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bam_import.c

#include <zlib.h>
#include <stdio.h>
#include <ctype.h>
#include <string.h>
#include <stdlib.h>
#include <unistd.h>
#include <assert.h>
#ifdef _WIN32
#include <fcntl.h>
#endif
#include "kstring.h"
#include "bam.h"
#include "sam_header.h"
#include "kseq.h"
#include "khash.h"

KSTREAM_INIT(gzFile, gzread, 8192)
KHASH_MAP_INIT_STR(ref, uint64_t)

void bam_init_header_hash(bam_header_t *header);
void bam_destroy_header_hash(bam_header_t *header);
int32_t bam_get_tid(const bam_header_t *header, const char *seq_name);

unsigned char bam_nt16_table[256] = {
      15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
      15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
      15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
       1, 2, 4, 8, 15,15,15,15, 15,15,15,15, 15, 0 /*=*/,15,15,
      15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,
      15,15, 5, 6,  8,15, 7, 9, 15,10,15,15, 15,15,15,15,
      15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,
      15,15, 5, 6,  8,15, 7, 9, 15,10,15,15, 15,15,15,15,
      15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
      15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
      15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
      15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
      15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
      15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
      15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
      15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15
};

unsigned short bam_char2flag_table[256] = {
      0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
      0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
      0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
      0,BAM_FREAD1,BAM_FREAD2,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
      0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
      BAM_FPROPER_PAIR,0,BAM_FMREVERSE,0, 0,BAM_FMUNMAP,0,0, 0,0,0,0, 0,0,0,0,
      0,0,0,0, BAM_FDUP,0,BAM_FQCFAIL,0, 0,0,0,0, 0,0,0,0,
      BAM_FPAIRED,0,BAM_FREVERSE,BAM_FSECONDARY, 0,BAM_FUNMAP,0,0, 0,0,0,0, 0,0,0,0,
      0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
      0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
      0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
      0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
      0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
      0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
      0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0,
      0,0,0,0, 0,0,0,0, 0,0,0,0, 0,0,0,0
};

char *bam_nt16_rev_table = "=ACMGRSVTWYHKDBN";

struct __tamFile_t {
      gzFile fp;
      kstream_t *ks;
      kstring_t *str;
      uint64_t n_lines;
      int is_first;
};

char **__bam_get_lines(const char *fn, int *_n) // for bam_plcmd.c only
{
      char **list = 0, *s;
      int n = 0, dret, m = 0;
      gzFile fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
      kstream_t *ks;
      kstring_t *str;
      str = (kstring_t*)calloc(1, sizeof(kstring_t));
      ks = ks_init(fp);
      while (ks_getuntil(ks, '\n', str, &dret) > 0) {
            if (n == m) {
                  m = m? m << 1 : 16;
                  list = (char**)realloc(list, m * sizeof(char*));
            }
            if (str->s[str->l-1] == '\r')
                  str->s[--str->l] = '\0';
            s = list[n++] = (char*)calloc(str->l + 1, 1);
            strcpy(s, str->s);
      }
      ks_destroy(ks);
      gzclose(fp);
      free(str->s); free(str);
      *_n = n;
      return list;
}

static bam_header_t *hash2header(const kh_ref_t *hash)
{
      bam_header_t *header;
      khiter_t k;
      header = bam_header_init();
      header->n_targets = kh_size(hash);
      header->target_name = (char**)calloc(kh_size(hash), sizeof(char*));
      header->target_len = (uint32_t*)calloc(kh_size(hash), 4);
      for (k = kh_begin(hash); k != kh_end(hash); ++k) {
            if (kh_exist(hash, k)) {
                  int i = (int)kh_value(hash, k);
                  header->target_name[i] = (char*)kh_key(hash, k);
                  header->target_len[i] = kh_value(hash, k)>>32;
            }
      }
      bam_init_header_hash(header);
      return header;
}
bam_header_t *sam_header_read2(const char *fn)
{
      bam_header_t *header;
      int c, dret, ret, error = 0;
      gzFile fp;
      kstream_t *ks;
      kstring_t *str;
      kh_ref_t *hash;
      khiter_t k;
      if (fn == 0) return 0;
      fp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(fn, "r");
      if (fp == 0) return 0;
      hash = kh_init(ref);
      ks = ks_init(fp);
      str = (kstring_t*)calloc(1, sizeof(kstring_t));
      while (ks_getuntil(ks, 0, str, &dret) > 0) {
            char *s = strdup(str->s);
            int len, i;
            i = kh_size(hash);
            ks_getuntil(ks, 0, str, &dret);
            len = atoi(str->s);
            k = kh_put(ref, hash, s, &ret);
            if (ret == 0) {
                  fprintf(stderr, "[sam_header_read2] duplicated sequence name: %s\n", s);
                  error = 1;
            }
            kh_value(hash, k) = (uint64_t)len<<32 | i;
            if (dret != '\n')
                  while ((c = ks_getc(ks)) != '\n' && c != -1);
      }
      ks_destroy(ks);
      gzclose(fp);
      free(str->s); free(str);
      fprintf(stderr, "[sam_header_read2] %d sequences loaded.\n", kh_size(hash));
      if (error) return 0;
      header = hash2header(hash);
      kh_destroy(ref, hash);
      return header;
}
static inline uint8_t *alloc_data(bam1_t *b, int size)
{
      if (b->m_data < size) {
            b->m_data = size;
            kroundup32(b->m_data);
            b->data = (uint8_t*)realloc(b->data, b->m_data);
      }
      return b->data;
}
static inline void parse_error(int64_t n_lines, const char * __restrict msg)
{
      fprintf(stderr, "Parse error at line %lld: %s\n", (long long)n_lines, msg);
      abort();
}
static inline void append_text(bam_header_t *header, kstring_t *str)
{
      size_t x = header->l_text, y = header->l_text + str->l + 2; // 2 = 1 byte dret + 1 byte null
      kroundup32(x); kroundup32(y);
      if (x < y) 
    {
        header->n_text = y;
        header->text = (char*)realloc(header->text, y);
        if ( !header->text ) 
        {
            fprintf(stderr,"realloc failed to alloc %ld bytes\n", y);
            abort();
        }
    }
    // Sanity check
    if ( header->l_text+str->l+1 >= header->n_text )
    {
        fprintf(stderr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n",  header->l_text+str->l+1,header->n_text,x,y);
        abort();
    }
      strncpy(header->text + header->l_text, str->s, str->l+1); // we cannot use strcpy() here.
      header->l_text += str->l + 1;
      header->text[header->l_text] = 0;
}

int sam_header_parse(bam_header_t *h)
{
      char **tmp;
      int i;
      free(h->target_len); free(h->target_name);
      h->n_targets = 0; h->target_len = 0; h->target_name = 0;
      if (h->l_text < 3) return 0;
      if (h->dict == 0) h->dict = sam_header_parse2(h->text);
      tmp = sam_header2list(h->dict, "SQ", "SN", &h->n_targets);
      if (h->n_targets == 0) return 0;
      h->target_name = calloc(h->n_targets, sizeof(void*));
      for (i = 0; i < h->n_targets; ++i)
            h->target_name[i] = strdup(tmp[i]);
      free(tmp);
      tmp = sam_header2list(h->dict, "SQ", "LN", &h->n_targets);
      h->target_len = calloc(h->n_targets, 4);
      for (i = 0; i < h->n_targets; ++i)
            h->target_len[i] = atoi(tmp[i]);
      free(tmp);
      return h->n_targets;
}

bam_header_t *sam_header_read(tamFile fp)
{
      int ret, dret;
      bam_header_t *header = bam_header_init();
      kstring_t *str = fp->str;
      while ((ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret)) >= 0 && str->s[0] == '@') { // skip header
            str->s[str->l] = dret; // note that str->s is NOT null terminated!!
            append_text(header, str);
            if (dret != '\n') {
                  ret = ks_getuntil(fp->ks, '\n', str, &dret);
                  str->s[str->l] = '\n'; // NOT null terminated!!
                  append_text(header, str);
            }
            ++fp->n_lines;
      }
      sam_header_parse(header);
      bam_init_header_hash(header);
      fp->is_first = 1;
      return header;
}

int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
{
      int ret, doff, doff0, dret, z = 0;
      bam1_core_t *c = &b->core;
      kstring_t *str = fp->str;
      kstream_t *ks = fp->ks;

      if (fp->is_first) {
            fp->is_first = 0;
            ret = str->l;
      } else {
            do { // special consideration for empty lines
                  ret = ks_getuntil(fp->ks, KS_SEP_TAB, str, &dret);
                  if (ret >= 0) z += str->l + 1;
            } while (ret == 0);
      }
      if (ret < 0) return -1;
      ++fp->n_lines;
      doff = 0;

      { // name
            c->l_qname = strlen(str->s) + 1;
            memcpy(alloc_data(b, doff + c->l_qname) + doff, str->s, c->l_qname);
            doff += c->l_qname;
      }
      { // flag
            long flag;
            char *s;
            ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
            flag = strtol((char*)str->s, &s, 0);
            if (*s) { // not the end of the string
                  flag = 0;
                  for (s = str->s; *s; ++s)
                        flag |= bam_char2flag_table[(int)*s];
            }
            c->flag = flag;
      }
      { // tid, pos, qual
            ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->tid = bam_get_tid(header, str->s);
            if (c->tid < 0 && strcmp(str->s, "*")) {
                  if (header->n_targets == 0) {
                        fprintf(stderr, "[sam_read1] missing header? Abort!\n");
                        exit(1);
                  } else fprintf(stderr, "[sam_read1] reference '%s' is recognized as '*'.\n", str->s);
            }
            ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->pos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
            ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->qual = isdigit(str->s[0])? atoi(str->s) : 0;
            if (ret < 0) return -2;
      }
      { // cigar
            char *s, *t;
            int i, op;
            long x;
            c->n_cigar = 0;
            if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -3;
            z += str->l + 1;
            if (str->s[0] != '*') {
                  for (s = str->s; *s; ++s) {
                        if (isalpha(*s)) ++c->n_cigar;
                        else if (!isdigit(*s)) parse_error(fp->n_lines, "invalid CIGAR character");
                  }
                  b->data = alloc_data(b, doff + c->n_cigar * 4);
                  for (i = 0, s = str->s; i != c->n_cigar; ++i) {
                        x = strtol(s, &t, 10);
                        op = toupper(*t);
                        if (op == 'M' || op == '=' || op == 'X') op = BAM_CMATCH;
                        else if (op == 'I') op = BAM_CINS;
                        else if (op == 'D') op = BAM_CDEL;
                        else if (op == 'N') op = BAM_CREF_SKIP;
                        else if (op == 'S') op = BAM_CSOFT_CLIP;
                        else if (op == 'H') op = BAM_CHARD_CLIP;
                        else if (op == 'P') op = BAM_CPAD;
                        else parse_error(fp->n_lines, "invalid CIGAR operation");
                        s = t + 1;
                        bam1_cigar(b)[i] = x << BAM_CIGAR_SHIFT | op;
                  }
                  if (*s) parse_error(fp->n_lines, "unmatched CIGAR operation");
                  c->bin = bam_reg2bin(c->pos, bam_calend(c, bam1_cigar(b)));
                  doff += c->n_cigar * 4;
            } else {
                  if (!(c->flag&BAM_FUNMAP)) {
                        fprintf(stderr, "Parse warning at line %lld: mapped sequence without CIGAR\n", (long long)fp->n_lines);
                        c->flag |= BAM_FUNMAP;
                  }
                  c->bin = bam_reg2bin(c->pos, c->pos + 1);
            }
      }
      { // mtid, mpos, isize
            ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
            c->mtid = strcmp(str->s, "=")? bam_get_tid(header, str->s) : c->tid;
            ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
            c->mpos = isdigit(str->s[0])? atoi(str->s) - 1 : -1;
            ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
            c->isize = (str->s[0] == '-' || isdigit(str->s[0]))? atoi(str->s) : 0;
            if (ret < 0) return -4;
      }
      { // seq and qual
            int i;
            uint8_t *p = 0;
            if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -5; // seq
            z += str->l + 1;
            if (strcmp(str->s, "*")) {
                  c->l_qseq = strlen(str->s);
                  if (c->n_cigar && c->l_qseq != (int32_t)bam_cigar2qlen(c, bam1_cigar(b)))
                        parse_error(fp->n_lines, "CIGAR and sequence length are inconsistent");
                  p = (uint8_t*)alloc_data(b, doff + c->l_qseq + (c->l_qseq+1)/2) + doff;
                  memset(p, 0, (c->l_qseq+1)/2);
                  for (i = 0; i < c->l_qseq; ++i)
                        p[i/2] |= bam_nt16_table[(int)str->s[i]] << 4*(1-i%2);
            } else c->l_qseq = 0;
            if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -6; // qual
            z += str->l + 1;
            if (strcmp(str->s, "*") && c->l_qseq != strlen(str->s))
                  parse_error(fp->n_lines, "sequence and quality are inconsistent");
            p += (c->l_qseq+1)/2;
            if (strcmp(str->s, "*") == 0) for (i = 0; i < c->l_qseq; ++i) p[i] = 0xff;
            else for (i = 0; i < c->l_qseq; ++i) p[i] = str->s[i] - 33;
            doff += c->l_qseq + (c->l_qseq+1)/2;
      }
      doff0 = doff;
      if (dret != '\n' && dret != '\r') { // aux
            while (ks_getuntil(ks, KS_SEP_TAB, str, &dret) >= 0) {
                  uint8_t *s, type, key[2];
                  z += str->l + 1;
                  if (str->l < 6 || str->s[2] != ':' || str->s[4] != ':')
                        parse_error(fp->n_lines, "missing colon in auxiliary data");
                  key[0] = str->s[0]; key[1] = str->s[1];
                  type = str->s[3];
                  s = alloc_data(b, doff + 3) + doff;
                  s[0] = key[0]; s[1] = key[1]; s += 2; doff += 2;
                  if (type == 'A' || type == 'a' || type == 'c' || type == 'C') { // c and C for backward compatibility
                        s = alloc_data(b, doff + 2) + doff;
                        *s++ = 'A'; *s = str->s[5];
                        doff += 2;
                  } else if (type == 'I' || type == 'i') {
                        long long x;
                        s = alloc_data(b, doff + 5) + doff;
                        x = (long long)atoll(str->s + 5);
                        if (x < 0) {
                              if (x >= -127) {
                                    *s++ = 'c'; *(int8_t*)s = (int8_t)x;
                                    s += 1; doff += 2;
                              } else if (x >= -32767) {
                                    *s++ = 's'; *(int16_t*)s = (int16_t)x;
                                    s += 2; doff += 3;
                              } else {
                                    *s++ = 'i'; *(int32_t*)s = (int32_t)x;
                                    s += 4; doff += 5;
                                    if (x < -2147483648ll)
                                          fprintf(stderr, "Parse warning at line %lld: integer %lld is out of range.",
                                                      (long long)fp->n_lines, x);
                              }
                        } else {
                              if (x <= 255) {
                                    *s++ = 'C'; *s++ = (uint8_t)x;
                                    doff += 2;
                              } else if (x <= 65535) {
                                    *s++ = 'S'; *(uint16_t*)s = (uint16_t)x;
                                    s += 2; doff += 3;
                              } else {
                                    *s++ = 'I'; *(uint32_t*)s = (uint32_t)x;
                                    s += 4; doff += 5;
                                    if (x > 4294967295ll)
                                          fprintf(stderr, "Parse warning at line %lld: integer %lld is out of range.",
                                                      (long long)fp->n_lines, x);
                              }
                        }
                  } else if (type == 'f') {
                        s = alloc_data(b, doff + 5) + doff;
                        *s++ = 'f';
                        *(float*)s = (float)atof(str->s + 5);
                        s += 4; doff += 5;
                  } else if (type == 'd') {
                        s = alloc_data(b, doff + 9) + doff;
                        *s++ = 'd';
                        *(float*)s = (float)atof(str->s + 9);
                        s += 8; doff += 9;
                  } else if (type == 'Z' || type == 'H') {
                        int size = 1 + (str->l - 5) + 1;
                        if (type == 'H') { // check whether the hex string is valid
                              int i;
                              if ((str->l - 5) % 2 == 1) parse_error(fp->n_lines, "length of the hex string not even");
                              for (i = 0; i < str->l - 5; ++i) {
                                    int c = toupper(str->s[5 + i]);
                                    if (!((c >= '0' && c <= '9') || (c >= 'A' && c <= 'F')))
                                          parse_error(fp->n_lines, "invalid hex character");
                              }
                        }
                        s = alloc_data(b, doff + size) + doff;
                        *s++ = type;
                        memcpy(s, str->s + 5, str->l - 5);
                        s[str->l - 5] = 0;
                        doff += size;
                  } else parse_error(fp->n_lines, "unrecognized type");
                  if (dret == '\n' || dret == '\r') break;
            }
      }
      b->l_aux = doff - doff0;
      b->data_len = doff;
      return z;
}

tamFile sam_open(const char *fn)
{
      tamFile fp;
      gzFile gzfp = (strcmp(fn, "-") == 0)? gzdopen(fileno(stdin), "rb") : gzopen(fn, "rb");
      if (gzfp == 0) return 0;
      fp = (tamFile)calloc(1, sizeof(struct __tamFile_t));
      fp->str = (kstring_t*)calloc(1, sizeof(kstring_t));
      fp->fp = gzfp;
      fp->ks = ks_init(fp->fp);
      return fp;
}

void sam_close(tamFile fp)
{
      if (fp) {
            ks_destroy(fp->ks);
            gzclose(fp->fp);
            free(fp->str->s); free(fp->str);
            free(fp);
      }
}

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