text: #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;
  }
  