--- /dev/null
+#include <ctype.h>
+#include <assert.h>
+#include <stdarg.h>
+
+#define BAM_LITE
+#include "bam.h"
+
+#undef bam_open
+#undef bam_dopen
+#undef bam_close
+#undef bam_read
+#undef bam_write
+#undef bam_tell
+#undef bam_seek
+
+#define bam_open(fn, mode) gzopen(fn, mode)
+#define bam_dopen(fd, mode) gzdopen(fd, mode)
+#define bam_close(fp) gzclose(fp)
+#define bam_read(fp, buf, size) gzread(fp, buf, size)
+
+#define BAM_NO_HASH
+
+char *bam_nt16_rev_table = "=ACMGRSVTWYHKDBN";
+
+/*************************
+ *** from bam_endian.h ***
+ *************************/
+
+static inline int bam_is_big_endian()
+{
+ long one= 1;
+ return !(*((char *)(&one)));
+}
+static inline uint16_t bam_swap_endian_2(uint16_t v)
+{
+ return (uint16_t)(((v & 0x00FF00FFU) << 8) | ((v & 0xFF00FF00U) >> 8));
+}
+static inline void *bam_swap_endian_2p(void *x)
+{
+ *(uint16_t*)x = bam_swap_endian_2(*(uint16_t*)x);
+ return x;
+}
+static inline uint32_t bam_swap_endian_4(uint32_t v)
+{
+ v = ((v & 0x0000FFFFU) << 16) | (v >> 16);
+ return ((v & 0x00FF00FFU) << 8) | ((v & 0xFF00FF00U) >> 8);
+}
+static inline void *bam_swap_endian_4p(void *x)
+{
+ *(uint32_t*)x = bam_swap_endian_4(*(uint32_t*)x);
+ return x;
+}
+static inline uint64_t bam_swap_endian_8(uint64_t v)
+{
+ v = ((v & 0x00000000FFFFFFFFLLU) << 32) | (v >> 32);
+ v = ((v & 0x0000FFFF0000FFFFLLU) << 16) | ((v & 0xFFFF0000FFFF0000LLU) >> 16);
+ return ((v & 0x00FF00FF00FF00FFLLU) << 8) | ((v & 0xFF00FF00FF00FF00LLU) >> 8);
+}
+static inline void *bam_swap_endian_8p(void *x)
+{
+ *(uint64_t*)x = bam_swap_endian_8(*(uint64_t*)x);
+ return x;
+}
+
+/**********************
+ *** from kstring.* ***
+ **********************/
+
+typedef struct __kstring_t {
+ size_t l, m;
+ char *s;
+} kstring_t;
+
+#ifndef kroundup32
+#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
+#endif
+
+static inline int kputsn(const char *p, int l, kstring_t *s)
+{
+ if (s->l + l + 1 >= s->m) {
+ s->m = s->l + l + 2;
+ kroundup32(s->m);
+ s->s = (char*)realloc(s->s, s->m);
+ }
+ strncpy(s->s + s->l, p, l);
+ s->l += l;
+ s->s[s->l] = 0;
+ return l;
+}
+
+static inline int kputs(const char *p, kstring_t *s)
+{
+ return kputsn(p, strlen(p), s);
+}
+
+static inline int kputc(int c, kstring_t *s)
+{
+ if (s->l + 1 >= s->m) {
+ s->m = s->l + 2;
+ kroundup32(s->m);
+ s->s = (char*)realloc(s->s, s->m);
+ }
+ s->s[s->l++] = c;
+ s->s[s->l] = 0;
+ return c;
+}
+
+int ksprintf(kstring_t *s, const char *fmt, ...)
+{
+ va_list ap;
+ int l;
+ va_start(ap, fmt);
+ l = vsnprintf(s->s + s->l, s->m - s->l, fmt, ap); // This line does not work with glibc 2.0. See `man snprintf'.
+ va_end(ap);
+ if (l + 1 > s->m - s->l) {
+ s->m = s->l + l + 2;
+ kroundup32(s->m);
+ s->s = (char*)realloc(s->s, s->m);
+ va_start(ap, fmt);
+ l = vsnprintf(s->s + s->l, s->m - s->l, fmt, ap);
+ }
+ va_end(ap);
+ s->l += l;
+ return l;
+}
+
+/******************
+ *** from bam.c ***
+ ******************/
+
+int bam_is_be = 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;
+ 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;
+ }
+ return end;
+}
+
+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;
+ }
+ return l;
+}
+
+/********************
+ * BAM I/O routines *
+ ********************/
+
+bam_header_t *bam_header_init()
+{
+ bam_is_be = bam_is_big_endian();
+ return (bam_header_t*)calloc(1, sizeof(bam_header_t));
+}
+
+void bam_header_destroy(bam_header_t *header)
+{
+ int32_t i;
+ extern void bam_destroy_header_hash(bam_header_t *header);
+ if (header == 0) return;
+ if (header->target_name) {
+ for (i = 0; i < header->n_targets; ++i)
+ free(header->target_name[i]);
+ free(header->target_name);
+ free(header->target_len);
+ }
+ free(header->text);
+#ifndef BAM_NO_HASH
+ if (header->rg2lib) bam_strmap_destroy(header->rg2lib);
+ bam_destroy_header_hash(header);
+#endif
+ free(header);
+}
+
+bam_header_t *bam_header_read(bamFile fp)
+{
+ bam_header_t *header;
+ char buf[4];
+ int32_t i, name_len;
+ // 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");
+ return 0;
+ }
+ header = bam_header_init();
+ // read plain text and the number of reference sequences
+ bam_read(fp, &header->l_text, 4);
+ if (bam_is_be) bam_swap_endian_4p(&header->l_text);
+ header->text = (char*)calloc(header->l_text + 1, 1);
+ 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);
+ // 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);
+ for (i = 0; i != header->n_targets; ++i) {
+ bam_read(fp, &name_len, 4);
+ if (bam_is_be) bam_swap_endian_4p(&name_len);
+ header->target_name[i] = (char*)calloc(name_len, 1);
+ bam_read(fp, header->target_name[i], name_len);
+ bam_read(fp, &header->target_len[i], 4);
+ if (bam_is_be) bam_swap_endian_4p(&header->target_len[i]);
+ }
+ return header;
+}
+
+static void swap_endian_data(const bam1_core_t *c, int data_len, uint8_t *data)
+{
+ uint8_t *s;
+ uint32_t i, *cigar = (uint32_t*)(data + c->l_qname);
+ s = data + c->n_cigar*4 + c->l_qname + c->l_qseq + (c->l_qseq + 1)/2;
+ for (i = 0; i < c->n_cigar; ++i) bam_swap_endian_4p(&cigar[i]);
+ while (s < data + data_len) {
+ uint8_t type;
+ s += 2; // skip key
+ type = toupper(*s); ++s; // skip type
+ if (type == 'C' || type == 'A') ++s;
+ else if (type == 'S') { bam_swap_endian_2p(s); s += 2; }
+ 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; }
+ }
+}
+
+int bam_read1(bamFile fp, bam1_t *b)
+{
+ bam1_core_t *c = &b->core;
+ int32_t block_len, ret, i;
+ uint32_t x[8];
+
+ assert(BAM_CORE_SIZE == 32);
+ if ((ret = bam_read(fp, &block_len, 4)) != 4) {
+ if (ret == 0) return -1; // normal end-of-file
+ else return -2; // truncated
+ }
+ if (bam_read(fp, x, BAM_CORE_SIZE) != BAM_CORE_SIZE) return -3;
+ if (bam_is_be) {
+ bam_swap_endian_4p(&block_len);
+ for (i = 0; i < 8; ++i) bam_swap_endian_4p(x + i);
+ }
+ c->tid = x[0]; c->pos = x[1];
+ c->bin = x[2]>>16; c->qual = x[2]>>8&0xff; c->l_qname = x[2]&0xff;
+ c->flag = x[3]>>16; c->n_cigar = x[3]&0xffff;
+ c->l_qseq = x[4];
+ c->mtid = x[5]; c->mpos = x[6]; c->isize = x[7];
+ b->data_len = block_len - BAM_CORE_SIZE;
+ if (b->m_data < b->data_len) {
+ b->m_data = b->data_len;
+ kroundup32(b->m_data);
+ b->data = (uint8_t*)realloc(b->data, b->m_data);
+ }
+ 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);
+ return 4 + block_len;
+}
+
+char *bam_format1(const bam_header_t *header, const bam1_t *b)
+{
+ uint8_t *s = bam1_seq(b), *t = bam1_qual(b);
+ int i;
+ const bam1_core_t *c = &b->core;
+ kstring_t str;
+ str.l = str.m = 0; str.s = 0;
+
+ ksprintf(&str, "%s\t%d\t", bam1_qname(b), c->flag);
+ if (c->tid < 0) kputs("*\t", &str);
+ else ksprintf(&str, "%s\t", header->target_name[c->tid]);
+ ksprintf(&str, "%d\t%d\t", c->pos + 1, c->qual);
+ if (c->n_cigar == 0) kputc('*', &str);
+ else {
+ for (i = 0; i < c->n_cigar; ++i)
+ ksprintf(&str, "%d%c", bam1_cigar(b)[i]>>BAM_CIGAR_SHIFT, "MIDNSHP"[bam1_cigar(b)[i]&BAM_CIGAR_MASK]);
+ }
+ kputc('\t', &str);
+ if (c->mtid < 0) kputs("*\t", &str);
+ else if (c->mtid == c->tid) kputs("=\t", &str);
+ else ksprintf(&str, "%s\t", header->target_name[c->mtid]);
+ ksprintf(&str, "%d\t%d\t", c->mpos + 1, c->isize);
+ 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);
+ 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;
+ ksprintf(&str, "\t%c%c:", key[0], key[1]);
+ if (type == 'A') { ksprintf(&str, "A:%c", *s); ++s; }
+ else if (type == 'C') { ksprintf(&str, "i:%u", *s); ++s; }
+ else if (type == 'c') { ksprintf(&str, "i:%d", *s); ++s; }
+ else if (type == 'S') { ksprintf(&str, "i:%u", *(uint16_t*)s); s += 2; }
+ else if (type == 's') { ksprintf(&str, "i:%d", *(int16_t*)s); s += 2; }
+ else if (type == 'I') { ksprintf(&str, "i:%u", *(uint32_t*)s); s += 4; }
+ else if (type == 'i') { ksprintf(&str, "i:%d", *(int32_t*)s); 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') { ksprintf(&str, "%c:", type); while (*s) kputc(*s++, &str); ++s; }
+ }
+ return str.s;
+}
+
+/*************************
+ *** from bam_pileup.c ***
+ *************************/
+
+typedef struct __linkbuf_t {
+ bam1_t b;
+ uint32_t beg, end;
+ struct __linkbuf_t *next;
+} lbnode_t;
+
+/* --- BEGIN: Memory pool */
+
+typedef struct {
+ int cnt, n, max;
+ lbnode_t **buf;
+} mempool_t;
+
+static mempool_t *mp_init()
+{
+ mempool_t *mp;
+ mp = (mempool_t*)calloc(1, sizeof(mempool_t));
+ return mp;
+}
+static void mp_destroy(mempool_t *mp)
+{
+ int k;
+ for (k = 0; k < mp->n; ++k) {
+ free(mp->buf[k]->b.data);
+ free(mp->buf[k]);
+ }
+ free(mp->buf);
+ free(mp);
+}
+static inline lbnode_t *mp_alloc(mempool_t *mp)
+{
+ ++mp->cnt;
+ if (mp->n == 0) return (lbnode_t*)calloc(1, sizeof(lbnode_t));
+ else return mp->buf[--mp->n];
+}
+static inline void mp_free(mempool_t *mp, lbnode_t *p)
+{
+ --mp->cnt; p->next = 0; // clear lbnode_t::next here
+ if (mp->n == mp->max) {
+ mp->max = mp->max? mp->max<<1 : 256;
+ mp->buf = (lbnode_t**)realloc(mp->buf, sizeof(lbnode_t*) * mp->max);
+ }
+ mp->buf[mp->n++] = p;
+}
+
+/* --- END: Memory pool */
+
+/* --- BEGIN: Auxiliary functions */
+
+static inline int resolve_cigar(bam_pileup1_t *p, uint32_t pos)
+{
+ unsigned k;
+ bam1_t *b = p->b;
+ bam1_core_t *c = &b->core;
+ uint32_t x = c->pos, y = 0;
+ int ret = 1, is_restart = 1;
+
+ if (c->flag&BAM_FUNMAP) return 0; // unmapped read
+ assert(x <= pos); // otherwise a bug
+ p->qpos = -1; p->indel = 0; p->is_del = p->is_head = p->is_tail = 0;
+ for (k = 0; k < c->n_cigar; ++k) {
+ int op = bam1_cigar(b)[k] & BAM_CIGAR_MASK; // operation
+ int l = bam1_cigar(b)[k] >> BAM_CIGAR_SHIFT; // length
+ if (op == BAM_CMATCH) { // NOTE: this assumes the first and the last operation MUST BE a match or a clip
+ if (x + l > pos) { // overlap with pos
+ p->indel = p->is_del = 0;
+ p->qpos = y + (pos - x);
+ if (x == pos && is_restart) p->is_head = 1;
+ if (x + l - 1 == pos) { // come to the end of a match
+ if (k < c->n_cigar - 1) { // there are additional operation(s)
+ uint32_t cigar = bam1_cigar(b)[k+1]; // next CIGAR
+ int op_next = cigar&BAM_CIGAR_MASK; // next CIGAR operation
+ if (op_next == BAM_CDEL) p->indel = -(int32_t)(cigar>>BAM_CIGAR_SHIFT); // del
+ else if (op_next == BAM_CINS) p->indel = cigar>>BAM_CIGAR_SHIFT; // ins
+ if (op_next == BAM_CSOFT_CLIP || op_next == BAM_CREF_SKIP || op_next == BAM_CHARD_CLIP)
+ p->is_tail = 1; // tail
+ } else p->is_tail = 1; // this is the last operation; set tail
+ }
+ }
+ x += l; y += l;
+ } else if (op == BAM_CDEL) { // then set ->is_del
+ if (x + l > pos) {
+ p->indel = 0; p->is_del = 1;
+ p->qpos = y + (pos - x);
+ }
+ x += l;
+ } else if (op == BAM_CREF_SKIP) x += l;
+ else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l;
+ is_restart = (op == BAM_CREF_SKIP || op == BAM_CSOFT_CLIP || op == BAM_CHARD_CLIP);
+ if (x > pos) {
+ if (op == BAM_CREF_SKIP) ret = 0; // then do not put it into pileup at all
+ break;
+ }
+ }
+ assert(x > pos); // otherwise a bug
+ return ret;
+}
+
+/* --- END: Auxiliary functions */
+
+struct __bam_plbuf_t {
+ mempool_t *mp;
+ lbnode_t *head, *tail, *dummy;
+ bam_pileup_f func;
+ void *func_data;
+ int32_t tid, pos, max_tid, max_pos;
+ int max_pu, is_eof;
+ bam_pileup1_t *pu;
+ int flag_mask;
+};
+
+void bam_plbuf_reset(bam_plbuf_t *buf)
+{
+ lbnode_t *p, *q;
+ buf->max_tid = buf->max_pos = -1;
+ buf->tid = buf->pos = 0;
+ buf->is_eof = 0;
+ for (p = buf->head; p->next;) {
+ q = p->next;
+ mp_free(buf->mp, p);
+ p = q;
+ }
+ buf->head = buf->tail;
+}
+
+void bam_plbuf_set_mask(bam_plbuf_t *buf, int mask)
+{
+ if (mask < 0) buf->flag_mask = BAM_DEF_MASK;
+ else buf->flag_mask = BAM_FUNMAP | mask;
+}
+
+bam_plbuf_t *bam_plbuf_init(bam_pileup_f func, void *data)
+{
+ bam_plbuf_t *buf;
+ buf = (bam_plbuf_t*)calloc(1, sizeof(bam_plbuf_t));
+ buf->func = func; buf->func_data = data;
+ buf->mp = mp_init();
+ buf->head = buf->tail = mp_alloc(buf->mp);
+ buf->dummy = mp_alloc(buf->mp);
+ buf->max_tid = buf->max_pos = -1;
+ buf->flag_mask = BAM_DEF_MASK;
+ return buf;
+}
+
+void bam_plbuf_destroy(bam_plbuf_t *buf)
+{
+ mp_free(buf->mp, buf->dummy);
+ mp_free(buf->mp, buf->head);
+ if (buf->mp->cnt != 0)
+ fprintf(stderr, "[bam_plbuf_destroy] memory leak: %d. Continue anyway.\n", buf->mp->cnt);
+ mp_destroy(buf->mp);
+ free(buf->pu);
+ free(buf);
+}
+
+int bam_plbuf_push(const bam1_t *b, bam_plbuf_t *buf)
+{
+ if (b) { // fill buffer
+ if (b->core.tid < 0) return 0;
+ if (b->core.flag & buf->flag_mask) return 0;
+ bam_copy1(&buf->tail->b, b);
+ buf->tail->beg = b->core.pos; buf->tail->end = bam_calend(&b->core, bam1_cigar(b));
+ if (!(b->core.tid >= buf->max_tid || (b->core.tid == buf->max_tid && buf->tail->beg >= buf->max_pos))) {
+ fprintf(stderr, "[bam_pileup_core] the input is not sorted. Abort!\n");
+ abort();
+ }
+ buf->max_tid = b->core.tid; buf->max_pos = buf->tail->beg;
+ if (buf->tail->end > buf->pos || buf->tail->b.core.tid > buf->tid) {
+ buf->tail->next = mp_alloc(buf->mp);
+ buf->tail = buf->tail->next;
+ }
+ } else buf->is_eof = 1;
+ while (buf->is_eof || buf->max_tid > buf->tid || (buf->max_tid == buf->tid && buf->max_pos > buf->pos)) {
+ int n_pu = 0;
+ lbnode_t *p, *q;
+ buf->dummy->next = buf->head;
+ for (p = buf->head, q = buf->dummy; p->next; q = p, p = p->next) {
+ if (p->b.core.tid < buf->tid || (p->b.core.tid == buf->tid && p->end <= buf->pos)) { // then remove from the list
+ q->next = p->next; mp_free(buf->mp, p); p = q;
+ } else if (p->b.core.tid == buf->tid && p->beg <= buf->pos) { // here: p->end > pos; then add to pileup
+ if (n_pu == buf->max_pu) { // then double the capacity
+ buf->max_pu = buf->max_pu? buf->max_pu<<1 : 256;
+ buf->pu = (bam_pileup1_t*)realloc(buf->pu, sizeof(bam_pileup1_t) * buf->max_pu);
+ }
+ buf->pu[n_pu].b = &p->b;
+ if (resolve_cigar(buf->pu + n_pu, buf->pos)) ++n_pu; // skip the read if we are looking at BAM_CREF_SKIP
+ }
+ }
+ buf->head = buf->dummy->next; // dummy->next may be changed
+ if (n_pu) { // then call user defined function
+ buf->func(buf->tid, buf->pos, n_pu, buf->pu, buf->func_data);
+ }
+ // update tid and pos
+ if (buf->head->next) {
+ if (buf->tid > buf->head->b.core.tid) {
+ fprintf(stderr, "[bam_plbuf_push] unsorted input. Pileup aborts.\n");
+ return 1;
+ }
+ }
+ if (buf->tid < buf->head->b.core.tid) { // come to a new reference sequence
+ buf->tid = buf->head->b.core.tid; buf->pos = buf->head->beg; // jump to the next reference
+ } else if (buf->pos < buf->head->beg) { // here: tid == head->b.core.tid
+ buf->pos = buf->head->beg; // jump to the next position
+ } else ++buf->pos; // scan contiguously
+ if (buf->is_eof && buf->head->next == 0) break;
+ }
+ return 0;
+}
+
+/**********************
+ *** from bam_aux.c ***
+ **********************/
+
+uint8_t *bam_aux_get(const bam1_t *b, const char tag[2])
+{
+ uint8_t *s;
+ int y = tag[0]<<8 | tag[1];
+ s = bam1_aux(b);
+ while (s < b->data + b->data_len) {
+ int type, x = (int)s[0]<<8 | s[1];
+ s += 2;
+ if (x == y) return s;
+ type = toupper(*s); ++s;
+ if (type == 'C') ++s;
+ else if (type == 'S') s += 2;
+ else if (type == 'I' || type == 'F') s += 4;
+ else if (type == 'D') s += 8;
+ else if (type == 'Z' || type == 'H') { while (*s) ++s; ++s; }
+ }
+ return 0;
+}
projects / samtools.git / commitdiff