uint64_t n_lines;
};
-char **bam_load_pos(const char *fn, int *_n)
+char **__bam_get_lines(const char *fn, int *_n) // for bam_plcmd.c only
{
char **list = 0, *s;
- int n = 0, dret, m = 0, c;
+ int n = 0, dret, m = 0;
gzFile fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
kstream_t *ks;
kstring_t *str;
str = (kstring_t*)calloc(1, sizeof(kstring_t));
ks = ks_init(fp);
- while (ks_getuntil(ks, 0, str, &dret) > 0) {
+ while (ks_getuntil(ks, '\n', str, &dret) > 0) {
if (n == m) {
m = m? m << 1 : 16;
list = (char**)realloc(list, m * sizeof(char*));
}
- s = list[n++] = (char*)calloc(str->l + 5, 1);
+ if (str->s[str->l-1] == '\r')
+ str->s[--str->l] = '\0';
+ s = list[n++] = (char*)calloc(str->l + 1, 1);
strcpy(s, str->s);
- s += str->l + 1;
- ks_getuntil(ks, 0, str, &dret);
- *((uint32_t*)s) = atoi(str->s);
- if (dret != '\n')
- while ((c = ks_getc(fp)) >= 0 && c != '\n');
}
ks_destroy(ks);
+ gzclose(fp);
free(str->s); free(str);
*_n = n;
return list;
assert(fp);
ks = ks_init(fp);
str = (kstring_t*)calloc(1, sizeof(kstring_t));
- while (ks_getuntil(ks, 0, str, &dret) >= 0) {
+ while (ks_getuntil(ks, 0, str, &dret) > 0) {
char *s = strdup(str->s);
int len, i;
i = kh_size(hash);
kstring_t *str = fp->str;
kstream_t *ks = fp->ks;
- while ((ret = ks_getuntil(fp->ks, 0, str, &dret)) >= 0 && str->s[0] == '@') { // skip header
+ while ((ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret)) >= 0 && str->s[0] == '@') { // skip header
str->s[str->l] = dret; // note that str->s is NOT null terminated!!
append_text(header, str);
if (dret != '\n') {
}
++fp->n_lines;
}
- while (ret == 0) ret = ks_getuntil(fp->ks, 0, str, &dret); // special consideration for "\r\n"
+ while (ret == 0) ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret); // special consideration for "\r\n"
if (ret < 0) return -1;
++fp->n_lines;
doff = 0;
doff += c->l_qname;
}
{ // flag, tid, pos, qual
- ret = ks_getuntil(ks, 0, str, &dret); c->flag = atoi(str->s);
- ret = ks_getuntil(ks, 0, str, &dret); c->tid = bam_get_tid(header, str->s);
- ret = ks_getuntil(ks, 0, str, &dret); c->pos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
- ret = ks_getuntil(ks, 0, str, &dret); c->qual = isdigit(str->s[0])? atoi(str->s) : 0;
+ ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); c->flag = atoi(str->s);
+ ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); c->tid = bam_get_tid(header, str->s);
+ ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); c->pos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
+ ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); c->qual = isdigit(str->s[0])? atoi(str->s) : 0;
if (ret < 0) return -2;
}
{ // cigar
int i, op;
long x;
c->n_cigar = 0;
- if (ks_getuntil(ks, 0, str, &dret) < 0) return -3;
+ if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -3;
if (str->s[0] != '*') {
for (s = str->s; *s; ++s) {
if (isalpha(*s)) ++c->n_cigar;
if (*s) parse_error(fp->n_lines, "unmatched CIGAR operation");
c->bin = bam_reg2bin(c->pos, bam_calend(c, bam1_cigar(b)));
doff += c->n_cigar * 4;
- }
+ } else c->bin = bam_reg2bin(c->pos, c->pos + 1);
}
{ // mtid, mpos, isize
- ret = ks_getuntil(ks, 0, str, &dret); c->mtid = strcmp(str->s, "=")? bam_get_tid(header, str->s) : c->tid;
- ret = ks_getuntil(ks, 0, str, &dret); c->mpos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
- ret = ks_getuntil(ks, 0, str, &dret); c->isize = (str->s[0] == '-' || isdigit(str->s[0]))? atoi(str->s) : 0;
+ ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); c->mtid = strcmp(str->s, "=")? bam_get_tid(header, str->s) : c->tid;
+ ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); c->mpos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
+ ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); c->isize = (str->s[0] == '-' || isdigit(str->s[0]))? atoi(str->s) : 0;
if (ret < 0) return -4;
}
{ // seq and qual
int i;
uint8_t *p;
- if (ks_getuntil(ks, 0, str, &dret) < 0) return -5; // seq
+ if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -5; // seq
c->l_qseq = strlen(str->s);
if (c->n_cigar && c->l_qseq != (int32_t)bam_cigar2qlen(c, bam1_cigar(b)))
parse_error(fp->n_lines, "CIGAR and sequence length are inconsistent");
bzero(p, (c->l_qseq+1)/2);
for (i = 0; i < c->l_qseq; ++i)
p[i/2] |= bam_nt16_table[(int)str->s[i]] << 4*(1-i%2);
- if (ks_getuntil(ks, 0, str, &dret) < 0) return -6; // qual
- if (c->l_qseq != strlen(str->s))
+ if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -6; // qual
+ if (strcmp(str->s, "*") && c->l_qseq != strlen(str->s))
parse_error(fp->n_lines, "sequence and quality are inconsistent");
p += (c->l_qseq+1)/2;
- for (i = 0; i < c->l_qseq; ++i) p[i] = str->s[i] - 33;
+ if (strcmp(str->s, "*") == 0) for (i = 0; i < c->l_qseq; ++i) p[i] = 0xff;
+ else for (i = 0; i < c->l_qseq; ++i) p[i] = str->s[i] - 33;
doff += c->l_qseq + (c->l_qseq+1)/2;
}
doff0 = doff;
if (dret != '\n' && dret != '\r') { // aux
- while (ks_getuntil(ks, 0, str, &dret) >= 0) {
+ while (ks_getuntil(ks, KS_SEP_TAB, str, &dret) >= 0) {
uint8_t *s, type, key[2];
if (str->l < 6 || str->s[2] != ':' || str->s[4] != ':')
parse_error(fp->n_lines, "missing colon in auxiliary data");
type = str->s[3];
s = alloc_data(b, doff + 3) + doff;
s[0] = key[0]; s[1] = key[1]; s += 2; doff += 2;
- if (type == 'A' || type == 'a') {
+ if (type == 'A' || type == 'a' || type == 'c' || type == 'C') { // c and C for backward compatibility
s = alloc_data(b, doff + 2) + doff;
- *s++ = type; *s = str->s[5];
+ *s++ = 'A'; *s = str->s[5];
doff += 2;
} else if (type == 'I' || type == 'i') {
long long x;
*s++ = 'f';
*(float*)s = (float)atof(str->s + 5);
s += 4; doff += 5;
+ } else if (type == 'd') {
+ s = alloc_data(b, doff + 9) + doff;
+ *s++ = 'd';
+ *(float*)s = (float)atof(str->s + 9);
+ s += 8; doff += 9;
} else if (type == 'Z' || type == 'H') {
int size = 1 + (str->l - 5) + 1;
if (type == 'H') { // check whether the hex string is valid
int ret;
b = (bam1_t*)calloc(1, sizeof(bam1_t));
- fpbaf = bam_open(fnbaf, "w");
+ fpbaf = (strcmp(fnbaf, "-") == 0)? bam_dopen(fileno(stdout), "w") : bam_open(fnbaf, "w");
fp = sam_open(fntaf);
ret = sam_read1(fp, header, b);
bam_header_write(fpbaf, header);
projects / samtools.git / blobdiff