#include "bam.h"
#ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.4-6 (r334)"
+#define PACKAGE_VERSION "0.1.4-7 (r337)"
#endif
int bam_taf2baf(int argc, char *argv[]);
* or functionality.
*/
+/* 2009-06-12 by lh3: support a mode string like "wu" where 'u' for uncompressed output */
+
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
fp = malloc(sizeof(BGZF));
fp->file_descriptor = fd;
fp->open_mode = 'r';
- fp->owned_file = 0;
+ fp->owned_file = 0; fp->is_uncompressed = 0;
fp->file = file;
fp->uncompressed_block_size = MAX_BLOCK_SIZE;
fp->uncompressed_block = malloc(MAX_BLOCK_SIZE);
static
BGZF*
-open_write(int fd)
+open_write(int fd, bool is_uncompressed)
{
FILE* file = fdopen(fd, "w");
BGZF* fp;
fp = malloc(sizeof(BGZF));
fp->file_descriptor = fd;
fp->open_mode = 'w';
- fp->owned_file = 0;
+ fp->owned_file = 0; fp->is_uncompressed = is_uncompressed;
fp->file = file;
fp->uncompressed_block_size = DEFAULT_BLOCK_SIZE;
fp->uncompressed_block = NULL;
bgzf_open(const char* __restrict path, const char* __restrict mode)
{
BGZF* fp = NULL;
- if (strcasecmp(mode, "r") == 0) {
+ if (mode[0] == 'r' || mode[0] == 'R') { /* The reading mode is preferred. */
int oflag = O_RDONLY;
int fd = open(path, oflag);
if (fd == -1) return 0;
fp = open_read(fd);
- } else if (strcasecmp(mode, "w") == 0) {
+ } else if (mode[0] == 'w' || mode[0] == 'W') {
int oflag = O_WRONLY | O_CREAT | O_TRUNC;
int fd = open(path, oflag, 0644);
if (fd == -1) return 0;
- fp = open_write(fd);
+ fp = open_write(fd, strstr(mode, "u")? 1 : 0);
}
if (fp != NULL) {
fp->owned_file = 1;
bgzf_fdopen(int fd, const char * __restrict mode)
{
if (fd == -1) return 0;
- if (strcasecmp(mode, "r") == 0) {
+ if (mode[0] == 'r' || mode[0] == 'R') {
return open_read(fd);
- } else if (strcasecmp(mode, "w") == 0) {
- return open_write(fd);
+ } else if (mode[0] == 'w' || mode[0] == 'W') {
+ return open_write(fd, strstr(mode, "u")? 1 : 0);
} else {
return NULL;
}
int input_length = block_length;
int compressed_length = 0;
while (1) {
-
+ int compress_level = fp->is_uncompressed? 0 : Z_DEFAULT_COMPRESSION;
z_stream zs;
zs.zalloc = NULL;
zs.zfree = NULL;
zs.next_out = (void*)&buffer[BLOCK_HEADER_LENGTH];
zs.avail_out = buffer_size - BLOCK_HEADER_LENGTH - BLOCK_FOOTER_LENGTH;
- int status = deflateInit2(&zs, Z_DEFAULT_COMPRESSION, Z_DEFLATED,
+ int status = deflateInit2(&zs, compress_level, Z_DEFLATED,
GZIP_WINDOW_BITS, Z_DEFAULT_MEM_LEVEL, Z_DEFAULT_STRATEGY);
if (status != Z_OK) {
report_error(fp, "deflate init failed");
#include <stdint.h>
#include <stdio.h>
-#include "zlib.h"
#include <stdbool.h>
-//#include "zutil.h"
+#include <zlib.h>
//typedef int8_t bool;
typedef struct {
int file_descriptor;
char open_mode; // 'r' or 'w'
- bool owned_file;
+ bool owned_file, is_uncompressed;
FILE* file;
int uncompressed_block_size;
int compressed_block_size;
} else if (mode[0] == 'w') { // write
fp->header = bam_header_dup((const bam_header_t*)aux);
if (mode[1] == 'b') { // binary
+ char bmode[3];
+ bmode[0] = 'w'; bmode[1] = strstr(mode, "u")? 'u' : 0; bmode[2] = 0;
fp->type |= TYPE_BAM;
- fp->x.bam = strcmp(fn, "-")? bam_open(fn, "w") : bam_dopen(fileno(stdout), "w");
+ fp->x.bam = strcmp(fn, "-")? bam_open(fn, bmode) : bam_dopen(fileno(stdout), bmode);
if (fp->x.bam == 0) goto open_err_ret;
bam_header_write(fp->x.bam, fp->header);
} else { // text
int main_samview(int argc, char *argv[])
{
- int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0;
+ int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, is_uncompressed = 0, is_bamout = 0;
samfile_t *in = 0, *out = 0;
- char in_mode[4], out_mode[4], *fn_out = 0, *fn_list = 0;
+ char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0;
/* parse command-line options */
strcpy(in_mode, "r"); strcpy(out_mode, "w");
- while ((c = getopt(argc, argv, "Sbt:hHo:q:f:F:")) >= 0) {
+ while ((c = getopt(argc, argv, "Sbt:hHo:q:f:F:u")) >= 0) {
switch (c) {
case 'S': is_bamin = 0; break;
- case 'b': strcat(out_mode, "b"); break;
+ case 'b': is_bamout = 1; break;
case 't': fn_list = strdup(optarg); is_bamin = 0; break;
case 'h': is_header = 1; break;
case 'H': is_header_only = 1; break;
case 'f': g_flag_on = strtol(optarg, 0, 0); break;
case 'F': g_flag_off = strtol(optarg, 0, 0); break;
case 'q': g_min_mapQ = atoi(optarg); break;
+ case 'u': is_uncompressed = 1; break;
default: return usage();
}
}
+ if (is_uncompressed) is_bamout = 1;
if (is_header_only) is_header = 1;
+ if (is_bamout) strcat(out_mode, "b");
if (is_bamin) strcat(in_mode, "b");
if (is_header) strcat(out_mode, "h");
+ if (is_uncompressed) strcat(out_mode, "u");
if (argc == optind) return usage();
// open file handlers
fprintf(stderr, " -h print header for the SAM output\n");
fprintf(stderr, " -H print header only (no alignments)\n");
fprintf(stderr, " -S input is SAM\n");
+ fprintf(stderr, " -u uncompressed BAM output (force -b)\n");
fprintf(stderr, " -t FILE list of reference names and lengths (force -S) [null]\n");
fprintf(stderr, " -o FILE output file name [stdout]\n");
fprintf(stderr, " -f INT required flag, 0 for unset [0]\n");