int samwrite(samfile_t *fp, const bam1_t *b)
{
if (fp == 0 || (fp->type & TYPE_READ)) return -1; // not open for writing
if (fp->type & TYPE_BAM) return bam_write1(fp->x.bam, b);
else {
char *s = bam_format1(fp->header, b);
int l = strlen(s);
fputs(s, fp->x.tamw); fputc('\n', fp->x.tamw);
free(s);
return l + 1;
}
}
void convert_bam_to_sam(char* bam_input, char* sam_input) {
int read_bytes;
bam1_t* bam_p = bam_init1();
char* bam_string;
LOG_DEBUG("CONVERT-START: bam to sam\n");
//open BAM file for read
if (time_flag) {
start_timer(t1_convert);
}
bam_file_t* bam_file_p = bam_fopen_mode(bam_input, NULL, "r");
//open SAM file for write, SAM file is a text file!!!
FILE* sam_fd = fopen(sam_input, "w");
if (sam_fd == NULL) {
char log_message[200];
sprintf(log_message, "Error opening file '%.150s' in mode 'r' !!!!!\n", sam_input);
LOG_FATAL(log_message);
}
//header for BAM file has been done in the opening
bam_header_t* bam_header_p = bam_file_p->bam_header_p;
//write header text to SAM file
fprintf(sam_fd, "%s", bam_header_p->text);
//write string alignments to SAM file
while ((read_bytes = bam_read1(bam_file_p->bam_fd, bam_p)) > 0) {
bam_string = bam_format1(bam_header_p, bam_p);
fprintf(sam_fd, "%s\n", bam_string);
free(bam_string); // it was allocated by the sam-tools, we must free it !!
num_alignments++;
}
//close BAM and SAM files, free bam alignment and bam file object
bam_fclose(bam_file_p);
fclose(sam_fd);
bam_destroy1(bam_p);
if (time_flag) {
stop_timer(t1_convert, t2_convert, convert_time);
}
//number_of_batchs = 1, convention value for statistics (not real batch)
number_of_batchs = 1;
LOG_DEBUG("CONVERT-START: bam to sam\n");
}
void CBamLine::b_init(bam_header_t* header) {
if (b) {
char *name = bam1_qname(b);
if (raw_merge) {
read_id=0;
return;
}
read_id=(uint64_t)atol(name);
if (read_id<1 && header) {
char* samline=bam_format1(header, b);
err_die("Error: invalid read Id (must be numeric) for BAM record:\n%s\n",
samline);
}
}
}
void bam_view1(const bam_header_t *header, const bam1_t *b)
{
char *s = bam_format1(header, b);
puts(s);
free(s);
}
void bam_view1(const bam_header_t *header, const bam1_t *b)
{
char *s = bam_format1(header, b);
printf("%s\n", s);
}
