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maq2sam.c

#include <string.h>
#include <zlib.h>
#include <stdio.h>
#include <inttypes.h>
#include <stdlib.h>
#include <assert.h>

#define PACKAGE_VERSION "r439"

//#define MAQ_LONGREADS

#ifdef MAQ_LONGREADS
#  define MAX_READLEN 128
#else
#  define MAX_READLEN 64
#endif

#define MAX_NAMELEN 36
#define MAQMAP_FORMAT_OLD 0
#define MAQMAP_FORMAT_NEW -1

#define PAIRFLAG_FF      0x01
#define PAIRFLAG_FR      0x02
#define PAIRFLAG_RF      0x04
#define PAIRFLAG_RR      0x08
#define PAIRFLAG_PAIRED  0x10
#define PAIRFLAG_DIFFCHR 0x20
#define PAIRFLAG_NOMATCH 0x40
#define PAIRFLAG_SW      0x80

typedef struct
{
      uint8_t seq[MAX_READLEN]; /* the last base is the single-end mapping quality. */
      uint8_t size, map_qual, info1, info2, c[2], flag, alt_qual;
      uint32_t seqid, pos;
      int dist;
      char name[MAX_NAMELEN];
} maqmap1_t;

typedef struct
{
      int format, n_ref;
      char **ref_name;
      uint64_t n_mapped_reads;
      maqmap1_t *mapped_reads;
} maqmap_t;

maqmap_t *maq_new_maqmap()
{
      maqmap_t *mm = (maqmap_t*)calloc(1, sizeof(maqmap_t));
      mm->format = MAQMAP_FORMAT_NEW;
      return mm;
}
void maq_delete_maqmap(maqmap_t *mm)
{
      int i;
      if (mm == 0) return;
      for (i = 0; i < mm->n_ref; ++i)
            free(mm->ref_name[i]);
      free(mm->ref_name);
      free(mm->mapped_reads);
      free(mm);
}
maqmap_t *maqmap_read_header(gzFile fp)
{
      maqmap_t *mm;
      int k, len;
      mm = maq_new_maqmap();
      gzread(fp, &mm->format, sizeof(int));
      if (mm->format != MAQMAP_FORMAT_NEW) {
            if (mm->format > 0) {
                  fprintf(stderr, "** Obsolete map format is detected. Please use 'mapass2maq' command to convert the format.\n");
                  exit(3);
            }
            assert(mm->format == MAQMAP_FORMAT_NEW);
      }
      gzread(fp, &mm->n_ref, sizeof(int));
      mm->ref_name = (char**)calloc(mm->n_ref, sizeof(char*));
      for (k = 0; k != mm->n_ref; ++k) {
            gzread(fp, &len, sizeof(int));
            mm->ref_name[k] = (char*)malloc(len * sizeof(char));
            gzread(fp, mm->ref_name[k], len);
      }
      /* read number of mapped reads */
      gzread(fp, &mm->n_mapped_reads, sizeof(uint64_t));
      return mm;
}

void maq2tam_core(gzFile fp, const char *rg)
{
      maqmap_t *mm;
      maqmap1_t mm1, *m1;
      int ret;
      m1 = &mm1;
      mm = maqmap_read_header(fp);
      while ((ret = gzread(fp, m1, sizeof(maqmap1_t))) == sizeof(maqmap1_t)) {
            int j, flag = 0, se_mapq = m1->seq[MAX_READLEN-1];
            if (m1->flag) flag |= 1;
            if ((m1->flag&PAIRFLAG_PAIRED) || ((m1->flag&PAIRFLAG_SW) && m1->flag != 192)) flag |= 2;
            if (m1->flag == 192) flag |= 4;
            if (m1->flag == 64) flag |= 8;
            if (m1->pos&1) flag |= 0x10;
            if ((flag&1) && m1->dist != 0) {
                  int c;
                  if (m1->dist > 0) {
                        if (m1->flag&(PAIRFLAG_FF|PAIRFLAG_RF)) c = 0;
                        else if (m1->flag&(PAIRFLAG_FR|PAIRFLAG_RR)) c = 1;
                        else c = m1->pos&1;                       
                  } else {
                        if (m1->flag&(PAIRFLAG_FF|PAIRFLAG_FR)) c = 0;
                        else if (m1->flag&(PAIRFLAG_RF|PAIRFLAG_RR)) c = 1;
                        else c = m1->pos&1;
                  }
                  if (c) flag |= 0x20;
            }
            if (m1->flag) {
                  int l = strlen(m1->name);
                  if (m1->name[l-2] == '/') {
                        flag |= (m1->name[l-1] == '1')? 0x40 : 0x80;
                        m1->name[l-2] = '\0';
                  }
            }
            printf("%s\t%d\t", m1->name, flag);
            printf("%s\t%d\t", mm->ref_name[m1->seqid], (m1->pos>>1)+1);
            if (m1->flag == 130) {
                  int c = (int8_t)m1->seq[MAX_READLEN-1];
                  printf("%d\t", m1->alt_qual);
                  if (c == 0) printf("%dM\t", m1->size);
                  else {
                        if (c > 0) printf("%dM%dI%dM\t", m1->map_qual, c, m1->size - m1->map_qual - c);
                        else printf("%dM%dD%dM\t", m1->map_qual, -c, m1->size - m1->map_qual);
                  }
                  se_mapq = 0; // zero SE mapQ for reads aligned by SW
            } else {
                  if (flag&4) printf("0\t*\t");
                  else printf("%d\t%dM\t", m1->map_qual, m1->size);
            }
            printf("*\t0\t%d\t", m1->dist);
            for (j = 0; j != m1->size; ++j) {
                  if (m1->seq[j] == 0) putchar('N');
                  else putchar("ACGT"[m1->seq[j]>>6&3]);
            }
            putchar('\t');
            for (j = 0; j != m1->size; ++j)
                  putchar((m1->seq[j]&0x3f) + 33);
            putchar('\t');
            if (rg) printf("RG:Z:%s\t", rg);
            if (flag&4) { // unmapped
                  printf("MF:i:%d\n", m1->flag);
            } else {
                  printf("MF:i:%d\t", m1->flag);
                  if (m1->flag) printf("AM:i:%d\tSM:i:%d\t", m1->alt_qual, se_mapq);
                  printf("NM:i:%d\tUQ:i:%d\tH0:i:%d\tH1:i:%d\n", m1->info1&0xf, m1->info2, m1->c[0], m1->c[1]);
            }
      }
      if (ret > 0)
            fprintf(stderr, "Truncated! Continue anyway.\n");
      maq_delete_maqmap(mm);
}

int main(int argc, char *argv[])
{
      gzFile fp;
      if (argc == 1) {
            fprintf(stderr, "Version: %s\n", PACKAGE_VERSION);
            fprintf(stderr, "Usage: maq2sam <in.map> [<readGroup>]\n");
            return 1;
      }
      fp = strcmp(argv[1], "-")? gzopen(argv[1], "r") : gzdopen(fileno(stdin), "r");
      maq2tam_core(fp, argc > 2? argv[2] : 0);
      gzclose(fp);
      return 0;
}

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