X-Git-Url: https://git.donarmstrong.com/?p=samtools.git;a=blobdiff_plain;f=bam.c;h=b00d6a6eb3ba8a8fa2ff86dca0a190b57f3fd961;hp=ee145a1f20587236e8b4b99567f9d9f23eb3ba02;hb=307c147168f7154e3755712797078c513e0b242a;hpb=3c65ee9af86aeb40302ce89eaa1d0516af2c4091 diff --git a/bam.c b/bam.c index ee145a1..b00d6a6 100644 --- a/bam.c +++ b/bam.c @@ -1,44 +1,41 @@ #include #include +#include +#include #include "bam.h" #include "bam_endian.h" +#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"; /************************** * CIGAR related routines * **************************/ -int bam_segreg(int32_t pos, const bam1_core_t *c, const uint32_t *cigar, bam_segreg_t *reg) -{ - unsigned k; - int32_t x = c->pos, y = 0; - int state = 0; - for (k = 0; k < c->n_cigar; ++k) { - int op = cigar[k] & BAM_CIGAR_MASK; // operation - int l = cigar[k] >> BAM_CIGAR_SHIFT; // length - if (state == 0 && (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CINS) && x + l > pos) { - reg->tbeg = x; reg->qbeg = y; reg->cbeg = k; - state = 1; - } - if (op == BAM_CMATCH) { x += l; y += l; } - else if (op == BAM_CDEL || op == BAM_CREF_SKIP) x += l; - else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l; - if (state == 1 && (op == BAM_CSOFT_CLIP || op == BAM_CHARD_CLIP || op == BAM_CREF_SKIP || k == c->n_cigar - 1)) { - reg->tend = x; reg->qend = y; reg->cend = k; - } - } - return state? 0 : -1; -} - 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; } @@ -47,11 +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; } @@ -77,9 +72,9 @@ void bam_header_destroy(bam_header_t *header) free(header->target_len); } free(header->text); -#ifndef BAM_NO_HASH + if (header->dict) sam_header_free(header->dict); + if (header->rg2lib) sam_tbl_destroy(header->rg2lib); bam_destroy_header_hash(header); -#endif free(header); } @@ -87,11 +82,20 @@ bam_header_t *bam_header_read(bamFile fp) { bam_header_t *header; char buf[4]; - int32_t i, name_len; + int magic_len; + int32_t i = 1, name_len; + // check EOF + i = bgzf_check_EOF(fp); + if (i < 0) { + // If the file is a pipe, checking the EOF marker will *always* fail + // 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. The input is probably truncated.\n"); // read "BAM1" - if (bam_read(fp, buf, 4) != 4) return 0; - if (strncmp(buf, "BAM\001", 4)) { - fprintf(stderr, "[bam_header_read] wrong header\n"); + magic_len = bam_read(fp, buf, 4); + if (magic_len != 4 || strncmp(buf, "BAM\001", 4) != 0) { + fprintf(stderr, "[bam_header_read] invalid BAM binary header (this is not a BAM file).\n"); return 0; } header = bam_header_init(); @@ -102,7 +106,6 @@ bam_header_t *bam_header_read(bamFile fp) bam_read(fp, header->text, header->l_text); bam_read(fp, &header->n_targets, 4); if (bam_is_be) bam_swap_endian_4p(&header->n_targets); - assert(header->n_targets > 0); // read reference sequence names and lengths header->target_name = (char**)calloc(header->n_targets, sizeof(char*)); header->target_len = (uint32_t*)calloc(header->n_targets, 4); @@ -150,6 +153,7 @@ int bam_header_write(bamFile fp, const bam_header_t *header) bam_write(fp, &x, 4); } else bam_write(fp, &header->target_len[i], 4); } + bgzf_flush(fp); return 0; } @@ -168,6 +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); + } } } @@ -201,6 +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; } @@ -217,6 +235,7 @@ inline int bam_write1_core(bamFile fp, const bam1_core_t *c, int data_len, uint8 x[5] = c->mtid; x[6] = c->mpos; x[7] = c->isize; + bgzf_flush_try(fp, 4 + block_len); if (bam_is_be) { for (i = 0; i < 8; ++i) bam_swap_endian_4p(x + i); y = block_len; @@ -234,45 +253,222 @@ int bam_write1(bamFile fp, const bam1_t *b) return bam_write1_core(fp, &b->core, b->data_len, b->data); } -void bam_view1(const bam_header_t *header, const bam1_t *b) +char *bam_format1_core(const bam_header_t *header, const bam1_t *b, int of) { uint8_t *s = bam1_seq(b), *t = bam1_qual(b); int i; const bam1_core_t *c = &b->core; - printf("%s\t%d\t", bam1_qname(b), c->flag); - if (c->tid < 0) printf("*\t"); - else printf("%s\t", header->target_name[c->tid]); - printf("%d\t%d\t", c->pos + 1, c->qual); - if (c->n_cigar == 0) putchar('*'); + kstring_t str; + str.l = str.m = 0; str.s = 0; + + kputsn(bam1_qname(b), c->l_qname-1, &str); kputc('\t', &str); + if (of == BAM_OFDEC) { kputw(c->flag, &str); kputc('\t', &str); } + else if (of == BAM_OFHEX) ksprintf(&str, "0x%x\t", c->flag); + else { // BAM_OFSTR + for (i = 0; i < 16; ++i) + if ((c->flag & 1<tid < 0) kputsn("*\t", 2, &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(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 { - for (i = 0; i < c->n_cigar; ++i) - printf("%d%c", bam1_cigar(b)[i]>>BAM_CIGAR_SHIFT, "MIDNSHP"[bam1_cigar(b)[i]&BAM_CIGAR_MASK]); + if (header) kputs(header->target_name[c->mtid], &str); + else kputw(c->mtid, &str); + kputc('\t', &str); } - putchar('\t'); - if (c->mtid < 0) printf("*\t"); - else if (c->mtid == c->tid) printf("=\t"); - else printf("%s\t", header->target_name[c->mtid]); - printf("%d\t%d\t", c->mpos + 1, c->isize); - for (i = 0; i < c->l_qseq; ++i) putchar(bam_nt16_rev_table[bam1_seqi(s, i)]); - putchar('\t'); - if (t[0] == 0xff) putchar('*'); - else for (i = 0; i < c->l_qseq; ++i) putchar(t[i] + 33); + 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); + kputc('\t', &str); + if (t[0] == 0xff) kputc('*', &str); + else for (i = 0; i < c->l_qseq; ++i) kputc(t[i] + 33, &str); + } else kputsn("*\t*", 3, &str); s = bam1_aux(b); while (s < b->data + b->data_len) { uint8_t type, key[2]; key[0] = s[0]; key[1] = s[1]; s += 2; type = *s; ++s; - printf("\t%c%c:", key[0], key[1]); - if (type == 'A') { printf("A:%c", *s); ++s; } - else if (type == 'C') { printf("i:%u", *s); ++s; } - else if (type == 'c') { printf("i:%d", *s); ++s; } - else if (type == 'S') { printf("i:%u", *(uint16_t*)s); s += 2; } - else if (type == 's') { printf("i:%d", *(int16_t*)s); s += 2; } - else if (type == 'I') { printf("i:%u", *(uint32_t*)s); s += 4; } - else if (type == 'i') { printf("i:%d", *(int32_t*)s); s += 4; } - else if (type == 'f') { printf("f:%g", *(float*)s); s += 4; } - else if (type == 'd') { printf("d:%lg", *(double*)s); s += 8; } - else if (type == 'Z' || type == 'H') { printf("%c:", type); while (*s) putchar(*s++); ++s; } + kputc('\t', &str); kputsn((char*)key, 2, &str); kputc(':', &str); + if (type == 'A') { kputsn("A:", 2, &str); kputc(*s, &str); ++s; } + else if (type == 'C') { kputsn("i:", 2, &str); kputw(*s, &str); ++s; } + else if (type == 'c') { kputsn("i:", 2, &str); kputw(*(int8_t*)s, &str); ++s; } + else if (type == 'S') { kputsn("i:", 2, &str); kputw(*(uint16_t*)s, &str); s += 2; } + else if (type == 's') { kputsn("i:", 2, &str); kputw(*(int16_t*)s, &str); s += 2; } + else if (type == 'I') { kputsn("i:", 2, &str); kputuw(*(uint32_t*)s, &str); s += 4; } + else if (type == 'i') { kputsn("i:", 2, &str); kputw(*(int32_t*)s, &str); s += 4; } + 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; +} + +char *bam_format1(const bam_header_t *header, const bam1_t *b) +{ + return bam_format1_core(header, b, BAM_OFDEC); +} + +void bam_view1(const bam_header_t *header, const bam1_t *b) +{ + char *s = bam_format1(header, b); + puts(s); + 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) +{ + const uint8_t *rg; + if (h->dict == 0) h->dict = sam_header_parse2(h->text); + if (h->rg2lib == 0) h->rg2lib = sam_header2tbl(h->dict, "RG", "ID", "LB"); + 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; + } + } } - putchar('\n'); + 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; }