--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyPRADA_1.2/tools/samtools-0.1.16/phase.c	Thu Feb 20 00:44:58 2014 -0500
@@ -0,0 +1,687 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <stdint.h>
+#include <math.h>
+#include <zlib.h>
+#include "bam.h"
+#include "errmod.h"
+
+#include "kseq.h"
+KSTREAM_INIT(gzFile, gzread, 16384)
+
+#define MAX_VARS 256
+#define FLIP_PENALTY 2
+#define FLIP_THRES 4
+#define MASK_THRES 3
+
+#define FLAG_FIX_CHIMERA 0x1
+#define FLAG_LIST_EXCL   0x4
+#define FLAG_DROP_AMBI   0x8
+
+typedef struct {
+	// configurations, initialized in the main function
+	int flag, k, min_baseQ, min_varLOD, max_depth;
+	// other global variables
+	int vpos_shift;
+	bamFile fp;
+	char *pre;
+	bamFile out[3];
+	// alignment queue
+	int n, m;
+	bam1_t **b;
+} phaseg_t;
+
+typedef struct {
+	int8_t seq[MAX_VARS]; // TODO: change to dynamic memory allocation!
+	int vpos, beg, end;
+	uint32_t vlen:16, single:1, flip:1, phase:1, phased:1, ambig:1;
+	uint32_t in:16, out:16; // in-phase and out-phase
+} frag_t, *frag_p;
+
+#define rseq_lt(a,b) ((a)->vpos < (b)->vpos)
+
+#include "khash.h"
+KHASH_SET_INIT_INT64(set64)
+KHASH_MAP_INIT_INT64(64, frag_t)
+
+typedef khash_t(64) nseq_t;
+
+#include "ksort.h"
+KSORT_INIT(rseq, frag_p, rseq_lt)
+
+static char nt16_nt4_table[] = { 4, 0, 1, 4, 2, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4 };
+
+static inline uint64_t X31_hash_string(const char *s)
+{
+	uint64_t h = *s;
+	if (h) for (++s ; *s; ++s) h = (h << 5) - h + *s;
+	return h;
+}
+
+static void count1(int l, const uint8_t *seq, int *cnt)
+{
+	int i, j, n_ambi;
+	uint32_t z, x;
+	if (seq[l-1] == 0) return; // do nothing is the last base is ambiguous
+	for (i = n_ambi = 0; i < l; ++i) // collect ambiguous bases
+		if (seq[i] == 0) ++n_ambi;
+	if (l - n_ambi <= 1) return; // only one SNP
+	for (x = 0; x < 1u<<n_ambi; ++x) { // count
+		for (i = j = 0, z = 0; i < l; ++i) {
+			int c;
+			if (seq[i]) c = seq[i] - 1;
+			else {
+				c = x>>j&1;
+				++j;
+			}
+			z = z<<1 | c;
+		}
+		++cnt[z];
+	}
+}
+
+static int **count_all(int l, int vpos, nseq_t *hash)
+{
+	khint_t k;
+	int i, j, **cnt;
+	uint8_t *seq;
+	seq = calloc(l, 1);
+	cnt = calloc(vpos, sizeof(void*));
+	for (i = 0; i < vpos; ++i) cnt[i] = calloc(1<<l, sizeof(int));
+	for (k = 0; k < kh_end(hash); ++k) {
+		if (kh_exist(hash, k)) {
+			frag_t *f = &kh_val(hash, k);
+			if (f->vpos >= vpos || f->single) continue; // out of region; or singleton
+			if (f->vlen == 1) { // such reads should be flagged as deleted previously if everything is right
+				f->single = 1;
+				continue;
+			}
+			for (j = 1; j < f->vlen; ++j) {
+				for (i = 0; i < l; ++i)
+					seq[i] = j < l - 1 - i? 0 : f->seq[j - (l - 1 - i)];
+				count1(l, seq, cnt[f->vpos + j]);
+			}
+		}
+	}
+	free(seq);
+	return cnt;
+}
+
+// phasing
+static int8_t *dynaprog(int l, int vpos, int **w)
+{
+	int *f[2], *curr, *prev, max, i;
+	int8_t **b, *h = 0;
+	uint32_t x, z = 1u<<(l-1), mask = (1u<<l) - 1;
+	f[0] = calloc(z, sizeof(int));
+	f[1] = calloc(z, sizeof(int));
+	b = calloc(vpos, sizeof(void*));
+	prev = f[0]; curr = f[1];
+	// fill the backtrack matrix
+	for (i = 0; i < vpos; ++i) {
+		int *wi = w[i], *tmp;
+		int8_t *bi;
+		bi = b[i] = calloc(z, 1);
+		/* In the following, x is the current state, which is the
+		 * lexicographically smaller local haplotype. xc is the complement of
+		 * x, or the larger local haplotype; y0 and y1 are the two predecessors
+		 * of x. */
+		for (x = 0; x < z; ++x) { // x0 is the smaller 
+			uint32_t y0, y1, xc;
+			int c0, c1;
+			xc = ~x&mask; y0 = x>>1; y1 = xc>>1;
+			c0 = prev[y0] + wi[x] + wi[xc];
+			c1 = prev[y1] + wi[x] + wi[xc];
+			if (c0 > c1) bi[x] = 0, curr[x] = c0;
+			else bi[x] = 1, curr[x] = c1;
+		}
+		tmp = prev; prev = curr; curr = tmp; // swap
+	}
+	{ // backtrack
+		uint32_t max_x = 0;
+		int which = 0;
+		h = calloc(vpos, 1);
+		for (x = 0, max = 0, max_x = 0; x < z; ++x)
+			if (prev[x] > max) max = prev[x], max_x = x;
+		for (i = vpos - 1, x = max_x; i >= 0; --i) {
+			h[i] = which? (~x&1) : (x&1);
+			which = b[i][x]? !which : which;
+			x = b[i][x]? (~x&mask)>>1 : x>>1;
+		}
+	}
+	// free
+	for (i = 0; i < vpos; ++i) free(b[i]);
+	free(f[0]); free(f[1]); free(b);
+	return h;
+}
+
+// phase each fragment
+static uint64_t *fragphase(int vpos, const int8_t *path, nseq_t *hash, int flip)
+{
+	khint_t k;
+	uint64_t *pcnt;
+	uint32_t *left, *rght, max;
+	left = rght = 0; max = 0;
+	pcnt = calloc(vpos, 8);
+	for (k = 0; k < kh_end(hash); ++k) {
+		if (kh_exist(hash, k)) {
+			int i, c[2];
+			frag_t *f = &kh_val(hash, k);
+			if (f->vpos >= vpos) continue;
+			// get the phase
+			c[0] = c[1] = 0;
+			for (i = 0; i < f->vlen; ++i) {
+				if (f->seq[i] == 0) continue;
+				++c[f->seq[i] == path[f->vpos + i] + 1? 0 : 1];
+			}
+			f->phase = c[0] > c[1]? 0 : 1;
+			f->in = c[f->phase]; f->out = c[1 - f->phase];
+			f->phased = f->in == f->out? 0 : 1;
+			f->ambig = (f->in && f->out && f->out < 3 && f->in <= f->out + 1)? 1 : 0;
+			// fix chimera
+			f->flip = 0;
+			if (flip && c[0] >= 3 && c[1] >= 3) {
+				int sum[2], m, mi, md;
+				if (f->vlen > max) { // enlarge the array
+					max = f->vlen;
+					kroundup32(max);
+					left = realloc(left, max * 4);
+					rght = realloc(rght, max * 4);
+				}
+				for (i = 0, sum[0] = sum[1] = 0; i < f->vlen; ++i) { // get left counts
+					if (f->seq[i]) {
+						int c = f->phase? 2 - f->seq[i] : f->seq[i] - 1;
+						++sum[c == path[f->vpos + i]? 0 : 1];
+					}
+					left[i] = sum[1]<<16 | sum[0];
+				}
+				for (i = f->vlen - 1, sum[0] = sum[1] = 0; i >= 0; --i) { // get right counts
+					if (f->seq[i]) {
+						int c = f->phase? 2 - f->seq[i] : f->seq[i] - 1;
+						++sum[c == path[f->vpos + i]? 0 : 1];
+					}
+					rght[i] = sum[1]<<16 | sum[0];
+				}
+				// find the best flip point
+				for (i = m = 0, mi = -1, md = -1; i < f->vlen - 1; ++i) {
+					int a[2];
+					a[0] = (left[i]&0xffff) + (rght[i+1]>>16&0xffff) - (rght[i+1]&0xffff) * FLIP_PENALTY;
+					a[1] = (left[i]>>16&0xffff) + (rght[i+1]&0xffff) - (rght[i+1]>>16&0xffff) * FLIP_PENALTY;
+					if (a[0] > a[1]) {
+						if (a[0] > m) m = a[0], md = 0, mi = i;
+					} else {
+						if (a[1] > m) m = a[1], md = 1, mi = i;
+					}
+				}
+				if (m - c[0] >= FLIP_THRES && m - c[1] >= FLIP_THRES) { // then flip
+					f->flip = 1;
+					if (md == 0) { // flip the tail
+						for (i = mi + 1; i < f->vlen; ++i)
+							if (f->seq[i] == 1) f->seq[i] = 2;
+							else if (f->seq[i] == 2) f->seq[i] = 1;
+					} else { // flip the head
+						for (i = 0; i <= mi; ++i)
+							if (f->seq[i] == 1) f->seq[i] = 2;
+							else if (f->seq[i] == 2) f->seq[i] = 1;
+					}
+				}
+			}
+			// update pcnt[]
+			if (!f->single) {
+				for (i = 0; i < f->vlen; ++i) {
+					int c;
+					if (f->seq[i] == 0) continue;
+					c = f->phase? 2 - f->seq[i] : f->seq[i] - 1;
+					if (c == path[f->vpos + i]) {
+						if (f->phase == 0) ++pcnt[f->vpos + i];
+						else pcnt[f->vpos + i] += 1ull<<32;
+					} else {
+						if (f->phase == 0) pcnt[f->vpos + i] += 1<<16;
+						else pcnt[f->vpos + i] += 1ull<<48;
+					}
+				}
+			}
+		}
+	}
+	free(left); free(rght);
+	return pcnt;
+}
+
+static uint64_t *genmask(int vpos, const uint64_t *pcnt, int *_n)
+{
+	int i, max = 0, max_i = -1, m = 0, n = 0, beg = 0, score = 0;
+	uint64_t *list = 0;
+	for (i = 0; i < vpos; ++i) {
+		uint64_t x = pcnt[i];
+		int c[4], pre = score, s;
+		c[0] = x&0xffff; c[1] = x>>16&0xffff; c[2] = x>>32&0xffff; c[3] = x>>48&0xffff;
+		s = (c[1] + c[3] == 0)? -(c[0] + c[2]) : (c[1] + c[3] - 1);
+		if (c[3] > c[2]) s += c[3] - c[2];
+		if (c[1] > c[0]) s += c[1] - c[0];
+		score += s;
+		if (score < 0) score = 0;
+		if (pre == 0 && score > 0) beg = i; // change from zero to non-zero
+		if ((i == vpos - 1 || score == 0) && max >= MASK_THRES) {
+			if (n == m) {
+				m = m? m<<1 : 4;
+				list = realloc(list, m * 8);
+			}
+			list[n++] = (uint64_t)beg<<32 | max_i;
+			i = max_i; // reset i to max_i
+			score = 0;
+		} else if (score > max) max = score, max_i = i;
+		if (score == 0) max = 0;
+	}
+	*_n = n;
+	return list;
+}
+
+// trim heading and tailing ambiguous bases; mark deleted and remove sequence
+static int clean_seqs(int vpos, nseq_t *hash)
+{
+	khint_t k;
+	int ret = 0;
+	for (k = 0; k < kh_end(hash); ++k) {
+		if (kh_exist(hash, k)) {
+			frag_t *f = &kh_val(hash, k);
+			int beg, end, i;
+			if (f->vpos >= vpos) {
+				ret = 1;
+				continue;
+			}
+			for (i = 0; i < f->vlen; ++i)
+				if (f->seq[i] != 0) break;
+			beg = i;
+			for (i = f->vlen - 1; i >= 0; --i)
+				if (f->seq[i] != 0) break;
+			end = i + 1;
+			if (end - beg <= 0) kh_del(64, hash, k);
+			else {
+				if (beg != 0) memmove(f->seq, f->seq + beg, end - beg);
+				f->vpos += beg; f->vlen = end - beg;
+				f->single = f->vlen == 1? 1 : 0;
+			}
+		}
+	}
+	return ret;
+}
+
+static void dump_aln(phaseg_t *g, int min_pos, const nseq_t *hash)
+{
+	int i, is_flip, drop_ambi;
+	drop_ambi = g->flag & FLAG_DROP_AMBI;
+	is_flip = (drand48() < 0.5);
+	for (i = 0; i < g->n; ++i) {
+		int end, which;
+		uint64_t key;
+		khint_t k;
+		bam1_t *b = g->b[i];
+		key = X31_hash_string(bam1_qname(b));
+		end = bam_calend(&b->core, bam1_cigar(b));
+		if (end > min_pos) break;
+		k = kh_get(64, hash, key);
+		if (k == kh_end(hash)) which = 3;
+		else {
+			frag_t *f = &kh_val(hash, k);
+			if (f->ambig) which = drop_ambi? 2 : 3;
+			else if (f->phased && f->flip) which = 2;
+			else if (f->phased == 0) which = 3;
+			else { // phased and not flipped
+				char c = 'Y';
+				which = f->phase;
+				bam_aux_append(b, "ZP", 'A', 1, (uint8_t*)&c);
+			}
+			if (which < 2 && is_flip) which = 1 - which; // increase the randomness
+		}
+		if (which == 3) which = (drand48() < 0.5);
+		bam_write1(g->out[which], b);
+		bam_destroy1(b);
+		g->b[i] = 0;
+	}
+	memmove(g->b, g->b + i, (g->n - i) * sizeof(void*));
+	g->n -= i;
+}
+
+static int phase(phaseg_t *g, const char *chr, int vpos, uint64_t *cns, nseq_t *hash)
+{
+	int i, j, n_seqs = kh_size(hash), n_masked = 0, min_pos;
+	khint_t k;
+	frag_t **seqs;
+	int8_t *path, *sitemask;
+	uint64_t *pcnt, *regmask;
+
+	if (vpos == 0) return 0;
+	i = clean_seqs(vpos, hash); // i is true if hash has an element with its vpos >= vpos
+	min_pos = i? cns[vpos]>>32 : 0x7fffffff;
+	if (vpos == 1) {
+		printf("PS\t%s\t%d\t%d\n", chr, (int)(cns[0]>>32) + 1, (int)(cns[0]>>32) + 1);
+		printf("M0\t%s\t%d\t%d\t%c\t%c\t%d\t0\t0\t0\t0\n//\n", chr, (int)(cns[0]>>32) + 1, (int)(cns[0]>>32) + 1,
+			"ACGTX"[cns[0]&3], "ACGTX"[cns[0]>>16&3], g->vpos_shift + 1);
+		for (k = 0; k < kh_end(hash); ++k) {
+			if (kh_exist(hash, k)) {
+				frag_t *f = &kh_val(hash, k);
+				if (f->vpos) continue;
+				f->flip = 0;
+				if (f->seq[0] == 0) f->phased = 0;
+				else f->phased = 1, f->phase = f->seq[0] - 1;
+			}
+		}
+		dump_aln(g, min_pos, hash);
+		++g->vpos_shift;
+		return 1;
+	}
+	{ // phase
+		int **cnt;
+		uint64_t *mask;
+		printf("PS\t%s\t%d\t%d\n", chr, (int)(cns[0]>>32) + 1, (int)(cns[vpos-1]>>32) + 1);
+		sitemask = calloc(vpos, 1);
+		cnt = count_all(g->k, vpos, hash);
+		path = dynaprog(g->k, vpos, cnt);
+		for (i = 0; i < vpos; ++i) free(cnt[i]);
+		free(cnt);
+		pcnt = fragphase(vpos, path, hash, 0); // do not fix chimeras when masking
+		mask = genmask(vpos, pcnt, &n_masked);
+		regmask = calloc(n_masked, 8);
+		for (i = 0; i < n_masked; ++i) {
+			regmask[i] = cns[mask[i]>>32]>>32<<32 | cns[(uint32_t)mask[i]]>>32;
+			for (j = mask[i]>>32; j <= (int32_t)mask[i]; ++j)
+				sitemask[j] = 1;
+		}
+		free(mask);
+		if (g->flag & FLAG_FIX_CHIMERA) {
+			free(pcnt);
+			pcnt = fragphase(vpos, path, hash, 1);
+		}
+	}
+	for (i = 0; i < n_masked; ++i)
+		printf("FL\t%s\t%d\t%d\n", chr, (int)(regmask[i]>>32) + 1, (int)regmask[i] + 1);
+	for (i = 0; i < vpos; ++i) {
+		uint64_t x = pcnt[i];
+		int8_t c[2];
+		c[0] = (cns[i]&0xffff)>>2 == 0? 4 : (cns[i]&3);
+		c[1] = (cns[i]>>16&0xffff)>>2 == 0? 4 : (cns[i]>>16&3);
+		printf("M%d\t%s\t%d\t%d\t%c\t%c\t%d\t%d\t%d\t%d\t%d\n", sitemask[i]+1, chr, (int)(cns[0]>>32) + 1, (int)(cns[i]>>32) + 1, "ACGTX"[c[path[i]]], "ACGTX"[c[1-path[i]]],
+			i + g->vpos_shift + 1, (int)(x&0xffff), (int)(x>>16&0xffff), (int)(x>>32&0xffff), (int)(x>>48&0xffff));
+	}
+	free(path); free(pcnt); free(regmask); free(sitemask);
+	seqs = calloc(n_seqs, sizeof(void*));
+	for (k = 0, i = 0; k < kh_end(hash); ++k) 
+		if (kh_exist(hash, k) && kh_val(hash, k).vpos < vpos && !kh_val(hash, k).single)
+			seqs[i++] = &kh_val(hash, k);
+	n_seqs = i;
+	ks_introsort_rseq(n_seqs, seqs);
+	for (i = 0; i < n_seqs; ++i) {
+		frag_t *f = seqs[i];
+		printf("EV\t0\t%s\t%d\t40\t%dM\t*\t0\t0\t", chr, f->vpos + 1 + g->vpos_shift, f->vlen);
+		for (j = 0; j < f->vlen; ++j) {
+			uint32_t c = cns[f->vpos + j];
+			if (f->seq[j] == 0) putchar('N');
+			else putchar("ACGT"[f->seq[j] == 1? (c&3) : (c>>16&3)]);
+		}
+		printf("\t*\tYP:i:%d\tYF:i:%d\tYI:i:%d\tYO:i:%d\tYS:i:%d\n", f->phase, f->flip, f->in, f->out, f->beg+1);
+	}
+	free(seqs);
+	printf("//\n");
+	fflush(stdout);
+	g->vpos_shift += vpos;
+	dump_aln(g, min_pos, hash);
+	return vpos;
+}
+
+static void update_vpos(int vpos, nseq_t *hash)
+{
+	khint_t k;
+	for (k = 0; k < kh_end(hash); ++k) {
+		if (kh_exist(hash, k)) {
+			frag_t *f = &kh_val(hash, k);
+			if (f->vpos < vpos) kh_del(64, hash, k); // TODO: if frag_t::seq is allocated dynamically, free it
+			else f->vpos -= vpos;
+		}
+	}
+}
+
+static nseq_t *shrink_hash(nseq_t *hash) // TODO: to implement
+{
+	return hash;
+}
+
+static int readaln(void *data, bam1_t *b)
+{
+	phaseg_t *g = (phaseg_t*)data;
+	int ret;
+	ret = bam_read1(g->fp, b);
+	if (ret < 0) return ret;
+	if (!(b->core.flag & (BAM_FUNMAP|BAM_FSECONDARY|BAM_FQCFAIL|BAM_FDUP)) && g->pre) {
+		if (g->n == g->m) {
+			g->m = g->m? g->m<<1 : 16;
+			g->b = realloc(g->b, g->m * sizeof(void*));
+		}
+		g->b[g->n++] = bam_dup1(b);
+	}
+	return ret;
+}
+
+static khash_t(set64) *loadpos(const char *fn, bam_header_t *h)
+{
+	gzFile fp;
+	kstream_t *ks;
+	int ret, dret;
+	kstring_t *str;
+	khash_t(set64) *hash;
+
+	hash = kh_init(set64);
+	str = calloc(1, sizeof(kstring_t));
+	fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
+	ks = ks_init(fp);
+	while (ks_getuntil(ks, 0, str, &dret) >= 0) {
+		int tid = bam_get_tid(h, str->s);
+		if (tid >= 0 && dret != '\n') {
+			if (ks_getuntil(ks, 0, str, &dret) >= 0) {
+				uint64_t x = (uint64_t)tid<<32 | (atoi(str->s) - 1);
+				kh_put(set64, hash, x, &ret);
+			} else break;
+		}
+		if (dret != '\n') while ((dret = ks_getc(ks)) > 0 && dret != '\n');
+		if (dret < 0) break;
+	}
+	ks_destroy(ks);
+	gzclose(fp);
+	free(str->s); free(str);
+	return hash;
+}
+
+static int gl2cns(float q[16])
+{
+	int i, j, min_ij;
+	float min, min2;
+	min = min2 = 1e30; min_ij = -1;
+	for (i = 0; i < 4; ++i) {
+		for (j = i; j < 4; ++j) {
+			if (q[i<<2|j] < min) min_ij = i<<2|j, min2 = min, min = q[i<<2|j];
+			else if (q[i<<2|j] < min2) min2 = q[i<<2|j];
+		}
+	}
+	return (min_ij>>2&3) == (min_ij&3)? 0 : 1<<18 | (min_ij>>2&3)<<16 | (min_ij&3) | (int)(min2 - min + .499) << 2;
+}
+
+int main_phase(int argc, char *argv[])
+{
+	extern void bam_init_header_hash(bam_header_t *header);
+	int c, tid, pos, vpos = 0, n, lasttid = -1, max_vpos = 0;
+	const bam_pileup1_t *plp;
+	bam_plp_t iter;
+	bam_header_t *h;
+	nseq_t *seqs;
+	uint64_t *cns = 0;
+	phaseg_t g;
+	char *fn_list = 0;
+	khash_t(set64) *set = 0;
+	errmod_t *em;
+	uint16_t *bases;
+
+	memset(&g, 0, sizeof(phaseg_t));
+	g.flag = FLAG_FIX_CHIMERA;
+	g.min_varLOD = 37; g.k = 13; g.min_baseQ = 13; g.max_depth = 256;
+	while ((c = getopt(argc, argv, "Q:eFq:k:b:l:D:A:")) >= 0) {
+		switch (c) {
+			case 'D': g.max_depth = atoi(optarg); break;
+			case 'q': g.min_varLOD = atoi(optarg); break;
+			case 'Q': g.min_baseQ = atoi(optarg); break;
+			case 'k': g.k = atoi(optarg); break;
+			case 'F': g.flag &= ~FLAG_FIX_CHIMERA; break;
+			case 'e': g.flag |= FLAG_LIST_EXCL; break;
+			case 'A': g.flag |= FLAG_DROP_AMBI; break;
+			case 'b': g.pre = strdup(optarg); break;
+			case 'l': fn_list = strdup(optarg); break;
+		}
+	}
+	if (argc == optind) {
+		fprintf(stderr, "\n");
+		fprintf(stderr, "Usage:   samtools phase [options] <in.bam>\n\n");
+		fprintf(stderr, "Options: -k INT    block length [%d]\n", g.k);
+		fprintf(stderr, "         -b STR    prefix of BAMs to output [null]\n");
+		fprintf(stderr, "         -q INT    min het phred-LOD [%d]\n", g.min_varLOD);
+		fprintf(stderr, "         -Q INT    min base quality in het calling [%d]\n", g.min_baseQ);
+		fprintf(stderr, "         -D INT    max read depth [%d]\n", g.max_depth);
+//		fprintf(stderr, "         -l FILE   list of sites to phase [null]\n");
+		fprintf(stderr, "         -F        do not attempt to fix chimeras\n");
+		fprintf(stderr, "         -A        drop reads with ambiguous phase\n");
+//		fprintf(stderr, "         -e        do not discover SNPs (effective with -l)\n");
+		fprintf(stderr, "\n");
+		return 1;
+	}
+	g.fp = strcmp(argv[optind], "-")? bam_open(argv[optind], "r") : bam_dopen(fileno(stdin), "r");
+	h = bam_header_read(g.fp);
+	if (fn_list) { // read the list of sites to phase
+		bam_init_header_hash(h);
+		set = loadpos(fn_list, h);
+		free(fn_list);
+	} else g.flag &= ~FLAG_LIST_EXCL;
+	if (g.pre) { // open BAMs to write
+		char *s = malloc(strlen(g.pre) + 20);
+		strcpy(s, g.pre); strcat(s, ".0.bam"); g.out[0] = bam_open(s, "w");
+		strcpy(s, g.pre); strcat(s, ".1.bam"); g.out[1] = bam_open(s, "w");
+		strcpy(s, g.pre); strcat(s, ".chimera.bam"); g.out[2] = bam_open(s, "w");
+		for (c = 0; c <= 2; ++c) bam_header_write(g.out[c], h);
+		free(s);
+	}
+
+	iter = bam_plp_init(readaln, &g);
+	g.vpos_shift = 0;
+	seqs = kh_init(64);
+	em = errmod_init(1. - 0.83);
+	bases = calloc(g.max_depth, 2);
+	printf("CC\n");
+	printf("CC\tDescriptions:\nCC\n");
+	printf("CC\t  CC      comments\n");
+	printf("CC\t  PS      start of a phase set\n");
+	printf("CC\t  FL      filtered region\n");
+	printf("CC\t  M[012]  markers; 0 for singletons, 1 for phased and 2 for filtered\n");
+	printf("CC\t  EV      supporting reads; SAM format\n");
+	printf("CC\t  //      end of a phase set\nCC\n");
+	printf("CC\tFormats of PS, FL and M[012] lines (1-based coordinates):\nCC\n");
+	printf("CC\t  PS  chr  phaseSetStart  phaseSetEnd\n");
+	printf("CC\t  FL  chr  filterStart    filterEnd\n");
+	printf("CC\t  M?  chr  PS  pos  allele0  allele1  hetIndex  #supports0  #errors0  #supp1  #err1\n");
+	printf("CC\nCC\n");
+	fflush(stdout);
+	while ((plp = bam_plp_auto(iter, &tid, &pos, &n)) != 0) {
+		int i, k, c, tmp, dophase = 1, in_set = 0;
+		float q[16];
+		if (tid < 0) break;
+		if (tid != lasttid) { // change of chromosome
+			g.vpos_shift = 0;
+			if (lasttid >= 0) {
+				seqs = shrink_hash(seqs);
+				phase(&g, h->target_name[lasttid], vpos, cns, seqs);
+				update_vpos(0x7fffffff, seqs);
+			}
+			lasttid = tid;
+			vpos = 0;
+		}
+		if (set && kh_get(set64, set, (uint64_t)tid<<32 | pos) != kh_end(set)) in_set = 1;
+		if (n > g.max_depth) continue; // do not proceed if the depth is too high
+		// fill the bases array and check if there is a variant
+		for (i = k = 0; i < n; ++i) {
+			const bam_pileup1_t *p = plp + i;
+			uint8_t *seq;
+			int q, baseQ, b;
+			if (p->is_del || p->is_refskip) continue;
+			baseQ = bam1_qual(p->b)[p->qpos];
+			if (baseQ < g.min_baseQ) continue;
+			seq = bam1_seq(p->b);
+			b = bam_nt16_nt4_table[bam1_seqi(seq, p->qpos)];
+			if (b > 3) continue;
+			q = baseQ < p->b->core.qual? baseQ : p->b->core.qual;
+			if (q < 4) q = 4;
+			if (q > 63) q = 63;
+			bases[k++] = q<<5 | (int)bam1_strand(p->b)<<4 | b;
+		}
+		if (k == 0) continue;
+		errmod_cal(em, k, 4, bases, q); // compute genotype likelihood
+		c = gl2cns(q); // get the consensus
+		// tell if to proceed
+		if (set && (g.flag&FLAG_LIST_EXCL) && !in_set) continue; // not in the list
+		if (!in_set && (c&0xffff)>>2 < g.min_varLOD) continue; // not a variant
+		// add the variant
+		if (vpos == max_vpos) {
+			max_vpos = max_vpos? max_vpos<<1 : 128;
+			cns = realloc(cns, max_vpos * 8);
+		}
+		cns[vpos] = (uint64_t)pos<<32 | c;
+		for (i = 0; i < n; ++i) {
+			const bam_pileup1_t *p = plp + i;
+			uint64_t key;
+			khint_t k;
+			uint8_t *seq = bam1_seq(p->b);
+			frag_t *f;
+			if (p->is_del || p->is_refskip) continue;
+			if (p->b->core.qual == 0) continue;
+			// get the base code
+			c = nt16_nt4_table[(int)bam1_seqi(seq, p->qpos)];
+			if (c == (cns[vpos]&3)) c = 1;
+			else if (c == (cns[vpos]>>16&3)) c = 2;
+			else c = 0;
+			// write to seqs
+			key = X31_hash_string(bam1_qname(p->b));
+			k = kh_put(64, seqs, key, &tmp);
+			f = &kh_val(seqs, k);
+			if (tmp == 0) { // present in the hash table
+				if (vpos - f->vpos + 1 < MAX_VARS) {
+					f->vlen = vpos - f->vpos + 1;
+					f->seq[f->vlen-1] = c;
+					f->end = bam_calend(&p->b->core, bam1_cigar(p->b));
+				}
+				dophase = 0;
+			} else { // absent
+				memset(f->seq, 0, MAX_VARS);
+				f->beg = p->b->core.pos;
+				f->end = bam_calend(&p->b->core, bam1_cigar(p->b));
+				f->vpos = vpos, f->vlen = 1, f->seq[0] = c, f->single = f->phased = f->flip = f->ambig = 0;
+			}
+		}
+		if (dophase) {
+			seqs = shrink_hash(seqs);
+			phase(&g, h->target_name[tid], vpos, cns, seqs);
+			update_vpos(vpos, seqs);
+			cns[0] = cns[vpos];
+			vpos = 0;
+		}
+		++vpos;
+	}
+	if (tid >= 0) phase(&g, h->target_name[tid], vpos, cns, seqs);
+	bam_header_destroy(h);
+	bam_plp_destroy(iter);
+	bam_close(g.fp);
+	kh_destroy(64, seqs);
+	kh_destroy(set64, set);
+	free(cns);
+	errmod_destroy(em);
+	free(bases);
+	if (g.pre) {
+		for (c = 0; c <= 2; ++c) bam_close(g.out[c]);
+		free(g.pre); free(g.b);
+	}
+	return 0;
+}