#include <stdlib.h>
#include <string.h>
#include <stdio.h>
-#include <assert.h>
#include <zlib.h>
#include "bam.h"
fprintf(stderr, "[bam_rmdup_core] %llu unmatched pairs\n", (long long)kh_size(del_set));
clear_del_set(del_set);
}
+ if ((int)c->tid == -1) { // append unmapped reads
+ bam_write1(out, b);
+ while (bam_read1(in, b) >= 0) bam_write1(out, b);
+ break;
+ }
last_tid = c->tid;
fprintf(stderr, "[bam_rmdup_core] processing reference %s...\n", header->target_name[c->tid]);
}
{
bamFile in, out;
if (argc < 3) {
- fprintf(stderr, "Usage: samtools rmdup <input.srt.bam> <output.bam>\n");
+ fprintf(stderr, "Usage: samtools rmdup <input.srt.bam> <output.bam>\n\n");
+ fprintf(stderr, "Note: Picard is recommended for this task.\n");
return 1;
}
in = (strcmp(argv[1], "-") == 0)? bam_dopen(fileno(stdin), "r") : bam_open(argv[1], "r");