X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=blobdiff_plain;f=bam.c;h=b00d6a6eb3ba8a8fa2ff86dca0a190b57f3fd961;hp=94b0aa8bb85bef4ae4a787af3337f1765ed8899e;hb=307c147168f7154e3755712797078c513e0b242a;hpb=ea7a6d0435f694556f0221140d58e3b80711f6e8 diff --git a/bam.c b/bam.c index 94b0aa8..b00d6a6 100644 --- a/bam.c +++ b/bam.c @@ -7,7 +7,7 @@ #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"; /************************** @@ -16,12 +16,26 @@ 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; } @@ -30,11 +44,9 @@ int32_t bam_cigar2qlen(const bam1_core_t *c, const uint32_t *cigar) { 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; } @@ -79,7 +91,7 @@ bam_header_t *bam_header_read(bamFile fp) // 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) { @@ -160,6 +172,19 @@ static void swap_endian_data(const bam1_core_t *c, int data_len, uint8_t *data) 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); + } } } @@ -193,6 +218,7 @@ int bam_read1(bamFile fp, bam1_t *b) 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; } @@ -245,19 +271,28 @@ char *bam_format1_core(const bam_header_t *header, const bam1_t *b, int of) kputc('\t', &str); } if (c->tid < 0) kputsn("*\t", 2, &str); - else { kputs(header->target_name[c->tid], &str); kputc('\t', &str); } + else { + if (header) kputs(header->target_name[c->tid] , &str); + else kputw(c->tid, &str); + kputc('\t', &str); + } 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); if (c->mtid < 0) kputsn("*\t", 2, &str); else if (c->mtid == c->tid) kputsn("=\t", 2, &str); - else { kputs(header->target_name[c->mtid], &str); kputc('\t', &str); } + else { + if (header) kputs(header->target_name[c->mtid], &str); + else kputw(c->mtid, &str); + kputc('\t', &str); + } kputw(c->mpos + 1, &str); kputc('\t', &str); kputw(c->isize, &str); kputc('\t', &str); if (c->l_qseq) { for (i = 0; i < c->l_qseq; ++i) kputc(bam_nt16_rev_table[bam1_seqi(s, i)], &str); @@ -281,6 +316,23 @@ char *bam_format1_core(const bam_header_t *header, const bam1_t *b, int of) 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; } @@ -297,6 +349,22 @@ void bam_view1(const bam_header_t *header, const bam1_t *b) free(s); } +int bam_validate1(const bam_header_t *header, const bam1_t *b) +{ + char *s; + + if (b->core.tid < -1 || b->core.mtid < -1) return 0; + if (header && (b->core.tid >= header->n_targets || b->core.mtid >= header->n_targets)) return 0; + + if (b->data_len < b->core.l_qname) return 0; + s = memchr(bam1_qname(b), '\0', b->core.l_qname); + if (s != &bam1_qname(b)[b->core.l_qname-1]) return 0; + + // FIXME: Other fields could also be checked, especially the auxiliary data + + return 1; +} + // FIXME: we should also check the LB tag associated with each alignment const char *bam_get_library(bam_header_t *h, const bam1_t *b) { @@ -306,3 +374,101 @@ const char *bam_get_library(bam_header_t *h, const bam1_t *b) 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; +}