+ fprintf(stderr, "\n");
+ fprintf(stderr, "Usage: samtools fillmd [-eubS] <aln.bam> <ref.fasta>\n\n");
+ fprintf(stderr, "Options: -e change identical bases to '='\n");
+ fprintf(stderr, " -u uncompressed BAM output (for piping)\n");
+ fprintf(stderr, " -b compressed BAM output\n");
+ fprintf(stderr, " -S the input is SAM with header\n\n");
+ return 1;
+ }
+ fp = samopen(argv[optind], mode_r, 0);
+ if (fp == 0) return 1;
+ if (is_sam_in && (fp->header == 0 || fp->header->n_targets == 0)) {
+ fprintf(stderr, "[bam_fillmd] input SAM does not have header. Abort!\n");