text: #include "pysam.h"
  
  #include <assert.h>
  #include <ctype.h>
  #include <string.h>
  #include "bam.h"
  #include "bam2bcf.h"
  #include "kaln.h"
  #include "kprobaln.h"
  #include "khash.h"
  KHASH_SET_INIT_STR(rg)
  
  #include "ksort.h"
  KSORT_INIT_GENERIC(uint32_t)
  
  #define MINUS_CONST 0x10000000
  #define INDEL_WINDOW_SIZE 50
  
  void *bcf_call_add_rg(void *_hash, const char *hdtext, const char *list)
  {
  	const char *s, *p, *q, *r, *t;
  	khash_t(rg) *hash;
  	if (list == 0 || hdtext == 0) return _hash;
  	if (_hash == 0) _hash = kh_init(rg);
  	hash = (khash_t(rg)*)_hash;
  	if ((s = strstr(hdtext, "@RG\t")) == 0) return hash;
  	do {
  		t = strstr(s + 4, "@RG\t"); // the next @RG
  		if ((p = strstr(s, "\tID:")) != 0) p += 4;
  		if ((q = strstr(s, "\tPL:")) != 0) q += 4;
  		if (p && q && (t == 0 || (p < t && q < t))) { // ID and PL are both present
  			int lp, lq;
  			char *x;
  			for (r = p; *r && *r != '\t' && *r != '\n'; ++r); lp = r - p;
  			for (r = q; *r && *r != '\t' && *r != '\n'; ++r); lq = r - q;
  			x = calloc((lp > lq? lp : lq) + 1, 1);
  			for (r = q; *r && *r != '\t' && *r != '\n'; ++r) x[r-q] = *r;
  			if (strstr(list, x)) { // insert ID to the hash table
  				khint_t k;
  				int ret;
  				for (r = p; *r && *r != '\t' && *r != '\n'; ++r) x[r-p] = *r;
  				x[r-p] = 0;
  				k = kh_get(rg, hash, x);
  				if (k == kh_end(hash)) k = kh_put(rg, hash, x, &ret);
  				else free(x);
  			} else free(x);
  		}
  		s = t;
  	} while (s);
  	return hash;
  }
  
  void bcf_call_del_rghash(void *_hash)
  {
  	khint_t k;
  	khash_t(rg) *hash = (khash_t(rg)*)_hash;
  	if (hash == 0) return;
  	for (k = kh_begin(hash); k < kh_end(hash); ++k)
  		if (kh_exist(hash, k))
  			free((char*)kh_key(hash, k));
  	kh_destroy(rg, hash);
  }
  
  static int tpos2qpos(const bam1_core_t *c, const uint32_t *cigar, int32_t tpos, int is_left, int32_t *_tpos)
  {
  	int k, x = c->pos, y = 0, last_y = 0;
  	*_tpos = c->pos;
  	for (k = 0; k < c->n_cigar; ++k) {
  		int op = cigar[k] & BAM_CIGAR_MASK;
  		int l = cigar[k] >> BAM_CIGAR_SHIFT;
  		if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
  			if (c->pos > tpos) return y;
  			if (x + l > tpos) {
  				*_tpos = tpos;
  				return y + (tpos - x);
  			}
  			x += l; y += l;
  			last_y = y;
  		} else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l;
  		else if (op == BAM_CDEL || op == BAM_CREF_SKIP) {
  			if (x + l > tpos) {
  				*_tpos = is_left? x : x + l;
  				return y;
  			}
  			x += l;
  		}
  	}
  	*_tpos = x;
  	return last_y;
  }
  // FIXME: check if the inserted sequence is consistent with the homopolymer run
  // l is the relative gap length and l_run is the length of the homopolymer on the reference
  static inline int est_seqQ(const bcf_callaux_t *bca, int l, int l_run)
  {
  	int q, qh;
  	q = bca->openQ + bca->extQ * (abs(l) - 1);
  	qh = l_run >= 3? (int)(bca->tandemQ * (double)abs(l) / l_run + .499) : 1000;
  	return q < qh? q : qh;
  }
  
  static inline int est_indelreg(int pos, const char *ref, int l, char *ins4)
  {
  	int i, j, max = 0, max_i = pos, score = 0;
  	l = abs(l);
  	for (i = pos + 1, j = 0; ref[i]; ++i, ++j) {
  		if (ins4) score += (toupper(ref[i]) != "ACGTN"[(int)ins4[j%l]])? -10 : 1;
  		else score += (toupper(ref[i]) != toupper(ref[pos+1+j%l]))? -10 : 1;
  		if (score < 0) break;
  		if (max < score) max = score, max_i = i;
  	}
  	return max_i - pos;
  }
  
  /*
   *  @n:  number of samples
   */
  int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref,
  					  const void *rghash)
  {
  	int i, s, j, k, t, n_types, *types, max_rd_len, left, right, max_ins, *score1, *score2, max_ref2;
  	int N, K, l_run, ref_type, n_alt;
  	char *inscns = 0, *ref2, *query, **ref_sample;
  	khash_t(rg) *hash = (khash_t(rg)*)rghash;
  	if (ref == 0 || bca == 0) return -1;
  	// mark filtered reads
  	if (rghash) {
  		N = 0;
  		for (s = N = 0; s < n; ++s) {
  			for (i = 0; i < n_plp[s]; ++i) {
  				bam_pileup1_t *p = plp[s] + i;
  				const uint8_t *rg = bam_aux_get(p->b, "RG");
  				p->aux = 1; // filtered by default
  				if (rg) {
  					khint_t k = kh_get(rg, hash, (const char*)(rg + 1));
  					if (k != kh_end(hash)) p->aux = 0, ++N; // not filtered
  				}
  			}
  		}
  		if (N == 0) return -1; // no reads left
  	}
  	// determine if there is a gap
  	for (s = N = 0; s < n; ++s) {
  		for (i = 0; i < n_plp[s]; ++i)
  			if (plp[s][i].indel != 0) break;
  		if (i < n_plp[s]) break;
  	}
  	if (s == n) return -1; // there is no indel at this position.
  	for (s = N = 0; s < n; ++s) N += n_plp[s]; // N is the total number of reads
  	{ // find out how many types of indels are present
          bca->max_support = bca->max_frac = 0;
  		int m, n_alt = 0, n_tot = 0, indel_support_ok = 0;
  		uint32_t *aux;
  		aux = calloc(N + 1, 4);
  		m = max_rd_len = 0;
  		aux[m++] = MINUS_CONST; // zero indel is always a type
  		for (s = 0; s < n; ++s) {
              int na = 0, nt = 0; 
  			for (i = 0; i < n_plp[s]; ++i) {
  				const bam_pileup1_t *p = plp[s] + i;
  				if (rghash == 0 || p->aux == 0) {
  					++nt;
  					if (p->indel != 0) {
  						++na;
  						aux[m++] = MINUS_CONST + p->indel;
  					}
  				}
  				j = bam_cigar2qlen(&p->b->core, bam1_cigar(p->b));
  				if (j > max_rd_len) max_rd_len = j;
  			}
              float frac = (float)na/nt;
              if ( !indel_support_ok && na >= bca->min_support && frac >= bca->min_frac )
                  indel_support_ok = 1;
              if ( na > bca->max_support && frac > 0 ) bca->max_support = na, bca->max_frac = frac;
              n_alt += na; 
              n_tot += nt;
  		}
          // To prevent long stretches of N's to be mistaken for indels (sometimes thousands of bases),
          //  check the number of N's in the sequence and skip places where half or more reference bases are Ns.
          int nN=0; for (i=pos; i-pos<max_rd_len && ref[i]; i++) if ( ref[i]=='N' ) nN++;
          if ( nN*2>i ) { free(aux); return -1; }
  
  		ks_introsort(uint32_t, m, aux);
  		// squeeze out identical types
  		for (i = 1, n_types = 1; i < m; ++i)
  			if (aux[i] != aux[i-1]) ++n_types;
          // Taking totals makes it hard to call rare indels
          if ( !bca->per_sample_flt )
              indel_support_ok = ( (float)n_alt / n_tot < bca->min_frac || n_alt < bca->min_support ) ? 0 : 1;
          if ( n_types == 1 || !indel_support_ok ) { // then skip
              free(aux); return -1;
          }
  		if (n_types >= 64) {
  			free(aux);
  			if (bam_verbose >= 2) 
  				fprintf(pysamerr, "[%s] excessive INDEL alleles at position %d. Skip the position.\n", __func__, pos + 1);
  			return -1;
  		}
  		types = (int*)calloc(n_types, sizeof(int));
  		t = 0;
  		types[t++] = aux[0] - MINUS_CONST; 
  		for (i = 1; i < m; ++i)
  			if (aux[i] != aux[i-1])
  				types[t++] = aux[i] - MINUS_CONST;
  		free(aux);
  		for (t = 0; t < n_types; ++t)
  			if (types[t] == 0) break;
  		ref_type = t; // the index of the reference type (0)
  	}
  	{ // calculate left and right boundary
  		left = pos > INDEL_WINDOW_SIZE? pos - INDEL_WINDOW_SIZE : 0;
  		right = pos + INDEL_WINDOW_SIZE;
  		if (types[0] < 0) right -= types[0];
  		// in case the alignments stand out the reference
  		for (i = pos; i < right; ++i)
  			if (ref[i] == 0) break;
  		right = i;
  	}
  	/* The following block fixes a long-existing flaw in the INDEL
  	 * calling model: the interference of nearby SNPs. However, it also
  	 * reduces the power because sometimes, substitutions caused by
  	 * indels are not distinguishable from true mutations. Multiple
  	 * sequence realignment helps to increase the power.
       *
       * Masks mismatches present in at least 70% of the reads with 'N'.
  	 */
  	{ // construct per-sample consensus
  		int L = right - left + 1, max_i, max2_i;
  		uint32_t *cns, max, max2;
  		char *ref0, *r;
  		ref_sample = calloc(n, sizeof(void*));
  		cns = calloc(L, 4);
  		ref0 = calloc(L, 1);
  		for (i = 0; i < right - left; ++i)
  			ref0[i] = bam_nt16_table[(int)ref[i+left]];
  		for (s = 0; s < n; ++s) {
  			r = ref_sample[s] = calloc(L, 1);
  			memset(cns, 0, sizeof(int) * L);
  			// collect ref and non-ref counts
  			for (i = 0; i < n_plp[s]; ++i) {
  				bam_pileup1_t *p = plp[s] + i;
  				bam1_t *b = p->b;
  				uint32_t *cigar = bam1_cigar(b);
  				uint8_t *seq = bam1_seq(b);
  				int x = b->core.pos, y = 0;
  				for (k = 0; k < b->core.n_cigar; ++k) {
  					int op = cigar[k]&0xf;
  					int j, l = cigar[k]>>4;
  					if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
  						for (j = 0; j < l; ++j)
  							if (x + j >= left && x + j < right)
  								cns[x+j-left] += (bam1_seqi(seq, y+j) == ref0[x+j-left])? 1 : 0x10000;
  						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;
  				}
  			}
  			// determine the consensus
  			for (i = 0; i < right - left; ++i) r[i] = ref0[i];
  			max = max2 = 0; max_i = max2_i = -1;
  			for (i = 0; i < right - left; ++i) {
  				if (cns[i]>>16 >= max>>16) max2 = max, max2_i = max_i, max = cns[i], max_i = i;
  				else if (cns[i]>>16 >= max2>>16) max2 = cns[i], max2_i = i;
  			}
  			if ((double)(max&0xffff) / ((max&0xffff) + (max>>16)) >= 0.7) max_i = -1;
  			if ((double)(max2&0xffff) / ((max2&0xffff) + (max2>>16)) >= 0.7) max2_i = -1;
  			if (max_i >= 0) r[max_i] = 15;
  			if (max2_i >= 0) r[max2_i] = 15;
  			//for (i = 0; i < right - left; ++i) fputc("=ACMGRSVTWYHKDBN"[(int)r[i]], pysamerr); fputc('\n', pysamerr);
  		}
  		free(ref0); free(cns);
  	}
  	{ // the length of the homopolymer run around the current position
  		int c = bam_nt16_table[(int)ref[pos + 1]];
  		if (c == 15) l_run = 1;
  		else {
  			for (i = pos + 2; ref[i]; ++i)
  				if (bam_nt16_table[(int)ref[i]] != c) break;
  			l_run = i;
  			for (i = pos; i >= 0; --i)
  				if (bam_nt16_table[(int)ref[i]] != c) break;
  			l_run -= i + 1;
  		}
  	}
  	// construct the consensus sequence
  	max_ins = types[n_types - 1];   // max_ins is at least 0
  	if (max_ins > 0) {
  		int *inscns_aux = calloc(5 * n_types * max_ins, sizeof(int));
  		// count the number of occurrences of each base at each position for each type of insertion
  		for (t = 0; t < n_types; ++t) {
  			if (types[t] > 0) {
  				for (s = 0; s < n; ++s) {
  					for (i = 0; i < n_plp[s]; ++i) {
  						bam_pileup1_t *p = plp[s] + i;
  						if (p->indel == types[t]) {
  							uint8_t *seq = bam1_seq(p->b);
  							for (k = 1; k <= p->indel; ++k) {
  								int c = bam_nt16_nt4_table[bam1_seqi(seq, p->qpos + k)];
                                  assert(c<5);
  								++inscns_aux[(t*max_ins+(k-1))*5 + c];
  							}
  						}
  					}
  				}
  			}
  		}
  		// use the majority rule to construct the consensus
  		inscns = calloc(n_types * max_ins, 1);
  		for (t = 0; t < n_types; ++t) {
  			for (j = 0; j < types[t]; ++j) {
  				int max = 0, max_k = -1, *ia = &inscns_aux[(t*max_ins+j)*5];
  				for (k = 0; k < 5; ++k)
  					if (ia[k] > max)
  						max = ia[k], max_k = k;
  				inscns[t*max_ins + j] = max? max_k : 4;
                  if ( max_k==4 ) { types[t] = 0; break; } // discard insertions which contain N's
  			}
  		}
  		free(inscns_aux);
  	}
  	// compute the likelihood given each type of indel for each read
  	max_ref2 = right - left + 2 + 2 * (max_ins > -types[0]? max_ins : -types[0]);
  	ref2  = calloc(max_ref2, 1);
  	query = calloc(right - left + max_rd_len + max_ins + 2, 1);
  	score1 = calloc(N * n_types, sizeof(int));
  	score2 = calloc(N * n_types, sizeof(int));
  	bca->indelreg = 0;
  	for (t = 0; t < n_types; ++t) {
  		int l, ir;
  		kpa_par_t apf1 = { 1e-4, 1e-2, 10 }, apf2 = { 1e-6, 1e-3, 10 };
  		apf1.bw = apf2.bw = abs(types[t]) + 3;
  		// compute indelreg
  		if (types[t] == 0) ir = 0;
  		else if (types[t] > 0) ir = est_indelreg(pos, ref, types[t], &inscns[t*max_ins]);
  		else ir = est_indelreg(pos, ref, -types[t], 0);
  		if (ir > bca->indelreg) bca->indelreg = ir;
  //		fprintf(pysamerr, "%d, %d, %d\n", pos, types[t], ir);
  		// realignment
  		for (s = K = 0; s < n; ++s) {
  			// write ref2
  			for (k = 0, j = left; j <= pos; ++j)
  				ref2[k++] = bam_nt16_nt4_table[(int)ref_sample[s][j-left]];
  			if (types[t] <= 0) j += -types[t];
  			else for (l = 0; l < types[t]; ++l)
  					 ref2[k++] = inscns[t*max_ins + l];
  			for (; j < right && ref[j]; ++j)
  				ref2[k++] = bam_nt16_nt4_table[(int)ref_sample[s][j-left]];
  			for (; k < max_ref2; ++k) ref2[k] = 4;
  			if (j < right) right = j;
  			// align each read to ref2
  			for (i = 0; i < n_plp[s]; ++i, ++K) {
  				bam_pileup1_t *p = plp[s] + i;
  				int qbeg, qend, tbeg, tend, sc, kk;
  				uint8_t *seq = bam1_seq(p->b);
  				uint32_t *cigar = bam1_cigar(p->b);
  				if (p->b->core.flag&4) continue; // unmapped reads
  				// FIXME: the following loop should be better moved outside; nonetheless, realignment should be much slower anyway.
  				for (kk = 0; kk < p->b->core.n_cigar; ++kk)
  					if ((cigar[kk]&BAM_CIGAR_MASK) == BAM_CREF_SKIP) break;
  				if (kk < p->b->core.n_cigar) continue;
  				// FIXME: the following skips soft clips, but using them may be more sensitive.
  				// determine the start and end of sequences for alignment
  				qbeg = tpos2qpos(&p->b->core, bam1_cigar(p->b), left,  0, &tbeg);
  				qend = tpos2qpos(&p->b->core, bam1_cigar(p->b), right, 1, &tend);
  				if (types[t] < 0) {
  					int l = -types[t];
  					tbeg = tbeg - l > left?  tbeg - l : left;
  				}
  				// write the query sequence
  				for (l = qbeg; l < qend; ++l)
  					query[l - qbeg] = bam_nt16_nt4_table[bam1_seqi(seq, l)];
  				{ // do realignment; this is the bottleneck
  					const uint8_t *qual = bam1_qual(p->b), *bq;
  					uint8_t *qq;
  					qq = calloc(qend - qbeg, 1);
  					bq = (uint8_t*)bam_aux_get(p->b, "ZQ");
  					if (bq) ++bq; // skip type
  					for (l = qbeg; l < qend; ++l) {
  						qq[l - qbeg] = bq? qual[l] + (bq[l] - 64) : qual[l];
  						if (qq[l - qbeg] > 30) qq[l - qbeg] = 30;
  						if (qq[l - qbeg] < 7) qq[l - qbeg] = 7;
  					}
  					sc = kpa_glocal((uint8_t*)ref2 + tbeg - left, tend - tbeg + abs(types[t]),
  									(uint8_t*)query, qend - qbeg, qq, &apf1, 0, 0);
  					l = (int)(100. * sc / (qend - qbeg) + .499); // used for adjusting indelQ below
  					if (l > 255) l = 255;
  					score1[K*n_types + t] = score2[K*n_types + t] = sc<<8 | l;
  					if (sc > 5) {
  						sc = kpa_glocal((uint8_t*)ref2 + tbeg - left, tend - tbeg + abs(types[t]),
  										(uint8_t*)query, qend - qbeg, qq, &apf2, 0, 0);
  						l = (int)(100. * sc / (qend - qbeg) + .499);
  						if (l > 255) l = 255;
  						score2[K*n_types + t] = sc<<8 | l;
  					}
  					free(qq);
  				}
  /*
  				for (l = 0; l < tend - tbeg + abs(types[t]); ++l)
  					fputc("ACGTN"[(int)ref2[tbeg-left+l]], pysamerr);
  				fputc('\n', pysamerr);
  				for (l = 0; l < qend - qbeg; ++l) fputc("ACGTN"[(int)query[l]], pysamerr);
  				fputc('\n', pysamerr);
  				fprintf(pysamerr, "pos=%d type=%d read=%d:%d name=%s qbeg=%d tbeg=%d score=%d\n", pos, types[t], s, i, bam1_qname(p->b), qbeg, tbeg, sc);
  */
  			}
  		}
  	}
  	free(ref2); free(query);
  	{ // compute indelQ
  		int *sc, tmp, *sumq;
  		sc   = alloca(n_types * sizeof(int));
  		sumq = alloca(n_types * sizeof(int));
  		memset(sumq, 0, sizeof(int) * n_types);
  		for (s = K = 0; s < n; ++s) {
  			for (i = 0; i < n_plp[s]; ++i, ++K) {
  				bam_pileup1_t *p = plp[s] + i;
  				int *sct = &score1[K*n_types], indelQ1, indelQ2, seqQ, indelQ;
  				for (t = 0; t < n_types; ++t) sc[t] = sct[t]<<6 | t;
  				for (t = 1; t < n_types; ++t) // insertion sort
  					for (j = t; j > 0 && sc[j] < sc[j-1]; --j)
  						tmp = sc[j], sc[j] = sc[j-1], sc[j-1] = tmp;
  				/* errmod_cal() assumes that if the call is wrong, the
  				 * likelihoods of other events are equal. This is about
  				 * right for substitutions, but is not desired for
  				 * indels. To reuse errmod_cal(), I have to make
  				 * compromise for multi-allelic indels.
  				 */
  				if ((sc[0]&0x3f) == ref_type) {
  					indelQ1 = (sc[1]>>14) - (sc[0]>>14);
  					seqQ = est_seqQ(bca, types[sc[1]&0x3f], l_run);
  				} else {
  					for (t = 0; t < n_types; ++t) // look for the reference type
  						if ((sc[t]&0x3f) == ref_type) break;
  					indelQ1 = (sc[t]>>14) - (sc[0]>>14);
  					seqQ = est_seqQ(bca, types[sc[0]&0x3f], l_run);
  				}
  				tmp = sc[0]>>6 & 0xff;
  				indelQ1 = tmp > 111? 0 : (int)((1. - tmp/111.) * indelQ1 + .499); // reduce indelQ
  				sct = &score2[K*n_types];
  				for (t = 0; t < n_types; ++t) sc[t] = sct[t]<<6 | t;
  				for (t = 1; t < n_types; ++t) // insertion sort
  					for (j = t; j > 0 && sc[j] < sc[j-1]; --j)
  						tmp = sc[j], sc[j] = sc[j-1], sc[j-1] = tmp;
  				if ((sc[0]&0x3f) == ref_type) {
  					indelQ2 = (sc[1]>>14) - (sc[0]>>14);
  				} else {
  					for (t = 0; t < n_types; ++t) // look for the reference type
  						if ((sc[t]&0x3f) == ref_type) break;
  					indelQ2 = (sc[t]>>14) - (sc[0]>>14);
  				}
  				tmp = sc[0]>>6 & 0xff;
  				indelQ2 = tmp > 111? 0 : (int)((1. - tmp/111.) * indelQ2 + .499);
  				// pick the smaller between indelQ1 and indelQ2
  				indelQ = indelQ1 < indelQ2? indelQ1 : indelQ2;
  				if (indelQ > 255) indelQ = 255;
  				if (seqQ > 255) seqQ = 255;
  				p->aux = (sc[0]&0x3f)<<16 | seqQ<<8 | indelQ; // use 22 bits in total
  				sumq[sc[0]&0x3f] += indelQ < seqQ? indelQ : seqQ;
  //				fprintf(pysamerr, "pos=%d read=%d:%d name=%s call=%d indelQ=%d seqQ=%d\n", pos, s, i, bam1_qname(p->b), types[sc[0]&0x3f], indelQ, seqQ);
  			}
  		}
  		// determine bca->indel_types[] and bca->inscns
  		bca->maxins = max_ins;
  		bca->inscns = realloc(bca->inscns, bca->maxins * 4);
  		for (t = 0; t < n_types; ++t)
  			sumq[t] = sumq[t]<<6 | t;
  		for (t = 1; t < n_types; ++t) // insertion sort
  			for (j = t; j > 0 && sumq[j] > sumq[j-1]; --j)
  				tmp = sumq[j], sumq[j] = sumq[j-1], sumq[j-1] = tmp;
  		for (t = 0; t < n_types; ++t) // look for the reference type
  			if ((sumq[t]&0x3f) == ref_type) break;
  		if (t) { // then move the reference type to the first
  			tmp = sumq[t];
  			for (; t > 0; --t) sumq[t] = sumq[t-1];
  			sumq[0] = tmp;
  		}
  		for (t = 0; t < 4; ++t) bca->indel_types[t] = B2B_INDEL_NULL;
  		for (t = 0; t < 4 && t < n_types; ++t) {
  			bca->indel_types[t] = types[sumq[t]&0x3f];
  			memcpy(&bca->inscns[t * bca->maxins], &inscns[(sumq[t]&0x3f) * max_ins], bca->maxins);
  		}
  		// update p->aux
  		for (s = n_alt = 0; s < n; ++s) {
  			for (i = 0; i < n_plp[s]; ++i) {
  				bam_pileup1_t *p = plp[s] + i;
  				int x = types[p->aux>>16&0x3f];
  				for (j = 0; j < 4; ++j)
  					if (x == bca->indel_types[j]) break;
  				p->aux = j<<16 | (j == 4? 0 : (p->aux&0xffff));
  				if ((p->aux>>16&0x3f) > 0) ++n_alt;
  //				fprintf(pysamerr, "X pos=%d read=%d:%d name=%s call=%d type=%d q=%d seqQ=%d\n", pos, s, i, bam1_qname(p->b), p->aux>>16&63, bca->indel_types[p->aux>>16&63], p->aux&0xff, p->aux>>8&0xff);
  			}
  		}		
  	}
  	free(score1); free(score2);
  	// free
  	for (i = 0; i < n; ++i) free(ref_sample[i]);
  	free(ref_sample);
  	free(types); free(inscns);
  	return n_alt > 0? 0 : -1;
  }
  