer_prefix("hg19bwaidx");

    tmp = calloc(strlen(prefix) + 5, 1);
    strcat(strcpy(tmp, prefix), ".bwt");
    bwt = bwt_restore_bwt(tmp);

  return 0;
}

I got the following error:

Undefined symbols for architecture x86_64:
  "_bwa_idx_infer_prefix", referenced from:
      _main in readbwt-3022ec.o
  "_bwt_restore_bwt", referenced from:
      _main in readbwt-3022ec.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)

Any help ?

Thanks.

Mariam
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