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bam.c

#include <stdio.h>
#include <ctype.h>
#include <errno.h>
#include <assert.h>
#include "bam.h"
#include "bam_endian.h"
#include "kstring.h"
#include "sam_header.h"

int bam_is_be = 0;
char *bam_flag2char_table = "pPuUrR12sfd\0\0\0\0\0";

/**************************
 * CIGAR related routines *
 **************************/

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);
      if (header->dict) sam_header_free(header->dict);
      if (header->rg2lib) sam_tbl_destroy(header->rg2lib);
      bam_destroy_header_hash(header);
      free(header);
}

bam_header_t *bam_header_read(bamFile fp)
{
      bam_header_t *header;
      char buf[4];
      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.\n");
      // read "BAM1"
      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();
      // 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;
}

int bam_header_write(bamFile fp, const bam_header_t *header)
{
      char buf[4];
      int32_t i, name_len, x;
      // write "BAM1"
      strncpy(buf, "BAM\001", 4);
      bam_write(fp, buf, 4);
      // write plain text and the number of reference sequences
      if (bam_is_be) {
            x = bam_swap_endian_4(header->l_text);
            bam_write(fp, &x, 4);
            if (header->l_text) bam_write(fp, header->text, header->l_text);
            x = bam_swap_endian_4(header->n_targets);
            bam_write(fp, &x, 4);
      } else {
            bam_write(fp, &header->l_text, 4);
            if (header->l_text) bam_write(fp, header->text, header->l_text);
            bam_write(fp, &header->n_targets, 4);
      }
      // write sequence names and lengths
      for (i = 0; i != header->n_targets; ++i) {
            char *p = header->target_name[i];
            name_len = strlen(p) + 1;
            if (bam_is_be) {
                  x = bam_swap_endian_4(name_len);
                  bam_write(fp, &x, 4);
            } else bam_write(fp, &name_len, 4);
            bam_write(fp, p, name_len);
            if (bam_is_be) {
                  x = bam_swap_endian_4(header->target_len[i]);
                  bam_write(fp, &x, 4);
            } else bam_write(fp, &header->target_len[i], 4);
      }
      bgzf_flush(fp);
      return 0;
}

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;
}

inline int bam_write1_core(bamFile fp, const bam1_core_t *c, int data_len, uint8_t *data)
{
      uint32_t x[8], block_len = data_len + BAM_CORE_SIZE, y;
      int i;
      assert(BAM_CORE_SIZE == 32);
      x[0] = c->tid;
      x[1] = c->pos;
      x[2] = (uint32_t)c->bin<<16 | c->qual<<8 | c->l_qname;
      x[3] = (uint32_t)c->flag<<16 | c->n_cigar;
      x[4] = c->l_qseq;
      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;
            bam_write(fp, bam_swap_endian_4p(&y), 4);
            swap_endian_data(c, data_len, data);
      } else bam_write(fp, &block_len, 4);
      bam_write(fp, x, BAM_CORE_SIZE);
      bam_write(fp, data, data_len);
      if (bam_is_be) swap_endian_data(c, data_len, data);
      return 4 + block_len;
}

int bam_write1(bamFile fp, const bam1_t *b)
{
      return bam_write1_core(fp, &b->core, b->data_len, b->data);
}

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;
      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<<i) && bam_flag2char_table[i])
                        kputc(bam_flag2char_table[i], &str);
            kputc('\t', &str);
      }
      if (c->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 {
            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('\t', &str);
      if (c->mtid < 0) kputsn("*\t", 2, &str);
      else if (c->mtid == c->tid) kputsn("=\t", 2, &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);
            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;
            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; }
      }
      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));
}

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