int main(int argc, char *argv[])
{
int min_span = 1000, min_match = 100, width = 600, height, diagonal = 1;
int color[2] = { 0xFF0000, 0x0080FF }, font_size = 11, no_label = 0;
float min_iden = .1;
paf_file_t *f;
sdict_t *d[2];
paf_rec_t r;
int32_t c, i, j;
uint64_t *acclen[2], totlen[2];
srtaux_t *a[2];
kvec_t(dt_hit_t) h = {0,0,0};
double sx, sy;
while ((c = getopt(argc, argv, "m:i:s:w:f:Ld")) >= 0) {
if (c == 'm') min_match = atoi(optarg);
else if (c == 'i') min_iden = atof(optarg);
else if (c == 's') min_span = atoi(optarg);
else if (c == 'w') width = atoi(optarg);
else if (c == 'f') font_size = atoi(optarg);
else if (c == 'L') no_label = 1;
else if (c == 'd') diagonal = 0;
}
if (argc == optind) {
fprintf(stderr, "Usage: minidot [options] <in.paf>\n");
fprintf(stderr, "Options:\n");
fprintf(stderr, " -m INT min match length [%d]\n", min_match);
fprintf(stderr, " -i FLOAT min identity [%.2f]\n", min_iden);
fprintf(stderr, " -s INT min span [%d]\n", min_span);
fprintf(stderr, " -w INT image width [%d]\n", width);
fprintf(stderr, " -f INT font size [%d]\n", font_size);
fprintf(stderr, " -L don't print labels\n");
fprintf(stderr, " -D don't try to put hits onto the diagonal\n");
return 1;
}
d[0] = sd_init();
d[1] = sd_init();
f = paf_open(argv[optind]);
while (paf_read(f, &r) >= 0) {
dt_hit_t *s;
if (r.qe - r.qs < min_span || r.te - r.ts < min_span || r.ml < min_match) continue;
if (r.ml < r.bl * min_iden) continue;
kv_pushp(dt_hit_t, h, &s);
s->qn = sd_put(d[0], r.qn, r.ql), s->qs = r.qs, s->qe = r.qe;
s->tn = sd_put(d[1], r.tn, r.tl);
s->ts = r.rev? r.te : r.ts, s->te = r.rev? r.ts : r.te;
s->ml = r.ml;
}
paf_close(f);
for (i = 0; i < 2; ++i) {
uint32_t n = d[i]->n_seq;
uint64_t l = 0;
a[i] = (srtaux_t*)calloc(n + 1, sizeof(srtaux_t));
if (i == 0 || !diagonal) {
for (j = 0; j < n; ++j)
a[i][j].name = d[i]->seq[j].name, a[i][j].i = j;
ks_introsort_dtx(n, a[i]);
} else {
srtaux_t *b = a[i];
uint32_t *inv;
inv = (uint32_t*)calloc(d[0]->n_seq, 4);
for (j = 0; j < d[0]->n_seq; ++j)
inv[a[0][j].i] = j;
for (j = 0; j < n; ++j)
b[j].name = d[i]->seq[j].name, b[j].tot = b[j].w = 0, b[j].i = j;
for (j = 0; j < h.n; ++j) {
uint64_t w, coor;
dt_hit_t *p = &h.a[j];
srtaux_t *q = &b[p->tn];
coor = acclen[0][inv[p->qn]] + (p->qs + p->qe) / 2;
w = (uint64_t)(.01 * p->ml * p->ml + .499);
q->tot += (double)coor * w;
q->w += w;
}
free(inv);
for (j = 0; j < n; ++j) b[j].tot /= b[j].w;
ks_introsort_dty(n, b);
}
acclen[i] = (uint64_t*)calloc(n, 8);
for (j = 0; j < n; ++j)
acclen[i][a[i][j].i] = l, l += d[i]->seq[a[i][j].i].len;
totlen[i] = l;
}
height = (int)((double)width / totlen[0] * totlen[1] + .499);
sx = (double)width / totlen[0];
sy = (double)height / totlen[1];
eps_header(stdout, width, height, .2);
eps_font(stdout, "Helvetica-Narrow", font_size);
eps_gray(stdout, .8);
if (!no_label) {
// write x labels
for (i = 0; i < d[0]->n_seq; ++i)
eps_Mstr(stdout, (acclen[0][a[0][i].i] + .5 * d[0]->seq[a[0][i].i].len) * sx, font_size*.5, a[0][i].name);
eps_stroke(stdout);
fprintf(stdout, "gsave %g 0 translate 90 rotate\n", font_size*1.25);
// write y labels
for (i = 0; i < d[1]->n_seq; ++i)
eps_Mstr(stdout, (acclen[1][a[1][i].i] + .5 * d[1]->seq[a[1][i].i].len) * sx, 0, a[1][i].name);
fprintf(stdout, "grestore\n");
eps_stroke(stdout);
}
// write grid lines
eps_linewidth(stdout, .1);
for (i = 0; i < d[1]->n_seq; ++i)
eps_linex(stdout, 1, width, i == 0? 1 : acclen[1][a[1][i].i] * sy);
eps_linex(stdout, 1, width, totlen[1] * sy);
for (i = 0; i < d[0]->n_seq; ++i)
eps_liney(stdout, 1, height, i == 0? 1 : acclen[0][a[0][i].i] * sx);
eps_liney(stdout, 1, height, totlen[0] * sx);
eps_stroke(stdout);
// write hits
eps_linewidth(stdout, .1);
for (j = 0; j < 2; ++j) {
eps_color(stdout, color[j]);
for (i = 0; i < h.n; ++i) {
dt_hit_t *p = &h.a[i];
double x0, y0, x1, y1;
uint64_t xo = acclen[0][p->qn], yo = acclen[1][p->tn];
if (j == 0 && p->ts > p->te) continue;
if (j == 1 && p->ts < p->te) continue;
x0 = (p->qs + xo) * sx, y0 = (p->ts + yo) * sy;
x1 = (p->qe + xo) * sx, y1 = (p->te + yo) * sy;
eps_line(stdout, x0, y0, x1, y1);
}
eps_stroke(stdout);
}
eps_bottom(stdout);
for (i = 0; i < 2; ++i) {
free(acclen[i]);
free(a[i]);
sd_destroy(d[i]);
}
free(h.a);
return 0;
}
int do_grep() {
#ifdef DEBUGa
printf("[!]do_grep\n");
#endif
BamInfo_t *pbam;
kh_cstr_t BamID;
khiter_t ki, bami;
kstring_t ks1 = { 0, 0, NULL };
kstring_t ks2 = { 0, 0, NULL };
kstring_t ks3 = { 0, 0, NULL };
samFile *in;
bam_hdr_t *h;
hts_idx_t *idx;
bam1_t *b, *d, *d2, *bR1, *bR2, *bR3;
bR1 = bam_init1(); bR2 = bam_init1(); bR3 = bam_init1();
//htsFile *out;
//hts_opt *in_opts = NULL, *out_opts = NULL;
int r = 0, exit_code = 0;
kvec_t(bam1_t) R1, R2, RV;
pierCluster_t *pierCluster;
//samdat_t tmp_samdat;
FILE *fs = fopen("./test.txt","w");
for (bami = kh_begin(bamNFOp); bami != kh_end(bamNFOp); ++bami) {
//printf(">[%d]:\n",bami);
if (kh_exist(bamNFOp, bami)) {
kv_init(R1); kv_init(R2); kv_init(RV);
//tmp_samdat = (const samdat_t){ 0 };
//memset(&tmp_samdat,0,sizeof(samdat_t));
//printf("-[%d]:\n",bami);
BamID = kh_key(bamNFOp, bami);
pbam = &kh_value(bamNFOp, bami);
fprintf(stderr, "%u [%s]=%s\t%u %u\n",bami,BamID,pbam->fileName,pbam->insertSize,pbam->SD);
in = sam_open(pbam->fileName, "r");
if (in == NULL) {
fprintf(stderr, "[x]Error opening \"%s\"\n", pbam->fileName);
return EXIT_FAILURE;
}
h = sam_hdr_read(in);
/* out = hts_open("-", "w");
if (out == NULL) {
fprintf(stderr, "[x]Error opening standard output\n");
return EXIT_FAILURE;
}
if (sam_hdr_write(out, h) < 0) {
fprintf(stderr, "[!]Error writing output header.\n");
exit_code = 1;
}
*/
int8_t *ChrIsHum;
if (h == NULL) {
fprintf(stderr, "[x]Couldn't read header for \"%s\"\n", pbam->fileName);
return EXIT_FAILURE;
} else {
ChrIsHum = malloc(h->n_targets * sizeof(int8_t));
for (int32_t i=0; i < h->n_targets; ++i) {
//ChrIsHum[i] = -1;
ki = kh_get(chrNFO, chrNFOp, h->target_name[i]);
if (ki == kh_end(chrNFOp)) {
errx(4,"[x]Cannot find ChrID for [%s] !",h->target_name[i]);
} else {
ChrInfo_t * tmp = &kh_value(chrNFOp, ki);
ChrIsHum[i] = tmp->isHum;
//printf(">>> %d Chr:%s %d\n",i,h->target_name[i],ChrIsHum[i]);
}
}
}
h->ignore_sam_err = 0;
b = bam_init1();
d = bam_init1();
d2 = bam_init1();
if ((idx = sam_index_load(in, pbam->fileName)) == 0) {
fprintf(stderr, "[E::%s] fail to load the BAM index\n", __func__);
return 1;
}
pierCluster = sam_plp_init();
while ((r = sam_read1(in, h, b)) >= 0) {
int8_t flag = false;
const bam1_core_t *c = &b->core;
if (c->flag & BAM_FSECONDARY) continue;
if (c->n_cigar) {
uint32_t *cigar = bam_get_cigar(b);
for (int i = 0; i < c->n_cigar; ++i) {
if (bam_cigar_opchr(cigar[i])=='S') { // soft clipping
if ( bam_cigar_oplen(cigar[i]) >= myConfig.minGrepSlen ) {
flag = true;
}
}
}
}
if (flag && ChrIsHum[c->tid]) { // Now, skip Virus items.
//bam_copy1(bR1, b);
flag = 0; // recycle
//int enoughMapQ = 0;
//kstring_t ks = { 0, 0, NULL };
/*if (sam_format1(h, b, &ks1) < 0) {
fprintf(stderr, "Error writing output.\n");
exit_code = 1;
break;
} else*/ if ((c->mtid == c->tid && ChrIsHum[c->tid]) || (ChrIsHum[c->tid] ^ ChrIsHum[c->mtid])) { // Only grep those mapped on same Human ChrID, or diff species/一方在病毒的情况.
//printf(">[%s]\n",ks_str(&ks1));
flag |= 1;
//tmp_samdat.b = bam_dup1(b);
//kv_push(samdat_t,R1,tmp_samdat);
/*if (checkMapQ(ChrIsHum, b, true)) {
++enoughMapQ;
}*/
}
if (getPairedSam(in, idx, b, d) != 0) {
flag &= ~1;
continue;
} else {
flag |= 2;
/*if (checkMapQ(ChrIsHum, d, false)) {
++enoughMapQ;
}*/
/*if (c->flag & BAM_FSECONDARY) {
if (getPairedSam(in, idx, d, d2) == 0) {
//sam_format1(h, d2, &ks3);
flag |= 4;
if (checkMapQ(ChrIsHum, d2, false)) {
++enoughMapQ;
}
}
}*/
}
/*
对于 BAM_FSECONDARY(256) 的 Read，跳两次 与 读 SA 项，效果一样。
>[sf95_Ref_48245009_48245108_48245208_Vir_-_2000_2044_R_100_90 353 chr2 13996555 0 50S40M chr18 48245109 0ACACAACAATGTTCCGGAGACTCTAAGGCCTCCCGATACAGAGCAGAGGCCACACACACACACACCATGGAATACTATTCAGCCAAAAAA CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC NM:i:0 MD:Z:40 AS:i:40 XS:i:40 RG:Z:Fsimout_mB SA:Z:rgi|59585|emb|X04615.1|,2000,-,40S46M4S,60,0; YC:Z:CT YD:Z:f]
-[sf95_Ref_48245009_48245108_48245208_Vir_-_2000_2044_R_100_90 177 chr18 48245109 9 40S50M gi|59585|emb|X04615.1|2000 0 GTTCCGGAGACTCTAAGGCCTCCCGATACAGAGCAGAGGCCACACACACACACACCATGGAATACTATTCAGCCAAAAAAAGGAATTCAA CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC NM:i:0 MD:Z:50 AS:i:50 XS:i:46 RG:Z:Fsimout_mB SA:Z:rgi|59585|emb|X04615.1|,2000,+,50S40M,9,0; YC:Z:GA YD:Z:f]
+[sf95_Ref_48245009_48245108_48245208_Vir_-_2000_2044_R_100_90 113 gi|59585|emb|X04615.1| 2000 60 40S46M4S chr18 48245109 0 TTTTTTGGCTGAATAGTATTCCATGGTGTGTGTGTGTGTGGCCTCTGCTCTGTATCGGGAGGCCTTAGAGTCTCCGGAACATTGTTGTGT CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC NM:i:0 MD:Z:46 AS:i:46 XS:i:27 RG:Z:Fsimout_mB SA:Z:fchr2,13996555,+,50S40M,0,0; YC:Z:CT YD:Z:r]
*/
/*if (sam_format1(h, d, &ks2) < 0) {
fprintf(stderr, "Error writing output.\n");
exit_code = 1;
break;
}*/
if (((flag & 3) == 3) /*&& enoughMapQ >= myConfig.samples*/) {
/*printf(">%d[%s]\n",checkMapQ(ChrIsHum, b, true),ks_str(&ks1));
printf("-%d[%s]\n",checkMapQ(ChrIsHum, d, false),ks_str(&ks2));
if (flag & 4) {
printf("+%d[%s]\n",checkMapQ(ChrIsHum, d2, false),ks_str(&ks3));
}
printf("<--%d\n",enoughMapQ);*/
if (sam_plp_push(ChrIsHum, pierCluster, b) == 0) {
//printf("--HumRange=%s:%d-%d\n", h->target_name[(pierCluster->HumanRange).tid], (pierCluster->HumanRange).pos, (pierCluster->HumanRange).endpos);
if ((!ChrIsHum[(d->core).tid]) && (flag & 2)) sam_plp_push(ChrIsHum, pierCluster, d);
//if ((!ChrIsHum[(d2->core).tid]) && (flag & 4)) sam_plp_push(ChrIsHum, pierCluster, d2);
} else {
//print
fprintf(fs,"[%s]\nHumRange=%s:%d-%d\n", BamID, h->target_name[(pierCluster->HumanRange).tid], (pierCluster->HumanRange).pos, (pierCluster->HumanRange).endpos);
fprintf(fs,"VirRange=%s:%d-%d\n", h->target_name[(pierCluster->VirusRange).tid], (pierCluster->VirusRange).pos, (pierCluster->VirusRange).endpos);
for (size_t i=0; i<kv_size(pierCluster->Reads);++i) {
bam1_t *bi = kv_A(pierCluster->Reads, i);
if (sam_format1(h, bi, &ks1) < 0) {
fprintf(stderr, "Error writing output.\n");
exit_code = 1;
break;
} else {
fprintf(fs,"%s\n",ks1.s);
}
}
fprintf(fs,"\n");
//printf("HumRange=%s:%d-%d\n", h->target_name[(pierCluster->HumanRange).tid], (pierCluster->HumanRange).pos, (pierCluster->HumanRange).endpos);
//fflush(fs);
sam_plp_dectroy(pierCluster);
pierCluster = sam_plp_init();
}
}
}
/*char *qname = bam_get_qname(b);
if (sam_write1(out, h, b) < 0) {
fprintf(stderr, "[x]Error writing output.\n");
exit_code = 1;
break;
}*/
}
/* r = sam_close(out); // stdout can only be closed once
if (r < 0) {
fprintf(stderr, "Error closing output.\n");
exit_code = 1;
}
*/
hts_idx_destroy(idx);
bam_destroy1(b);
bam_destroy1(d);
bam_destroy1(d2);
bam_hdr_destroy(h);
r = sam_close(in);
free(ChrIsHum);
#ifdef DEBUGa
fflush(NULL);
//pressAnyKey();
#endif
sam_plp_dectroy(pierCluster);
//printf("<[%d]:\n",bami);
}
}
fclose(fs);
getPairedSam(NULL, NULL, NULL, NULL); // sam_close(fp2);
//printf("---[%d]---\n",exit_code);
bam_destroy1(bR1); bam_destroy1(bR2); bam_destroy1(bR3);
ks_release(&ks1);
ks_release(&ks2);
ks_release(&ks3);
return exit_code;
}
mem_alnreg_v mem_fmeas_fliter_se(mem_alnreg_v a , int n , int l_seq , int mode)
{
mem_alnreg_v aa ;
int i , j ;
kvec_t(FF_t) k_ff_t ;
kv_init(k_ff_t);
kv_init(aa);
// caculate FMEAS value
if(n == 0) return aa ;
for( i = 0 ; i < a.n ; i++){
mem_alnreg_t *p_ar = a.a + i ;
for( j = i + 1 ; j < a.n ; j++){
FF_t tmp ;
mem_alnreg_t *q_ar = a.a + j ;
double sens , spec ;
int FN = 0 , TP = 0 ,TN = 0 , FP = 0 ;
int A,B,C,D;
if( p_ar->qb < q_ar->qb || (p_ar->qb == q_ar->qb && p_ar->qe >= q_ar->qe)){ // p q
A = p_ar->qb ;
B = p_ar->qe - 1 ;
C = q_ar->qb ;
D = q_ar->qe - 1 ;
}else { // p q
A = q_ar->qb ;
B = q_ar->qe - 1;
C = p_ar->qb ;
D = p_ar->qe - 1;
}
if(B < C){
TP = B - A + D - C + 2 ;
FN = l_seq - D - 1 + A + C - B - 1 ;
TN = l_seq ;
FP = 0 ;
}else if( D <= B){ // contain
continue ;
}else{
TP = D - A + 1 ;
FN = l_seq - D - 1 + A ;
FP = B - C + 1 ;
TN = l_seq - FP;
}
sens = (double)TP/(double)(TP+FN);
spec = (double)TN/(double)(TN+FP);
tmp.FMEAS = (2*spec*sens)/(spec+sens);
tmp.score = p_ar->score + q_ar->score;
tmp.x = i , tmp.y = j ;
if(tmp.FMEAS > 0.95) kv_push(FF_t,k_ff_t,tmp);
}
}
ks_introsort(ff_mem_flt, k_ff_t.n, k_ff_t.a);
kv_push(mem_alnreg_t,aa,a.a[0]);
double max_feas ;
// int score ;
if( k_ff_t.n == 0 ) return aa;
max_feas = k_ff_t.a[0].FMEAS ;
// score = k_ff_t.a[0].score ;
if(mode){
int cnt = 0 ;
for( i = 0 ; i < kv_size(k_ff_t) ; i++){
FF_t p = kv_A(k_ff_t,i);
if(p.x == 0 && cnt == 0){
kv_push(mem_alnreg_t,aa,a.a[p.y]);
cnt = 1 ;
}else if(p.x == 0){
kv_push(mem_alnreg_t,aa,a.a[0]);
kv_push(mem_alnreg_t,aa,a.a[p.y]);
}
}
for( i = 0 ; i < kv_size(k_ff_t); i++){
FF_t p = kv_A(k_ff_t,i);
if(max_feas != p.FMEAS ) break;
if(p.x == 0) continue ;
kv_push(mem_alnreg_t,aa,a.a[p.x]);
kv_push(mem_alnreg_t,aa,a.a[p.y]);
}
}else{
int cnt = 0 ;
for( i = 0 ; i < kv_size(k_ff_t); i++){
FF_t p = kv_A(k_ff_t,i);
if(max_feas != p.FMEAS ) break;
if(p.x == 0 && cnt == 0){
kv_push(mem_alnreg_t,aa,a.a[p.y]);
continue ;
}else if( p.x == 0 ){
kv_push(mem_alnreg_t,aa,a.a[0]);
kv_push(mem_alnreg_t,aa,a.a[p.y]);
continue ;
}
kv_push(mem_alnreg_t,aa,a.a[p.x]);
kv_push(mem_alnreg_t,aa,a.a[p.y]);
}
}
kv_destroy(k_ff_t);
#if 0
for( i = 0 ; i < kv_size(aa); i++){
mem_alnreg_t *q = aa.a + i;
printf("%db: %d %de:%d \t" , i, q->qb , i, q->qe);
if( i == kv_size(aa) -1 ) printf("\n");
}
#endif
return aa ;
}
