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main.c

#include <string.h>
#include <stdlib.h>
#include <sys/stat.h>
#include "bcf.h"

int bcfview(int argc, char *argv[]);
int bcf_main_index(int argc, char *argv[]);

#define BUF_SIZE 0x10000

int bcf_cat(int n, char * const *fn)
{
      int i;
      bcf_t *out;
      uint8_t *buf;
      buf = malloc(BUF_SIZE);
      out = bcf_open("-", "w");
      for (i = 0; i < n; ++i) {
            bcf_t *in;
            bcf_hdr_t *h;
            off_t end;
            struct stat s;
            in = bcf_open(fn[i], "r");
            h = bcf_hdr_read(in);
            if (i == 0) bcf_hdr_write(out, h);
            bcf_hdr_destroy(h);
#ifdef _USE_KNETFILE
            fstat(knet_fileno(in->fp->x.fpr), &s);
            end = s.st_size - 28;
            while (knet_tell(in->fp->x.fpr) < end) {
                  int size = knet_tell(in->fp->x.fpr) + BUF_SIZE < end? BUF_SIZE : end - knet_tell(in->fp->x.fpr);
                  knet_read(in->fp->x.fpr, buf, size);
                  fwrite(buf, 1, size, out->fp->x.fpw);
            }
#else
            abort(); // FIXME: not implemented
#endif
            bcf_close(in);
      }
      bcf_close(out);
      free(buf);
      return 0;
}

int main(int argc, char *argv[])
{
      if (argc == 1) {
            fprintf(stderr, "\n");
            fprintf(stderr, "Usage:   bcftools <command> <arguments>\n\n");
            fprintf(stderr, "Command: view      print, extract, convert and call SNPs from BCF\n");
            fprintf(stderr, "         index     index BCF\n");
            fprintf(stderr, "         cat       concatenate BCFs\n");
            fprintf(stderr, "\n");
            return 1;
      }
      if (strcmp(argv[1], "view") == 0) return bcfview(argc-1, argv+1);
      else if (strcmp(argv[1], "index") == 0) return bcf_main_index(argc-1, argv+1);
      else if (strcmp(argv[1], "cat") == 0) return bcf_cat(argc-2, argv+2);
      else {
            fprintf(stderr, "[main] Unrecognized command.\n");
            return 1;
      }
      return 0;
}

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