KNETFILE_O= knetfile.o
LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \
bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o \
- $(KNETFILE_O) bam_sort.o sam_header.o
+ $(KNETFILE_O) bam_sort.o sam_header.o bam_reheader.o
AOBJS= bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o \
bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o \
bamtk.o kaln.o
--- /dev/null
+#include <stdio.h>
+#include <stdlib.h>
+#include "bgzf.h"
+#include "bam.h"
+
+#define BUF_SIZE 0x10000
+
+int bam_reheader(BGZF *in, const bam_header_t *h, int fd)
+{
+ BGZF *fp;
+ bam_header_t *old;
+ int len;
+ uint8_t *buf;
+ if (in->open_mode != 'r') return -1;
+ buf = malloc(BUF_SIZE);
+ old = bam_header_read(in);
+ fp = bgzf_fdopen(fd, "w");
+ bam_header_write(fp, h);
+ if (in->block_offset < in->block_length) {
+ bgzf_write(fp, in->uncompressed_block + in->block_offset, in->block_length - in->block_offset);
+ bgzf_flush(fp);
+ }
+#ifdef _USE_KNETFILE
+ while ((len = knet_read(in->x.fpr, buf, BUF_SIZE)) > 0)
+#else
+ while (!feof(in->file) && (len = fread(buf, 1, BUF_SIZE, in->file)) > 0)
+#endif
+ fwrite(buf, 1, len, fp->x.fpw);
+ free(buf);
+ fp->block_offset = in->block_offset = 0;
+ bgzf_close(fp);
+ return 0;
+}
+
+int main_reheader(int argc, char *argv[])
+{
+ bam_header_t *h;
+ BGZF *in;
+ if (argc != 3) {
+ fprintf(stderr, "Usage: samtools reheader <in.header.sam> <in.bam>\n");
+ return 1;
+ }
+ { // read the header
+ tamFile fph = sam_open(argv[1]);
+ if (fph == 0) {
+ fprintf(stderr, "[%s] fail to read the header from %s.\n", __func__, argv[1]);
+ return 1;
+ }
+ h = sam_header_read(fph);
+ sam_close(fph);
+ }
+ in = strcmp(argv[2], "-")? bam_open(argv[2], "r") : bam_dopen(fileno(stdin), "r");
+ if (in == 0) {
+ fprintf(stderr, "[%s] fail to open file %s.\n", __func__, argv[2]);
+ return 1;
+ }
+ bam_reheader(in, h, fileno(stdout));
+ bgzf_close(in);
+ return 0;
+}
#endif
#ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.7-8 (r585)"
+#define PACKAGE_VERSION "0.1.7-9 (r586)"
#endif
int bam_taf2baf(int argc, char *argv[]);
int main_samview(int argc, char *argv[]);
int main_import(int argc, char *argv[]);
+int main_reheader(int argc, char *argv[]);
int faidx_main(int argc, char *argv[]);
int glf3_view_main(int argc, char *argv[]);
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, "\n");
return 1;
}
else if (strcmp(argv[1], "tagview") == 0) return bam_tagview(argc-1, argv+1);
else if (strcmp(argv[1], "calmd") == 0) return bam_fillmd(argc-1, argv+1);
else if (strcmp(argv[1], "fillmd") == 0) return bam_fillmd(argc-1, argv+1);
+ else if (strcmp(argv[1], "reheader") == 0) return main_reheader(argc-1, argv+1);
#if _CURSES_LIB != 0
else if (strcmp(argv[1], "tview") == 0) return bam_tview_main(argc-1, argv+1);
#endif
if (fd == -1) return 0;
fp = open_write(fd, strstr(mode, "u")? 1 : 0);
}
- if (fp != NULL) {
- fp->owned_file = 1;
- }
+ if (fp != NULL) fp->owned_file = 1;
return fp;
}
bgzf_read_block(BGZF* fp)
{
bgzf_byte_t header[BLOCK_HEADER_LENGTH];
- int size = 0;
+ int count, size = 0;
#ifdef _USE_KNETFILE
int64_t block_address = knet_tell(fp->x.fpr);
if (load_block_from_cache(fp, block_address)) return 0;
- int count = knet_read(fp->x.fpr, header, sizeof(header));
+ count = knet_read(fp->x.fpr, header, sizeof(header));
#else
int64_t block_address = ftello(fp->file);
if (load_block_from_cache(fp, block_address)) return 0;
- int count = fread(header, 1, sizeof(header), fp->file);
+ count = fread(header, 1, sizeof(header), fp->file);
#endif
if (count == 0) {
fp->block_length = 0;
}
size += count;
count = inflate_block(fp, block_length);
- if (count < 0) {
- return -1;
- }
+ if (count < 0) return -1;
if (fp->block_length != 0) {
// Do not reset offset if this read follows a seek.
fp->block_offset = 0;
else ret = knet_close(fp->x.fpr);
if (ret != 0) return -1;
#else
- if (fclose(fp->file) != 0) {
- return -1;
- }
+ if (fclose(fp->file) != 0) return -1;
#endif
}
free(fp->uncompressed_block);