#include "kstring.h"
#include "sam_header.h"
-int bam_is_be = 0;
+int bam_is_be = 0, bam_verbose = 2, bam_no_B = 0;
char *bam_flag2char_table = "pPuUrR12sfd\0\0\0\0\0";
/**************************
uint32_t bam_calend(const bam1_core_t *c, const uint32_t *cigar)
{
- uint32_t k, end;
- end = c->pos;
+ int k, end = c->pos;
for (k = 0; k < c->n_cigar; ++k) {
- int op = cigar[k] & BAM_CIGAR_MASK;
- if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CREF_SKIP)
- end += cigar[k] >> BAM_CIGAR_SHIFT;
+ int op = bam_cigar_op(cigar[k]);
+ int len = bam_cigar_oplen(cigar[k]);
+ if (op == BAM_CBACK) { // move backward
+ int l, u, v;
+ if (k == c->n_cigar - 1) break; // skip trailing 'B'
+ for (l = k - 1, u = v = 0; l >= 0; --l) {
+ int op1 = bam_cigar_op(cigar[l]);
+ int len1 = bam_cigar_oplen(cigar[l]);
+ if (bam_cigar_type(op1)&1) { // consume query
+ if (u + len1 >= len) { // stop
+ if (bam_cigar_type(op1)&2) v += len - u;
+ break;
+ } else u += len1;
+ }
+ if (bam_cigar_type(op1)&2) v += len1;
+ }
+ end = l < 0? c->pos : end - v;
+ } else if (bam_cigar_type(op)&2) end += bam_cigar_oplen(cigar[k]);
}
return end;
}
{
uint32_t k;
int32_t l = 0;
- for (k = 0; k < c->n_cigar; ++k) {
- int op = cigar[k] & BAM_CIGAR_MASK;
- if (op == BAM_CMATCH || op == BAM_CINS || op == BAM_CSOFT_CLIP)
- l += cigar[k] >> BAM_CIGAR_SHIFT;
- }
+ for (k = 0; k < c->n_cigar; ++k)
+ if (bam_cigar_type(bam_cigar_op(cigar[k]))&1)
+ l += bam_cigar_oplen(cigar[k]);
return l;
}
// with ESPIPE. Suppress the error message in this case.
if (errno != ESPIPE) perror("[bam_header_read] bgzf_check_EOF");
}
- else if (i == 0) fprintf(stderr, "[bam_header_read] EOF marker is absent.\n");
+ else if (i == 0) fprintf(stderr, "[bam_header_read] EOF marker is absent. The input is probably truncated.\n");
// read "BAM1"
magic_len = bam_read(fp, buf, 4);
if (magic_len != 4 || strncmp(buf, "BAM\001", 4) != 0) {
else if (type == 'I' || type == 'F') { bam_swap_endian_4p(s); s += 4; }
else if (type == 'D') { bam_swap_endian_8p(s); s += 8; }
else if (type == 'Z' || type == 'H') { while (*s) ++s; ++s; }
+ else if (type == 'B') {
+ int32_t n, Bsize = bam_aux_type2size(*s);
+ memcpy(&n, s + 1, 4);
+ if (1 == Bsize) {
+ } else if (2 == Bsize) {
+ for (i = 0; i < n; i += 2)
+ bam_swap_endian_2p(s + 5 + i);
+ } else if (4 == Bsize) {
+ for (i = 0; i < n; i += 4)
+ bam_swap_endian_4p(s + 5 + i);
+ }
+ bam_swap_endian_4p(s+1);
+ }
}
}
if (bam_read(fp, b->data, b->data_len) != b->data_len) return -4;
b->l_aux = b->data_len - c->n_cigar * 4 - c->l_qname - c->l_qseq - (c->l_qseq+1)/2;
if (bam_is_be) swap_endian_data(c, b->data_len, b->data);
+ if (bam_no_B) bam_remove_B(b);
return 4 + block_len;
}
kputw(c->pos + 1, &str); kputc('\t', &str); kputw(c->qual, &str); kputc('\t', &str);
if (c->n_cigar == 0) kputc('*', &str);
else {
+ uint32_t *cigar = bam1_cigar(b);
for (i = 0; i < c->n_cigar; ++i) {
kputw(bam1_cigar(b)[i]>>BAM_CIGAR_SHIFT, &str);
- kputc("MIDNSHP"[bam1_cigar(b)[i]&BAM_CIGAR_MASK], &str);
+ kputc(bam_cigar_opchr(cigar[i]), &str);
}
}
kputc('\t', &str);
else if (type == 'f') { ksprintf(&str, "f:%g", *(float*)s); s += 4; }
else if (type == 'd') { ksprintf(&str, "d:%lg", *(double*)s); s += 8; }
else if (type == 'Z' || type == 'H') { kputc(type, &str); kputc(':', &str); while (*s) kputc(*s++, &str); ++s; }
+ else if (type == 'B') {
+ uint8_t sub_type = *(s++);
+ int32_t n;
+ memcpy(&n, s, 4);
+ s += 4; // no point to the start of the array
+ kputc(type, &str); kputc(':', &str); kputc(sub_type, &str); // write the typing
+ for (i = 0; i < n; ++i) {
+ kputc(',', &str);
+ if ('c' == sub_type || 'c' == sub_type) { kputw(*(int8_t*)s, &str); ++s; }
+ else if ('C' == sub_type) { kputw(*(uint8_t*)s, &str); ++s; }
+ else if ('s' == sub_type) { kputw(*(int16_t*)s, &str); s += 2; }
+ else if ('S' == sub_type) { kputw(*(uint16_t*)s, &str); s += 2; }
+ else if ('i' == sub_type) { kputw(*(int32_t*)s, &str); s += 4; }
+ else if ('I' == sub_type) { kputuw(*(uint32_t*)s, &str); s += 4; }
+ else if ('f' == sub_type) { ksprintf(&str, "%g", *(float*)s); s += 4; }
+ }
+ }
}
return str.s;
}
rg = bam_aux_get(b, "RG");
return (rg == 0)? 0 : sam_tbl_get(h->rg2lib, (const char*)(rg + 1));
}
+
+/************
+ * Remove B *
+ ************/
+
+int bam_remove_B(bam1_t *b)
+{
+ int i, j, end_j, k, l, no_qual;
+ uint32_t *cigar, *new_cigar;
+ uint8_t *seq, *qual, *p;
+ // test if removal is necessary
+ if (b->core.flag & BAM_FUNMAP) return 0; // unmapped; do nothing
+ cigar = bam1_cigar(b);
+ for (k = 0; k < b->core.n_cigar; ++k)
+ if (bam_cigar_op(cigar[k]) == BAM_CBACK) break;
+ if (k == b->core.n_cigar) return 0; // no 'B'
+ if (bam_cigar_op(cigar[0]) == BAM_CBACK) goto rmB_err; // cannot be removed
+ // allocate memory for the new CIGAR
+ if (b->data_len + (b->core.n_cigar + 1) * 4 > b->m_data) { // not enough memory
+ b->m_data = b->data_len + b->core.n_cigar * 4;
+ kroundup32(b->m_data);
+ b->data = (uint8_t*)realloc(b->data, b->m_data);
+ cigar = bam1_cigar(b); // after realloc, cigar may be changed
+ }
+ new_cigar = (uint32_t*)(b->data + (b->m_data - b->core.n_cigar * 4)); // from the end of b->data
+ // the core loop
+ seq = bam1_seq(b); qual = bam1_qual(b);
+ no_qual = (qual[0] == 0xff); // test whether base quality is available
+ i = j = 0; end_j = -1;
+ for (k = l = 0; k < b->core.n_cigar; ++k) {
+ int op = bam_cigar_op(cigar[k]);
+ int len = bam_cigar_oplen(cigar[k]);
+ if (op == BAM_CBACK) { // the backward operation
+ int t, u;
+ if (k == b->core.n_cigar - 1) break; // ignore 'B' at the end of CIGAR
+ if (len > j) goto rmB_err; // an excessively long backward
+ for (t = l - 1, u = 0; t >= 0; --t) { // look back
+ int op1 = bam_cigar_op(new_cigar[t]);
+ int len1 = bam_cigar_oplen(new_cigar[t]);
+ if (bam_cigar_type(op1)&1) { // consume the query
+ if (u + len1 >= len) { // stop
+ new_cigar[t] -= (len - u) << BAM_CIGAR_SHIFT;
+ break;
+ } else u += len1;
+ }
+ }
+ if (bam_cigar_oplen(new_cigar[t]) == 0) --t; // squeeze out the zero-length operation
+ l = t + 1;
+ end_j = j; j -= len;
+ } else { // other CIGAR operations
+ new_cigar[l++] = cigar[k];
+ if (bam_cigar_type(op)&1) { // consume the query
+ if (i != j) { // no need to copy if i == j
+ int u, c, c0;
+ for (u = 0; u < len; ++u) { // construct the consensus
+ c = bam1_seqi(seq, i+u);
+ if (j + u < end_j) { // in an overlap
+ c0 = bam1_seqi(seq, j+u);
+ if (c != c0) { // a mismatch; choose the better base
+ if (qual[j+u] < qual[i+u]) { // the base in the 2nd segment is better
+ bam1_seq_seti(seq, j+u, c);
+ qual[j+u] = qual[i+u] - qual[j+u];
+ } else qual[j+u] -= qual[i+u]; // the 1st is better; reduce base quality
+ } else qual[j+u] = qual[j+u] > qual[i+u]? qual[j+u] : qual[i+u];
+ } else { // not in an overlap; copy over
+ bam1_seq_seti(seq, j+u, c);
+ qual[j+u] = qual[i+u];
+ }
+ }
+ }
+ i += len, j += len;
+ }
+ }
+ }
+ if (no_qual) qual[0] = 0xff; // in very rare cases, this may be modified
+ // merge adjacent operations if possible
+ for (k = 1; k < l; ++k)
+ if (bam_cigar_op(new_cigar[k]) == bam_cigar_op(new_cigar[k-1]))
+ new_cigar[k] += new_cigar[k-1] >> BAM_CIGAR_SHIFT << BAM_CIGAR_SHIFT, new_cigar[k-1] &= 0xf;
+ // kill zero length operations
+ for (k = i = 0; k < l; ++k)
+ if (new_cigar[k] >> BAM_CIGAR_SHIFT)
+ new_cigar[i++] = new_cigar[k];
+ l = i;
+ // update b
+ memcpy(cigar, new_cigar, l * 4); // set CIGAR
+ p = b->data + b->core.l_qname + l * 4;
+ memmove(p, seq, (j+1)>>1); p += (j+1)>>1; // set SEQ
+ memmove(p, qual, j); p += j; // set QUAL
+ memmove(p, bam1_aux(b), b->l_aux); p += b->l_aux; // set optional fields
+ b->core.n_cigar = l, b->core.l_qseq = j; // update CIGAR length and query length
+ b->data_len = p - b->data; // update record length
+ return 0;
+
+rmB_err:
+ b->core.flag |= BAM_FUNMAP;
+ return -1;
+}