#include <string.h>
+#include <unistd.h>
+#include "faidx.h"
#include "sam.h"
#define TYPE_BAM 1
int i;
h = bam_header_init();
*h = *h0;
- h->hash = 0;
+ h->hash = h->dict = h->rg2lib = 0;
h->text = (char*)calloc(h->l_text + 1, 1);
memcpy(h->text, h0->text, h->l_text);
h->target_len = (uint32_t*)calloc(h->n_targets, 4);
}
return h;
}
+static void append_header_text(bam_header_t *header, char* text, int len)
+{
+ int x = header->l_text + 1;
+ int y = header->l_text + len + 1; // 1 byte null
+ if (text == 0) return;
+ kroundup32(x);
+ kroundup32(y);
+ if (x < y) header->text = (char*)realloc(header->text, y);
+ strncpy(header->text + header->l_text, text, len); // we cannot use strcpy() here.
+ header->l_text += len;
+ header->text[header->l_text] = 0;
+}
samfile_t *samopen(const char *fn, const char *mode, const void *aux)
{
fp->header = sam_header_read(fp->x.tamr);
if (fp->header->n_targets == 0) { // no @SQ fields
if (aux) { // check if aux is present
- bam_header_destroy(fp->header);
+ bam_header_t *textheader = fp->header;
fp->header = sam_header_read2((const char*)aux);
+ if (fp->header == 0) goto open_err_ret;
+ append_header_text(fp->header, textheader->text, textheader->l_text);
+ bam_header_destroy(textheader);
}
if (fp->header->n_targets == 0)
- fprintf(stderr, "[samopen] empty header.\n");
+ fprintf(stderr, "[samopen] no @SQ lines in the header.\n");
} else fprintf(stderr, "[samopen] SAM header is present: %d sequences.\n", fp->header->n_targets);
}
} 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
// open file
fp->x.tamw = strcmp(fn, "-")? fopen(fn, "w") : stdout;
if (fp->x.tamr == 0) goto open_err_ret;
+ if (strstr(mode, "X")) fp->type |= BAM_OFSTR<<2;
+ else if (strstr(mode, "x")) fp->type |= BAM_OFHEX<<2;
+ else fp->type |= BAM_OFDEC<<2;
// write header
if (strstr(mode, "h")) {
int i;
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);
+ char *s = bam_format1_core(fp->header, b, fp->type>>2&3);
int l = strlen(s);
fputs(s, fp->x.tamw); fputc('\n', fp->x.tamw);
free(s);
bam_destroy1(b);
return 0;
}
+
+char *samfaipath(const char *fn_ref)
+{
+ char *fn_list = 0;
+ if (fn_ref == 0) return 0;
+ fn_list = calloc(strlen(fn_ref) + 5, 1);
+ strcat(strcpy(fn_list, fn_ref), ".fai");
+ if (access(fn_list, R_OK) == -1) { // fn_list is unreadable
+ if (access(fn_ref, R_OK) == -1) {
+ fprintf(stderr, "[samfaipath] fail to read file %s.\n", fn_ref);
+ } else {
+ fprintf(stderr, "[samfaipath] build FASTA index...\n");
+ if (fai_build(fn_ref) == -1) {
+ fprintf(stderr, "[samfaipath] fail to build FASTA index.\n");
+ free(fn_list); fn_list = 0;
+ }
+ }
+ }
+ return fn_list;
+}