15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15
};
+unsigned short bam_char2flag_table[256] = {
+ 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+ 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+ 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+ 0,BAM_FREAD1,BAM_FREAD2,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+ 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+ BAM_FPROPER_PAIR,0,BAM_FMREVERSE,0, 0,BAM_FMUNMAP,0,0, 0,0,0,0, 0,0,0,0,
+ 0,0,0,0, BAM_FDUP,0,BAM_FQCFAIL,0, 0,0,0,0, 0,0,0,0,
+ BAM_FPAIRED,0,BAM_FREVERSE,BAM_FSECONDARY, 0,BAM_FUNMAP,0,0, 0,0,0,0, 0,0,0,0,
+ 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+ 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+ 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+ 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+ 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+ 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+ 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
+ 0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0
+};
+
char *bam_nt16_rev_table = "=ACMGRSVTWYHKDBN";
struct __tamFile_t {
memcpy(alloc_data(b, doff + c->l_qname) + doff, str->s, c->l_qname);
doff += c->l_qname;
}
- { // flag, tid, pos, qual
+ { // flag
long flag;
char *s;
ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
flag = strtol((char*)str->s, &s, 0);
+ if (*s) { // not the end of the string
+ flag = 0;
+ for (s = str->s; *s; ++s)
+ flag |= bam_char2flag_table[(int)*s];
+ }
c->flag = flag;
+ }
+ { // tid, pos, qual
ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->tid = bam_get_tid(header, str->s);
if (c->tid < 0 && strcmp(str->s, "*")) {
if (header->n_targets == 0) {