#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;
}
