+ fprintf(stderr, " calmd recalculate MD/NM tags and '=' bases\n");
+ fprintf(stderr, " merge merge sorted alignments\n");
+ fprintf(stderr, " rmdup remove PCR duplicates\n");
+ fprintf(stderr, " reheader replace BAM header\n");
+ fprintf(stderr, " targetcut cut fosmid regions (for fosmid pool only)\n");
+ fprintf(stderr, " phase phase heterozygotes\n");