#include "bam.h"
#ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.2-6"
+#define PACKAGE_VERSION "0.1.2-24"
#endif
int bam_taf2baf(int argc, char *argv[]);
int bam_flagstat(int argc, char *argv[]);
int faidx_main(int argc, char *argv[]);
-int glf_view_main(int argc, char *argv[]);
+int glf3_view_main(int argc, char *argv[]);
static int view_aux(const bam1_t *b, void *data)
{
bamFile fp, fpout = 0;
bam_header_t *header;
bam1_t *b;
- int ret, c, is_bam = 0;
- while ((c = getopt(argc, argv, "b")) >= 0) {
+ int ret, c, is_bam = 0, is_header = 0, is_headeronly = 0;
+ while ((c = getopt(argc, argv, "bhH")) >= 0) {
switch (c) {
case 'b': is_bam = 1; break;
+ case 'h': is_header = 1; break;
+ case 'H': is_headeronly = 1; break;
default: fprintf(stderr, "Unrecognized option: -%c\n", c); return 1;
}
}
if (argc == optind) {
- fprintf(stderr, "Usage: samtools view [-b] <in.bam> [<region> [...]]\n");
+ fprintf(stderr, "Usage: samtools view [-bhH] <in.bam> [<region> [...]]\n");
return 1;
}
fp = strcmp(argv[optind], "-")? bam_open(argv[optind], "r") : bam_dopen(fileno(stdin), "r");
assert(fpout = bam_dopen(fileno(stdout), "w"));
bam_header_write(fpout, header);
}
+ if (is_header || is_headeronly) {
+ int i, c;
+ c = header->text[header->l_text-1];
+ header->text[header->l_text-1] = 0;
+ printf("%s", header->text);
+ if (c) putchar(c);
+ header->text[header->l_text-1] = c;
+ for (i = 0; i < header->n_targets; ++i)
+ printf("@SQ\tSN:%s\tLN:%d\n", header->target_name[i], header->target_len[i]);
+ if (is_headeronly) {
+ bam_header_destroy(header);
+ bam_close(fp);
+ return 0;
+ }
+ }
if (optind + 1 == argc) {
b = (bam1_t*)calloc(1, sizeof(bam1_t));
while ((ret = bam_read1(fp, b)) >= 0) bam_view1(header, b);
for (i = optind + 1; i < argc; ++i) {
int tid, beg, end;
bam_parse_region(header, argv[i], &tid, &beg, &end);
+ if (tid < 0) return 0;
if (is_bam) bam_fetch(fp, idx, tid, beg, end, fpout, view_auxb);
else bam_fetch(fp, idx, tid, beg, end, header, view_aux);
}
else if (strcmp(argv[1], "faidx") == 0) return faidx_main(argc-1, argv+1);
else if (strcmp(argv[1], "fixmate") == 0) return bam_mating(argc-1, argv+1);
else if (strcmp(argv[1], "rmdup") == 0) return bam_rmdup(argc-1, argv+1);
- else if (strcmp(argv[1], "glfview") == 0) return glf_view_main(argc-1, argv+1);
+ else if (strcmp(argv[1], "glfview") == 0) return glf3_view_main(argc-1, argv+1);
else if (strcmp(argv[1], "flagstat") == 0) return bam_flagstat(argc-1, argv+1);
#ifndef _NO_CURSES
else if (strcmp(argv[1], "tview") == 0) return bam_tview_main(argc-1, argv+1);