mrb_value
mrb_hash_keys(mrb_state *mrb, mrb_value hash)
{
khash_t(ht) *h = RHASH_TBL(hash);
khiter_t k;
mrb_value ary, *p;
if (!h || kh_size(h) == 0) return mrb_ary_new(mrb);
ary = mrb_ary_new_capa(mrb, kh_size(h));
mrb_ary_set(mrb, ary, kh_size(h)-1, mrb_nil_value());
p = RARRAY_PTR(ary);
for (k = kh_begin(h); k != kh_end(h); k++) {
if (kh_exist(h, k)) {
mrb_value kv = kh_key(h,k);
mrb_hash_value hv = kh_value(h,k);
p[hv.n] = kv;
}
}
return ary;
}
static mrb_value
recursive_eql(mrb_state *mrb, mrb_value hash, mrb_value dt, int recur)
{
khash_t(ht) *h1 = RHASH_TBL(hash);
khash_t(ht) *h2 = RHASH_TBL(dt);
khiter_t k1, k2;
mrb_value key1;
for (k1 = kh_begin(h1); k1 != kh_end(h1); k1++) {
if (!kh_exist(h1, k1)) continue;
key1 = kh_key(h1,k1);
k2 = kh_get(ht, h2, key1);
if ( k2 != kh_end(h2)) {
if (mrb_equal(mrb, kh_value(h1,k1), kh_value(h2,k2))) {
continue; /* next key */
}
}
return mrb_false_value();
}
return mrb_true_value();
}
static mrb_value
hash_equal(mrb_state *mrb, mrb_value hash1, mrb_value hash2, int eql)
{
khash_t(ht) *h1, *h2;
if (mrb_obj_equal(mrb, hash1, hash2)) return mrb_true_value();
if (!mrb_hash_p(hash2)) {
if (!mrb_respond_to(mrb, hash2, mrb_intern_lit(mrb, "to_hash"))) {
return mrb_false_value();
}
if (eql)
return mrb_fixnum_value(mrb_eql(mrb, hash2, hash1));
else
return mrb_fixnum_value(mrb_equal(mrb, hash2, hash1));
}
h1 = RHASH_TBL(hash1);
h2 = RHASH_TBL(hash2);
if (!h1) {
return mrb_bool_value(!h2);
}
if (!h2) return mrb_false_value();
if (kh_size(h1) != kh_size(h2)) return mrb_false_value();
else {
khiter_t k1, k2;
mrb_value key;
for (k1 = kh_begin(h1); k1 != kh_end(h1); k1++) {
if (!kh_exist(h1, k1)) continue;
key = kh_key(h1,k1);
k2 = kh_get(ht, mrb, h2, key);
if (k2 != kh_end(h2)) {
if (mrb_equal(mrb, kh_value(h1,k1), kh_value(h2,k2))) {
continue; /* next key */
}
}
return mrb_false_value();
}
}
return mrb_true_value();
}
/*
* call-seq:
* obj.instance_variables -> array
*
* Returns an array of instance variable names for the receiver. Note
* that simply defining an accessor does not create the corresponding
* instance variable.
*
* class Fred
* attr_accessor :a1
* def initialize
* @iv = 3
* end
* end
* Fred.new.instance_variables #=> [:@iv]
*/
mrb_value
mrb_obj_instance_variables(mrb_state *mrb, mrb_value self)
{
mrb_value ary;
kh_iv_t *h = RCLASS_IV_TBL(self);
int i;
const char* p;
ary = mrb_ary_new(mrb);
if (h) {
for (i=0;i<kh_end(h);i++) {
if (kh_exist(h, i)) {
p = mrb_sym2name(mrb, kh_key(h,i));
if (*p == '@') {
if (mrb_type(kh_value(h, i)) != MRB_TT_UNDEF)
mrb_ary_push(mrb, ary, mrb_str_new_cstr(mrb, p));
}
}
}
}
return ary;
}
static mrb_value
mrb_hash_dup(mrb_state *mrb, mrb_value hash)
{
struct RHash* ret;
khash_t(ht) *h, *ret_h;
khiter_t k, ret_k;
mrb_value ifnone, vret;
h = RHASH_TBL(hash);
ret = (struct RHash*)mrb_obj_alloc(mrb, MRB_TT_HASH, mrb->hash_class);
ret->ht = kh_init(ht, mrb);
if (h && kh_size(h) > 0) {
ret_h = ret->ht;
for (k = kh_begin(h); k != kh_end(h); k++) {
if (kh_exist(h, k)) {
int ai = mrb_gc_arena_save(mrb);
ret_k = kh_put(ht, mrb, ret_h, KEY(kh_key(h, k)));
mrb_gc_arena_restore(mrb, ai);
kh_val(ret_h, ret_k).v = kh_val(h, k).v;
kh_val(ret_h, ret_k).n = kh_size(ret_h)-1;
}
}
}
if (MRB_RHASH_DEFAULT_P(hash)) {
ret->flags |= MRB_HASH_DEFAULT;
}
if (MRB_RHASH_PROCDEFAULT_P(hash)) {
ret->flags |= MRB_HASH_PROC_DEFAULT;
}
vret = mrb_obj_value(ret);
ifnone = RHASH_IFNONE(hash);
if (!mrb_nil_p(ifnone)) {
mrb_iv_set(mrb, vret, mrb_intern_lit(mrb, "ifnone"), ifnone);
}
return vret;
}
uint32_t mm_idx_cal_max_occ(const mm_idx_t *mi, float f)
{
int i;
size_t n = 0;
uint32_t thres;
khint_t *a, k;
if (f <= 0.) return UINT32_MAX;
for (i = 0; i < 1<<mi->b; ++i)
if (mi->B[i].h) n += kh_size((idxhash_t*)mi->B[i].h);
a = (uint32_t*)malloc(n * 4);
for (i = n = 0; i < 1<<mi->b; ++i) {
idxhash_t *h = (idxhash_t*)mi->B[i].h;
if (h == 0) continue;
for (k = 0; k < kh_end(h); ++k) {
if (!kh_exist(h, k)) continue;
a[n++] = kh_key(h, k)&1? 1 : (uint32_t)kh_val(h, k);
}
}
thres = ks_ksmall_uint32_t(n, a, (uint32_t)((1. - f) * n)) + 1;
free(a);
return thres;
}
static mrb_sym
class_sym(mrb_state *mrb, struct RClass *c, struct RClass *outer)
{
mrb_value name;
name = mrb_obj_iv_get(mrb, (struct RObject*)c, mrb_intern(mrb, "__classid__"));
if (mrb_nil_p(name)) {
khash_t(iv)* h;
khiter_t k;
mrb_value v;
if (!outer) outer = mrb->object_class;
h = outer->iv;
for (k = kh_begin(h); k != kh_end(h); k++) {
if (!kh_exist(h,k)) continue;
v = kh_value(h,k);
if (mrb_type(v) == c->tt && mrb_class_ptr(v) == c) {
return kh_key(h,k);
}
}
}
return SYM2ID(name);
}
static mrb_bool
iv_foreach(mrb_state *mrb, iv_tbl *t, iv_foreach_func *func, void *p)
{
if (t == NULL) {
return TRUE;
}
else {
khash_t(iv) *h = &t->h;
khiter_t k;
int n;
for (k = kh_begin(h); k != kh_end(h); k++) {
if (kh_exist(h, k)) {
n = (*func)(mrb, kh_key(h, k), kh_value(h, k), p);
if (n > 0) return FALSE;
if (n < 0) {
kh_del(iv, mrb, h, k);
}
}
}
}
return TRUE;
}
mrb_value
mrb_hash_dup(mrb_state *mrb, mrb_value hash)
{
struct RHash* ret;
khash_t(ht) *h, *ret_h;
khiter_t k, ret_k;
h = RHASH_TBL(hash);
ret = (struct RHash*)mrb_obj_alloc(mrb, MRB_TT_HASH, mrb->hash_class);
ret->ht = kh_init(ht, mrb);
if (kh_size(h) > 0) {
ret_h = ret->ht;
for (k = kh_begin(h); k != kh_end(h); k++) {
if (kh_exist(h,k)) {
ret_k = kh_put(ht, ret_h, KEY(kh_key(h,k)));
kh_val(ret_h, ret_k) = kh_val(h,k);
}
}
}
return mrb_obj_value(ret);
}
static PyObject* pyext_epoll_free(PyObject *self,PyObject *args){
khiter_t hit;
int epfd;
struct pyep_data *pyep;
if(!PyArg_ParseTuple(args,"i",&epfd)){
PyErr_BadArgument();
return NULL;
}
if((pyep = pyep_getby_epfd(epfd)) == NULL){
PyErr_SetString(PyExc_KeyError,"epoll file descriptor not found");
return NULL;
}
if(ev_close(&pyep->evdata)){
PyErr_SetString(PyExc_SystemError,"epoll free failed");
return NULL;
}
for(hit = kh_begin(pyep->evhdr_ht);hit != kh_end(pyep->evhdr_ht);hit++){
if(kh_exist(pyep->evhdr_ht,hit)){
free((struct ev_header*)kh_value(pyep->evhdr_ht,hit));
}
}
kh_destroy(ptr,pyep->evhdr_ht);
hit = kh_get(ptr,pyep_ht,epfd);
kh_del(ptr,pyep_ht,hit);
free(pyep);
Py_INCREF(Py_None);
return Py_None;
}
static mrb_value
inspect_obj(mrb_state *mrb, mrb_value obj, mrb_value str, int recur)
{
if (recur) {
mrb_str_cat2(mrb, str, " ...");
}
else {
khiter_t k;
kh_iv_t *h = RCLASS_IV_TBL(obj);
if (h) {
for (k = kh_begin(h); k != kh_end(h); k++) {
if (kh_exist(h, k)){
mrb_sym id = kh_key(h, k);
mrb_value value = kh_value(h, k);
/* need not to show internal data */
if (RSTRING_PTR(str)[0] == '-') { /* first element */
RSTRING_PTR(str)[0] = '#';
mrb_str_cat2(mrb, str, " ");
}
else {
mrb_str_cat2(mrb, str, ", ");
}
mrb_str_cat2(mrb, str, mrb_sym2name(mrb, id));
mrb_str_cat2(mrb, str, "=");
mrb_str_append(mrb, str, mrb_inspect(mrb, value));
}
}
}
}
mrb_str_cat2(mrb, str, ">");
RSTRING_PTR(str)[0] = '#';
return str;
}
int
strm_env_copy(strm_state* s1, strm_state* s2)
{
strm_env *e1 = s1->env;
strm_env *e2 = s2->env;
khiter_t k, kk;
int r;
if (!e1) {
e1 = s1->env = kh_init(env);
}
if (!e2) {
e2 = s1->env = kh_init(env);
}
for (k = kh_begin(e2); k != kh_end(e2); k++) {
if (kh_exist(e2, k)) {
kk = kh_put(env, e1, kh_key(e2, k), &r);
if (r <= 0) return STRM_NG; /* r=0 key is present in the hash table */
/* r=-1 operation failed */
kh_value(e1, kk) = kh_value(e2, k);
}
}
return STRM_OK;
}
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;
}
/*
* Computes entropy from integer frequencies for various encoding methods and
* picks the best encoding.
*
* FIXME: we could reuse some of the code here for the actual encoding
* parameters too. Eg the best 'k' for SUBEXP or the code lengths for huffman.
*
* Returns the best codec to use.
*/
enum cram_encoding cram_stats_encoding(cram_fd *fd, cram_stats *st) {
enum cram_encoding best_encoding = E_NULL;
int best_size = INT_MAX, bits;
int nvals, i, ntot = 0, max_val = 0, min_val = INT_MAX, k;
int *vals = NULL, *freqs = NULL, vals_alloc = 0, *codes;
//cram_stats_dump(st);
/* Count number of unique symbols */
for (nvals = i = 0; i < MAX_STAT_VAL; i++) {
if (!st->freqs[i])
continue;
if (nvals >= vals_alloc) {
vals_alloc = vals_alloc ? vals_alloc*2 : 1024;
vals = realloc(vals, vals_alloc * sizeof(int));
freqs = realloc(freqs, vals_alloc * sizeof(int));
if (!vals || !freqs) {
if (vals) free(vals);
if (freqs) free(freqs);
return E_HUFFMAN; // Cannot do much else atm
}
}
vals[nvals] = i;
freqs[nvals] = st->freqs[i];
ntot += freqs[nvals];
if (max_val < i) max_val = i;
if (min_val > i) min_val = i;
nvals++;
}
if (st->h) {
khint_t k;
int i;
for (k = kh_begin(st->h); k != kh_end(st->h); k++) {
if (!kh_exist(st->h, k))
continue;
if (nvals >= vals_alloc) {
vals_alloc = vals_alloc ? vals_alloc*2 : 1024;
vals = realloc(vals, vals_alloc * sizeof(int));
freqs = realloc(freqs, vals_alloc * sizeof(int));
if (!vals || !freqs)
return E_HUFFMAN; // Cannot do much else atm
}
i = kh_key(st->h, k);
vals[nvals]=i;
freqs[nvals] = kh_val(st->h, k);
ntot += freqs[nvals];
if (max_val < i) max_val = i;
if (min_val > i) min_val = i;
nvals++;
}
}
st->nvals = nvals;
assert(ntot == st->nsamp);
if (nvals <= 1) {
free(vals);
free(freqs);
return E_HUFFMAN;
}
if (fd->verbose > 1)
fprintf(stderr, "Range = %d..%d, nvals=%d, ntot=%d\n",
min_val, max_val, nvals, ntot);
/* Theoretical entropy */
// if (fd->verbose > 1) {
// double dbits = 0;
// for (i = 0; i < nvals; i++) {
// dbits += freqs[i] * log((double)freqs[i]/ntot);
// }
// dbits /= -log(2);
// if (fd->verbose > 1)
// fprintf(stderr, "Entropy = %f\n", dbits);
// }
if (nvals > 1 && ntot > 256) {
#if 0
/*
* CRUDE huffman estimator. Round to closest and round up from 0
* to 1 bit.
*
* With and without ITF8 incase we have a few discrete values but with
* large magnitude.
*
* Note rans0/arith0 and Z_HUFFMAN_ONLY vs internal huffman can be
* compared in this way, but order-1 (eg rans1) or maybe LZ77 modes
* may detect the correlation of high bytes to low bytes in multi-
* byte values. So this predictor breaks down.
*/
double dbits = 0; // entropy + ~huffman
double dbitsH = 0;
double dbitsE = 0; // external entropy + ~huffman
double dbitsEH = 0;
int F[256] = {0}, n = 0;
double e = 0; // accumulated error bits
for (i = 0; i < nvals; i++) {
double x; int X;
unsigned int v = vals[i];
//Better encoding would cope with sign.
//v = ABS(vals[i])*2+(vals[i]<0);
if (!(v & ~0x7f)) {
F[v] += freqs[i], n+=freqs[i];
} else if (!(v & ~0x3fff)) {
F[(v>>8) |0x80] += freqs[i];
F[ v &0xff] += freqs[i], n+=2*freqs[i];
} else if (!(v & ~0x1fffff)) {
static int
cachefkcrt_exist_cb(cache_iter_t it)
{
return kh_exist(certmap, it);
}
static void TGM_FragLenHistToMature(TGM_FragLenHist* pHist)
{
khash_t(fragLen)* pRawHist = pHist->rawHist;
pHist->size = kh_size(pRawHist);
if (pHist->size > pHist->capacity)
{
free(pHist->fragLen);
free(pHist->freq);
pHist->capacity = 2 * pHist->size;
pHist->fragLen = (uint32_t*) malloc(pHist->capacity * sizeof(uint32_t));
if(pHist->fragLen == NULL)
TGM_ErrQuit("ERROR: Not enough memory for the storage of the fragment length array in the fragment length histogram object.\n");
pHist->freq = (uint64_t*) malloc(pHist->capacity * sizeof(uint64_t));
if(pHist->freq == NULL)
TGM_ErrQuit("ERROR: Not enough memory for the storage of the frequency array in the fragment length histogram object.\n");
}
unsigned int i = 0;
for (khiter_t khIter = kh_begin(pRawHist); khIter != kh_end(pRawHist); ++khIter)
{
if (kh_exist(pRawHist, khIter))
{
pHist->fragLen[i] = kh_key(pRawHist, khIter);
++i;
}
}
qsort(pHist->fragLen, pHist->size, sizeof(uint32_t), CompareFragLenBin);
double cumFreq = 0.0;
double totalFragLen = 0.0;
uint64_t totalFreq = pHist->modeCount[0];
double cdf = 0;
uint32_t fragLenQual = 0;
TGM_Bool foundMedian = FALSE;
for (unsigned int j = 0; j != pHist->size; ++j)
{
khiter_t khIter = kh_get(fragLen, pRawHist, pHist->fragLen[j]);
if (khIter == kh_end(pRawHist))
TGM_ErrQuit("ERROR: Cannot find the fragment length frequency from the hash table.\n");
pHist->freq[j] = kh_value(pRawHist, khIter);
totalFragLen += pHist->fragLen[j] * pHist->freq[j];
cumFreq += pHist->freq[j];
cdf = cumFreq / totalFreq;
if (!foundMedian && cdf >= 0.5)
{
pHist->median = pHist->fragLen[j];
foundMedian = TRUE;
}
cdf = cdf > 0.5 ? 1.0 - cdf : cdf;
fragLenQual = DoubleRoundToInt(-10.0 * log10(cdf));
kh_value(pRawHist, khIter) = fragLenQual;
}
pHist->mean = totalFragLen / totalFreq;
pHist->stdev = 0.0;
for (unsigned int j = 0; j != pHist->size; ++j)
{
pHist->stdev += (double) pHist->freq[j] * pow(pHist->mean - pHist->fragLen[j], 2);
}
if (totalFreq != 1)
pHist->stdev = sqrt(pHist->stdev / (double) (totalFreq - 1));
}
static int output_stats_and_reset(struct bgpcorsaro_pfxmonitor_state_t *state,
uint32_t interval_start)
{
khiter_t k;
khiter_t p;
khiter_t a;
int khret;
uint8_t pfx_visible;
uint32_t unique_pfxs = 0;
khash_t(peer_asn_map) * pam;
/* origin_asn -> num peer ASns*/
khash_t(asn_count_map) *asn_np = NULL;
if ((asn_np = kh_init(asn_count_map)) == NULL) {
return -1;
}
/* for each prefix go through all peers */
for (k = kh_begin(state->pfx_info); k != kh_end(state->pfx_info); ++k) {
if (kh_exist(state->pfx_info, k) == 0) {
continue;
}
/* reset counters */
kh_clear(asn_count_map, asn_np);
/* get peer-asn map for this prefix */
pam = kh_value(state->pfx_info, k);
/* save the origin asn visibility (i.e. how many peers' ASns
* observe such information */
/* for each peer, go through all origins */
for (p = kh_begin(pam); p != kh_end(pam); ++p) {
if (kh_exist(pam, p) == 0) {
continue;
}
/* increment the counter for this ASN */
if ((a = kh_get(asn_count_map, asn_np, kh_value(pam, p))) ==
kh_end(asn_np)) {
a = kh_put(asn_count_map, asn_np, kh_value(pam, p), &khret);
kh_value(asn_np, a) = 1;
} else {
kh_value(asn_np, a)++;
}
}
/* now asn_np has a complete count of the number of peers' ASns that
observed
each origin ASN */
/* count the prefix and origins if their visibility
* is above the threshold */
pfx_visible = 0;
for (a = kh_begin(asn_np); a != kh_end(asn_np); ++a) {
if (kh_exist(asn_np, a) == 0) {
continue;
}
/* the information is accounted only if it is
* consistent on at least threshold peers' ASns */
if (kh_value(asn_np, a) >= state->peer_asns_th) {
pfx_visible = 1;
bgpstream_id_set_insert(state->unique_origins, kh_key(asn_np, a));
}
}
/* updating counters */
unique_pfxs += pfx_visible;
}
DUMP_METRIC(unique_pfxs, state->interval_start, "%s.%s.%s.%s",
state->metric_prefix, PLUGIN_NAME, state->ip_space_name,
"prefixes_cnt");
DUMP_METRIC(bgpstream_id_set_size(state->unique_origins),
state->interval_start, "%s.%s.%s.%s", state->metric_prefix,
PLUGIN_NAME, state->ip_space_name, "origin_ASns_cnt");
bgpstream_id_set_clear(state->unique_origins);
kh_destroy(asn_count_map, asn_np);
return 0;
}
static void bcf_sr_sort_set(bcf_srs_t *readers, sr_sort_t *srt, const char *chr, int min_pos)
{
if ( !srt->grp_str2int )
{
// first time here, initialize
if ( !srt->pair )
{
if ( readers->collapse==COLLAPSE_NONE ) readers->collapse = BCF_SR_PAIR_EXACT;
bcf_sr_set_opt(readers, BCF_SR_PAIR_LOGIC, readers->collapse);
}
bcf_sr_init_scores(srt);
srt->grp_str2int = khash_str2int_init();
srt->var_str2int = khash_str2int_init();
}
int k;
khash_t(str2int) *hash;
hash = srt->grp_str2int;
for (k=0; k < kh_end(hash); k++)
if ( kh_exist(hash,k) ) free((char*)kh_key(hash,k));
hash = srt->var_str2int;
for (k=0; k < kh_end(hash); k++)
if ( kh_exist(hash,k) ) free((char*)kh_key(hash,k));
kh_clear(str2int, srt->grp_str2int);
kh_clear(str2int, srt->var_str2int);
srt->ngrp = srt->nvar = srt->nvset = 0;
grp_t grp;
memset(&grp,0,sizeof(grp_t));
// group VCFs into groups, each with a unique combination of variants in the duplicate lines
int ireader,ivar,irec,igrp,ivset,iact;
for (ireader=0; ireader<readers->nreaders; ireader++) srt->vcf_buf[ireader].nrec = 0;
for (iact=0; iact<srt->nactive; iact++)
{
ireader = srt->active[iact];
bcf_sr_t *reader = &readers->readers[ireader];
int rid = bcf_hdr_name2id(reader->header, chr);
grp.nvar = 0;
hts_expand(int,reader->nbuffer,srt->moff,srt->off);
srt->noff = 0;
srt->str.l = 0;
for (irec=1; irec<=reader->nbuffer; irec++)
{
bcf1_t *line = reader->buffer[irec];
if ( line->rid!=rid || line->pos!=min_pos ) break;
if ( srt->str.l ) kputc(';',&srt->str);
srt->off[srt->noff++] = srt->str.l;
size_t beg = srt->str.l;
for (ivar=1; ivar<line->n_allele; ivar++)
{
if ( ivar>1 ) kputc(',',&srt->str);
kputs(line->d.allele[0],&srt->str);
kputc('>',&srt->str);
kputs(line->d.allele[ivar],&srt->str);
}
if ( line->n_allele==1 )
{
kputs(line->d.allele[0],&srt->str);
kputsn(">.",2,&srt->str);
}
// Create new variant or attach to existing one. But careful, there can be duplicate
// records with the same POS,REF,ALT (e.g. in dbSNP-b142)
char *var_str = beg + srt->str.s;
int ret, var_idx = 0, var_end = srt->str.l;
while ( 1 )
{
ret = khash_str2int_get(srt->var_str2int, var_str, &ivar);
if ( ret==-1 ) break;
var_t *var = &srt->var[ivar];
if ( var->vcf[var->nvcf-1] != ireader ) break;
srt->str.l = var_end;
kputw(var_idx, &srt->str);
var_str = beg + srt->str.s;
var_idx++;
}
if ( ret==-1 )
{
ivar = srt->nvar++;
hts_expand0(var_t,srt->nvar,srt->mvar,srt->var);
srt->var[ivar].nvcf = 0;
khash_str2int_set(srt->var_str2int, strdup(var_str), ivar);
free(srt->var[ivar].str); // possible left-over from the previous position
}
var_t *var = &srt->var[ivar];
var->nalt = line->n_allele - 1;
var->type = bcf_get_variant_types(line);
srt->str.s[var_end] = 0;
if ( ret==-1 )
var->str = strdup(var_str);
int mvcf = var->mvcf;
var->nvcf++;
hts_expand0(int*, var->nvcf, var->mvcf, var->vcf);
if ( mvcf != var->mvcf ) var->rec = (bcf1_t **) realloc(var->rec,sizeof(bcf1_t*)*var->mvcf);
var->vcf[var->nvcf-1] = ireader;
var->rec[var->nvcf-1] = line;
grp.nvar++;
hts_expand(var_t,grp.nvar,grp.mvar,grp.var);
grp.var[grp.nvar-1] = ivar;
}
char *grp_key = grp_create_key(srt);
int ret = khash_str2int_get(srt->grp_str2int, grp_key, &igrp);
if ( ret==-1 )
{
igrp = srt->ngrp++;
hts_expand0(grp_t, srt->ngrp, srt->mgrp, srt->grp);
free(srt->grp[igrp].var);
srt->grp[igrp] = grp;
srt->grp[igrp].key = grp_key;
khash_str2int_set(srt->grp_str2int, grp_key, igrp);
memset(&grp,0,sizeof(grp_t));
}
else
free(grp_key);
srt->grp[igrp].nvcf++;
}
free(grp.var);
// initialize bitmask - which groups is the variant present in
for (ivar=0; ivar<srt->nvar; ivar++)
{
srt->var[ivar].mask = kbs_resize(srt->var[ivar].mask, srt->ngrp);
kbs_clear(srt->var[ivar].mask);
}
for (igrp=0; igrp<srt->ngrp; igrp++)
{
for (ivar=0; ivar<srt->grp[igrp].nvar; ivar++)
{
int i = srt->grp[igrp].var[ivar];
kbs_insert(srt->var[i].mask, igrp);
}
}
// create the initial list of variant sets
for (ivar=0; ivar<srt->nvar; ivar++)
{
ivset = srt->nvset++;
hts_expand0(varset_t, srt->nvset, srt->mvset, srt->vset);
varset_t *vset = &srt->vset[ivset];
vset->nvar = 1;
hts_expand0(var_t, vset->nvar, vset->mvar, vset->var);
vset->var[vset->nvar-1] = ivar;
var_t *var = &srt->var[ivar];
vset->cnt = var->nvcf;
vset->mask = kbs_resize(vset->mask, srt->ngrp);
kbs_clear(vset->mask);
kbs_bitwise_or(vset->mask, var->mask);
int type = 0;
if ( var->type==VCF_REF ) type |= SR_REF;
else
{
if ( var->type & VCF_SNP ) type |= SR_SNP;
if ( var->type & VCF_MNP ) type |= SR_SNP;
if ( var->type & VCF_INDEL ) type |= SR_INDEL;
if ( var->type & VCF_OTHER ) type |= SR_OTHER;
}
var->type = type;
}
#if DEBUG_VSETS
debug_vsets(srt);
#endif
// initialize the pairing matrix
hts_expand(int, srt->ngrp*srt->nvset, srt->mpmat, srt->pmat);
hts_expand(int, srt->nvset, srt->mcnt, srt->cnt);
memset(srt->pmat, 0, sizeof(*srt->pmat)*srt->ngrp*srt->nvset);
for (ivset=0; ivset<srt->nvset; ivset++)
{
varset_t *vset = &srt->vset[ivset];
for (igrp=0; igrp<srt->ngrp; igrp++) srt->pmat[ivset*srt->ngrp+igrp] = 0;
srt->cnt[ivset] = vset->cnt;
}
// pair the lines
while ( srt->nvset )
{
#if DEBUG_VSETS
fprintf(stderr,"\n");
debug_vsets(srt);
#endif
int imax = 0;
for (ivset=1; ivset<srt->nvset; ivset++)
if ( srt->cnt[imax] < srt->cnt[ivset] ) imax = ivset;
int ipair = -1;
uint32_t max_score = 0;
for (ivset=0; ivset<srt->nvset; ivset++)
{
if ( kbs_logical_and(srt->vset[imax].mask,srt->vset[ivset].mask) ) continue; // cannot be merged
uint32_t score = pairing_score(srt, imax, ivset);
// fprintf(stderr,"score: %d %d, logic=%d \t..\t %u\n", imax,ivset,srt->pair,score);
if ( max_score < score ) { max_score = score; ipair = ivset; }
}
// merge rows creating a new variant set this way
if ( ipair!=-1 && ipair!=imax )
{
imax = merge_vsets(srt, imax, ipair);
continue;
}
push_vset(srt, imax);
}
srt->chr = chr;
srt->pos = min_pos;
}
static void
gc_mark_phase(pic_state *pic)
{
struct context *cxt;
size_t j;
assert(pic->heap->weaks == NULL);
/* context */
for (cxt = pic->cxt; cxt != NULL; cxt = cxt->prev) {
if (cxt->fp) gc_mark_object(pic, (struct object *)cxt->fp);
if (cxt->sp) gc_mark_object(pic, (struct object *)cxt->sp);
if (cxt->irep) gc_mark_object(pic, (struct object *)cxt->irep);
}
/* arena */
for (j = 0; j < pic->ai; ++j) {
gc_mark_object(pic, (struct object *)pic->arena[j]);
}
/* global variables */
gc_mark(pic, pic->globals);
/* dynamic environment */
gc_mark(pic, pic->dyn_env);
/* top continuation */
gc_mark(pic, pic->halt);
/* features */
gc_mark(pic, pic->features);
/* weak maps */
do {
struct object *key;
pic_value val;
int it;
khash_t(weak) *h;
struct weak *weak;
j = 0;
weak = pic->heap->weaks;
while (weak != NULL) {
h = &weak->hash;
for (it = kh_begin(h); it != kh_end(h); ++it) {
if (! kh_exist(h, it))
continue;
key = kh_key(h, it);
val = kh_val(h, it);
if (is_alive(key)) {
if (obj_p(pic, val) && ! is_alive(obj_ptr(pic, val))) {
gc_mark(pic, val);
++j;
}
}
}
weak = weak->prev;
}
} while (j > 0);
}
static void rmdupse_buf(buffer_t *buf)
{
khash_t(32) *h;
uint32_t key;
khint_t k;
int mpos, i, upper;
listelem_t *p;
mpos = 0x7fffffff;
mpos = (buf->x == buf->n)? buf->buf[buf->x-1].b->core.pos : 0x7fffffff;
upper = (buf->x < 0)? buf->n : buf->x;
// fill the hash table
h = kh_init(32);
for (i = 0; i < upper; ++i) {
elem_t *e = buf->buf + i;
int ret;
if (e->score < 0) continue;
if (e->rpos >= 0) {
if (e->rpos <= mpos) key = (uint32_t)e->rpos<<1 | 1;
else continue;
} else {
if (e->b->core.pos < mpos) key = (uint32_t)e->b->core.pos<<1;
else continue;
}
k = kh_put(32, h, key, &ret);
p = &kh_val(h, k);
if (ret == 0) { // present in the hash table
if (p->n == p->m) {
p->m <<= 1;
p->a = (int*)realloc(p->a, p->m * sizeof(int));
}
p->a[p->n++] = i;
} else {
p->m = p->n = 1;
p->a = (int*)calloc(p->m, sizeof(int));
p->a[0] = i;
}
}
// rmdup
for (k = kh_begin(h); k < kh_end(h); ++k) {
if (kh_exist(h, k)) {
int max, maxi;
p = &kh_val(h, k);
// get the max
for (i = max = 0, maxi = -1; i < p->n; ++i) {
if (buf->buf[p->a[i]].score > max) {
max = buf->buf[p->a[i]].score;
maxi = i;
}
}
// mark the elements
for (i = 0; i < p->n; ++i) {
buf->buf[p->a[i]].score = -1;
if (i != maxi) {
bam_destroy1(buf->buf[p->a[i]].b);
buf->buf[p->a[i]].b = 0;
}
}
// free
free(p->a);
}
}
kh_destroy(32, h);
}
int git_strmap_has_data(git_strmap *map, size_t idx)
{
return kh_exist(map, idx);
}
bool HashMap_exists(HashMap* map, bstring key) {
khint_t k = kh_get(str, map->h, bdata(key));
return kh_exist(map->h, k);
}
int main_samview(int argc, char *argv[])
{
int index;
for(index = 0; index < argc; index++) {
printf("The %d is %s\n",index,argv[index]);
}
getchar();return 0;
int c, is_header = 0, is_header_only = 0, ret = 0, compress_level = -1, is_count = 0;
int is_long_help = 0, n_threads = 0;
int64_t count = 0;
samFile *in = 0, *out = 0, *un_out=0;
bam_hdr_t *header = NULL;
char out_mode[5], out_un_mode[5], *out_format = "";
char *fn_in = 0, *fn_out = 0, *fn_list = 0, *q, *fn_un_out = 0;
sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
samview_settings_t settings = {
.rghash = NULL,
.min_mapQ = 0,
.flag_on = 0,
.flag_off = 0,
.min_qlen = 0,
.remove_B = 0,
.subsam_seed = 0,
.subsam_frac = -1.,
.library = NULL,
.bed = NULL,
};
static const struct option lopts[] = {
SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', 0, 'T'),
{ "threads", required_argument, NULL, '@' },
{ NULL, 0, NULL, 0 }
};
/* parse command-line options */
strcpy(out_mode, "w");
strcpy(out_un_mode, "w");
while ((c = getopt_long(argc, argv,
"SbBcCt:h1Ho:O:q:f:F:ul:r:?T:R:L:s:@:m:x:U:",
lopts, NULL)) >= 0) {
switch (c) {
case 's':
if ((settings.subsam_seed = strtol(optarg, &q, 10)) != 0) {
srand(settings.subsam_seed);
settings.subsam_seed = rand();
}
settings.subsam_frac = strtod(q, &q);
break;
case 'm': settings.min_qlen = atoi(optarg); break;
case 'c': is_count = 1; break;
case 'S': break;
case 'b': out_format = "b"; break;
case 'C': out_format = "c"; break;
case 't': fn_list = strdup(optarg); break;
case 'h': is_header = 1; break;
case 'H': is_header_only = 1; break;
case 'o': fn_out = strdup(optarg); break;
case 'U': fn_un_out = strdup(optarg); break;
case 'f': settings.flag_on |= strtol(optarg, 0, 0); break;
case 'F': settings.flag_off |= strtol(optarg, 0, 0); break;
case 'q': settings.min_mapQ = atoi(optarg); break;
case 'u': compress_level = 0; break;
case '1': compress_level = 1; break;
case 'l': settings.library = strdup(optarg); break;
case 'L':
if ((settings.bed = bed_read(optarg)) == NULL) {
print_error_errno("view", "Could not read file \"%s\"", optarg);
ret = 1;
goto view_end;
}
break;
case 'r':
if (add_read_group_single("view", &settings, optarg) != 0) {
ret = 1;
goto view_end;
}
break;
case 'R':
if (add_read_groups_file("view", &settings, optarg) != 0) {
ret = 1;
goto view_end;
}
break;
/* REMOVED as htslib doesn't support this
//case 'x': out_format = "x"; break;
//case 'X': out_format = "X"; break;
*/
case '?': is_long_help = 1; break;
case 'B': settings.remove_B = 1; break;
case '@': n_threads = strtol(optarg, 0, 0); break;
case 'x':
{
if (strlen(optarg) != 2) {
fprintf(stderr, "main_samview: Error parsing -x auxiliary tags should be exactly two characters long.\n");
return usage(stderr, EXIT_FAILURE, is_long_help);
}
settings.remove_aux = (char**)realloc(settings.remove_aux, sizeof(char*) * (++settings.remove_aux_len));
settings.remove_aux[settings.remove_aux_len-1] = optarg;
}
break;
default:
if (parse_sam_global_opt(c, optarg, lopts, &ga) != 0)
return usage(stderr, EXIT_FAILURE, is_long_help);
break;
}
}
if (compress_level >= 0 && !*out_format) out_format = "b";
if (is_header_only) is_header = 1;
// File format auto-detection first
if (fn_out) sam_open_mode(out_mode+1, fn_out, NULL);
if (fn_un_out) sam_open_mode(out_un_mode+1, fn_un_out, NULL);
// Overridden by manual -b, -C
if (*out_format)
out_mode[1] = out_un_mode[1] = *out_format;
out_mode[2] = out_un_mode[2] = '\0';
// out_(un_)mode now 1 or 2 bytes long, followed by nul.
if (compress_level >= 0) {
char tmp[2];
tmp[0] = compress_level + '0'; tmp[1] = '\0';
strcat(out_mode, tmp);
strcat(out_un_mode, tmp);
}
if (argc == optind && isatty(STDIN_FILENO)) return usage(stdout, EXIT_SUCCESS, is_long_help); // potential memory leak...
fn_in = (optind < argc)? argv[optind] : "-";
// generate the fn_list if necessary
if (fn_list == 0 && ga.reference) fn_list = samfaipath(ga.reference);
// open file handlers
if ((in = sam_open_format(fn_in, "r", &ga.in)) == 0) {
print_error_errno("view", "failed to open \"%s\" for reading", fn_in);
ret = 1;
goto view_end;
}
if (fn_list) {
if (hts_set_fai_filename(in, fn_list) != 0) {
fprintf(stderr, "[main_samview] failed to use reference \"%s\".\n", fn_list);
ret = 1;
goto view_end;
}
}
if ((header = sam_hdr_read(in)) == 0) {
fprintf(stderr, "[main_samview] fail to read the header from \"%s\".\n", fn_in);
ret = 1;
goto view_end;
}
if (settings.rghash) { // FIXME: I do not know what "bam_header_t::n_text" is for...
char *tmp;
int l;
tmp = drop_rg(header->text, settings.rghash, &l);
free(header->text);
header->text = tmp;
header->l_text = l;
}
if (!is_count) {
if ((out = sam_open_format(fn_out? fn_out : "-", out_mode, &ga.out)) == 0) {
print_error_errno("view", "failed to open \"%s\" for writing", fn_out? fn_out : "standard output");
ret = 1;
goto view_end;
}
if (fn_list) {
if (hts_set_fai_filename(out, fn_list) != 0) {
fprintf(stderr, "[main_samview] failed to use reference \"%s\".\n", fn_list);
ret = 1;
goto view_end;
}
}
if (*out_format || is_header ||
out_mode[1] == 'b' || out_mode[1] == 'c' ||
(ga.out.format != sam && ga.out.format != unknown_format)) {
if (sam_hdr_write(out, header) != 0) {
fprintf(stderr, "[main_samview] failed to write the SAM header\n");
ret = 1;
goto view_end;
}
}
if (fn_un_out) {
if ((un_out = sam_open_format(fn_un_out, out_un_mode, &ga.out)) == 0) {
print_error_errno("view", "failed to open \"%s\" for writing", fn_un_out);
ret = 1;
goto view_end;
}
if (fn_list) {
if (hts_set_fai_filename(un_out, fn_list) != 0) {
fprintf(stderr, "[main_samview] failed to use reference \"%s\".\n", fn_list);
ret = 1;
goto view_end;
}
}
if (*out_format || is_header ||
out_un_mode[1] == 'b' || out_un_mode[1] == 'c' ||
(ga.out.format != sam && ga.out.format != unknown_format)) {
if (sam_hdr_write(un_out, header) != 0) {
fprintf(stderr, "[main_samview] failed to write the SAM header\n");
ret = 1;
goto view_end;
}
}
}
}
if (n_threads > 1) { if (out) hts_set_threads(out, n_threads); }
if (is_header_only) goto view_end; // no need to print alignments
if (optind + 1 >= argc) { // convert/print the entire file
bam1_t *b = bam_init1();
int r;
while ((r = sam_read1(in, header, b)) >= 0) { // read one alignment from `in'
if (!process_aln(header, b, &settings)) {
if (!is_count) { if (check_sam_write1(out, header, b, fn_out, &ret) < 0) break; }
count++;
} else {
if (un_out) { if (check_sam_write1(un_out, header, b, fn_un_out, &ret) < 0) break; }
}
}
if (r < -1) {
fprintf(stderr, "[main_samview] truncated file.\n");
ret = 1;
}
bam_destroy1(b);
} else { // retrieve alignments in specified regions
int i;
bam1_t *b;
hts_idx_t *idx = sam_index_load(in, fn_in); // load index
if (idx == 0) { // index is unavailable
fprintf(stderr, "[main_samview] random alignment retrieval only works for indexed BAM or CRAM files.\n");
ret = 1;
goto view_end;
}
b = bam_init1();
for (i = optind + 1; i < argc; ++i) {
int result;
hts_itr_t *iter = sam_itr_querys(idx, header, argv[i]); // parse a region in the format like `chr2:100-200'
if (iter == NULL) { // region invalid or reference name not found
int beg, end;
if (hts_parse_reg(argv[i], &beg, &end))
fprintf(stderr, "[main_samview] region \"%s\" specifies an unknown reference name. Continue anyway.\n", argv[i]);
else
fprintf(stderr, "[main_samview] region \"%s\" could not be parsed. Continue anyway.\n", argv[i]);
continue;
}
// fetch alignments
while ((result = sam_itr_next(in, iter, b)) >= 0) {
if (!process_aln(header, b, &settings)) {
if (!is_count) { if (check_sam_write1(out, header, b, fn_out, &ret) < 0) break; }
count++;
} else {
if (un_out) { if (check_sam_write1(un_out, header, b, fn_un_out, &ret) < 0) break; }
}
}
hts_itr_destroy(iter);
if (result < -1) {
fprintf(stderr, "[main_samview] retrieval of region \"%s\" failed due to truncated file or corrupt BAM index file\n", argv[i]);
ret = 1;
break;
}
}
bam_destroy1(b);
hts_idx_destroy(idx); // destroy the BAM index
}
view_end:
if (is_count && ret == 0)
printf("%" PRId64 "\n", count);
// close files, free and return
if (in) check_sam_close("view", in, fn_in, "standard input", &ret);
if (out) check_sam_close("view", out, fn_out, "standard output", &ret);
if (un_out) check_sam_close("view", un_out, fn_un_out, "file", &ret);
free(fn_list); free(fn_out); free(settings.library); free(fn_un_out);
sam_global_args_free(&ga);
if ( header ) bam_hdr_destroy(header);
if (settings.bed) bed_destroy(settings.bed);
if (settings.rghash) {
khint_t k;
for (k = 0; k < kh_end(settings.rghash); ++k)
if (kh_exist(settings.rghash, k)) free((char*)kh_key(settings.rghash, k));
kh_destroy(rg, settings.rghash);
}
if (settings.remove_aux_len) {
free(settings.remove_aux);
}
return ret;
}
static int usage(FILE *fp, int exit_status, int is_long_help)
{
fprintf(fp,
"\n"
"Usage: samtools view [options] <in.bam>|<in.sam>|<in.cram> [region ...]\n"
"\n"
"Options:\n"
// output options
" -b output BAM\n"
" -C output CRAM (requires -T)\n"
" -1 use fast BAM compression (implies -b)\n"
" -u uncompressed BAM output (implies -b)\n"
" -h include header in SAM output\n"
" -H print SAM header only (no alignments)\n"
" -c print only the count of matching records\n"
" -o FILE output file name [stdout]\n"
" -U FILE output reads not selected by filters to FILE [null]\n"
// extra input
" -t FILE FILE listing reference names and lengths (see long help) [null]\n"
// read filters
" -L FILE only include reads overlapping this BED FILE [null]\n"
" -r STR only include reads in read group STR [null]\n"
" -R FILE only include reads with read group listed in FILE [null]\n"
" -q INT only include reads with mapping quality >= INT [0]\n"
" -l STR only include reads in library STR [null]\n"
" -m INT only include reads with number of CIGAR operations consuming\n"
" query sequence >= INT [0]\n"
" -f INT only include reads with all bits set in INT set in FLAG [0]\n"
" -F INT only include reads with none of the bits set in INT set in FLAG [0]\n"
// read processing
" -x STR read tag to strip (repeatable) [null]\n"
" -B collapse the backward CIGAR operation\n"
" -s FLOAT integer part sets seed of random number generator [0];\n"
" rest sets fraction of templates to subsample [no subsampling]\n"
// general options
" -@, --threads INT\n"
" number of BAM/CRAM compression threads [0]\n"
" -? print long help, including note about region specification\n"
" -S ignored (input format is auto-detected)\n");
sam_global_opt_help(fp, "-.O.T");
fprintf(fp, "\n");
if (is_long_help)
fprintf(fp,
"Notes:\n"
"\n"
"1. This command now auto-detects the input format (BAM/CRAM/SAM).\n"
" Further control over the CRAM format can be specified by using the\n"
" --output-fmt-option, e.g. to specify the number of sequences per slice\n"
" and to use avoid reference based compression:\n"
"\n"
"\tsamtools view -C --output-fmt-option seqs_per_slice=5000 \\\n"
"\t --output-fmt-option no_ref -o out.cram in.bam\n"
"\n"
" Options can also be specified as a comma separated list within the\n"
" --output-fmt value too. For example this is equivalent to the above\n"
"\n"
"\tsamtools view --output-fmt cram,seqs_per_slice=5000,no_ref \\\n"
"\t -o out.cram in.bam\n"
"\n"
"2. The file supplied with `-t' is SPACE/TAB delimited with the first\n"
" two fields of each line consisting of the reference name and the\n"
" corresponding sequence length. The `.fai' file generated by \n"
" `samtools faidx' is suitable for use as this file. This may be an\n"
" empty file if reads are unaligned.\n"
"\n"
"3. SAM->BAM conversion: samtools view -bT ref.fa in.sam.gz\n"
"\n"
"4. BAM->SAM conversion: samtools view -h in.bam\n"
"\n"
"5. A region should be presented in one of the following formats:\n"
" `chr1', `chr2:1,000' and `chr3:1000-2,000'. When a region is\n"
" specified, the input alignment file must be a sorted and indexed\n"
" alignment (BAM/CRAM) file.\n"
"\n"
"6. Option `-u' is preferred over `-b' when the output is piped to\n"
" another samtools command.\n"
"\n");
return exit_status;
}
/** Implements the end_interval function of the plugin API */
int corsaro_dos_end_interval(corsaro_t *corsaro, corsaro_interval_t *int_end)
{
int this_interval = int_end->time-STATE(corsaro)->first_interval;
khiter_t i;
attack_vector_t *vector;
attack_vector_t **attack_arr = NULL;
int attack_arr_cnt = 0;
uint8_t gbuf[12];
uint8_t cntbuf[4];
if(this_interval < CORSARO_DOS_INTERVAL)
{
/* we haven't run for long enough to dump */
return 0;
}
else
{
/* we either have hit exactly the right amount of time,
or we have gone for too long, dump now and reset the counter */
STATE(corsaro)->first_interval = int_end->time;
/* fall through and continue to dump */
}
/* this is an interval we care about */
/* malloc an array big enough to hold the entire hash even though we wont
need it to be that big */
if((attack_arr =
malloc(sizeof(attack_vector_t *)*
kh_size(STATE(corsaro)->attack_hash))) == NULL)
{
corsaro_log(__func__, corsaro,
"could not malloc array for attack vectors");
return -1;
}
/* classify the flows and dump the attack ones */
for(i = kh_begin(STATE(corsaro)->attack_hash);
i != kh_end(STATE(corsaro)->attack_hash); ++i)
{
if(kh_exist(STATE(corsaro)->attack_hash, i))
{
vector = kh_key(STATE(corsaro)->attack_hash, i);
if(attack_vector_is_expired(vector, int_end->time) != 0)
{
kh_del(av, STATE(corsaro)->attack_hash, i);
attack_vector_free(vector);
vector = NULL;
}
else if(attack_vector_is_attack(corsaro, vector, int_end->time) != 0)
{
/* this is an attack */
/* add it to the attack array so we can know how many
before we dump it */
attack_arr[attack_arr_cnt] = vector;
attack_arr_cnt++;
}
else
{
attack_vector_reset(vector);
}
}
}
corsaro_io_write_interval_start(corsaro, STATE(corsaro)->outfile,
&corsaro->interval_start);
if(corsaro->global_file != NULL)
{
corsaro_io_write_plugin_start(corsaro, corsaro->global_file,
PLUGIN(corsaro));
}
if(CORSARO_FILE_MODE(STATE(corsaro)->outfile) == CORSARO_FILE_MODE_ASCII)
{
if(corsaro->global_file != NULL)
{
/* global stats */
/* dump the number of mismatched packets and vectors */
corsaro_file_printf(corsaro, corsaro->global_file,
"mismatch: %"PRIu32"\n"
"attack_vectors: %"PRIu32"\n"
"non-attack_vectors: %"PRIu32"\n",
STATE(corsaro)->number_mismatched_packets,
attack_arr_cnt,
kh_size(STATE(corsaro)->attack_hash)
-attack_arr_cnt);
}
/* dump the number of vectors */
corsaro_file_printf(corsaro, STATE(corsaro)->outfile, "%"PRIu32"\n",
attack_arr_cnt);
/* dump the vectors */
for(i = 0; i < attack_arr_cnt; i++)
{
if(ascii_dump(corsaro, attack_arr[i]) != 0)
{
corsaro_log(__func__, corsaro, "could not dump hash");
return -1;
}
/* reset the interval stats */
attack_vector_reset(attack_arr[i]);
}
}
else if(CORSARO_FILE_MODE(STATE(corsaro)->outfile) == CORSARO_FILE_MODE_BINARY)
{
if(corsaro->global_file != NULL)
{
/* global stats */
bytes_htonl(&gbuf[0], STATE(corsaro)->number_mismatched_packets);
bytes_htonl(&gbuf[4], attack_arr_cnt);
bytes_htonl(&gbuf[8],
kh_size(STATE(corsaro)->attack_hash)-attack_arr_cnt);
if(corsaro_file_write(corsaro, corsaro->global_file,
&gbuf[0], 12) != 12)
{
corsaro_log(__func__, corsaro,
"could not dump global stats to file");
return -1;
}
}
/* dump the number of vectors */
bytes_htonl(&cntbuf[0], attack_arr_cnt);
if(corsaro_file_write(corsaro, STATE(corsaro)->outfile,
&cntbuf[0], 4) != 4)
{
corsaro_log(__func__, corsaro,
"could not dump vector count to file");
return -1;
}
/* dump the vectors */
for(i = 0; i < attack_arr_cnt; i++)
{
if(binary_dump(corsaro, attack_arr[i]) != 0)
{
corsaro_log(__func__, corsaro, "could not dump hash");
return -1;
}
attack_vector_reset(attack_arr[i]);
}
}
else
{
corsaro_log(__func__, corsaro, "invalid mode");
return -1;
}
if(corsaro->global_file != NULL)
{
corsaro_io_write_plugin_end(corsaro, corsaro->global_file,
PLUGIN(corsaro));
}
corsaro_io_write_interval_end(corsaro, STATE(corsaro)->outfile, int_end);
STATE(corsaro)->number_mismatched_packets = 0;
free(attack_arr);
/* if we are rotating, now is when we should do it */
if(corsaro_is_rotate_interval(corsaro))
{
/* close the current file */
if(STATE(corsaro)->outfile != NULL)
{
corsaro_file_close(corsaro, STATE(corsaro)->outfile);
STATE(corsaro)->outfile = NULL;
}
}
return 0;
}
void
pic_gc(pic_state *pic)
{
struct context *cxt;
size_t j;
khash_t(oblist) *s = &pic->oblist;
struct symbol *sym;
int it;
struct object *obj, *prev, *next;
assert(pic->gc_attrs == NULL);
if (! pic->gc_enable) {
return;
}
/* scan objects */
for (cxt = pic->cxt; cxt != NULL; cxt = cxt->prev) {
if (cxt->fp) gc_mark_object(pic, (struct object *)cxt->fp);
if (cxt->sp) gc_mark_object(pic, (struct object *)cxt->sp);
if (cxt->irep) gc_mark_object(pic, (struct object *)cxt->irep);
gc_mark(pic, cxt->conts);
}
for (j = 0; j < pic->ai; ++j) {
gc_mark_object(pic, (struct object *)pic->arena[j]);
}
gc_mark(pic, pic->globals);
gc_mark(pic, pic->halt);
/* scan weak references */
do {
struct object *key;
pic_value val;
int it;
khash_t(attr) *h;
struct attr *attr;
j = 0;
attr = pic->gc_attrs;
while (attr != NULL) {
h = &attr->hash;
for (it = kh_begin(h); it != kh_end(h); ++it) {
if (! kh_exist(h, it))
continue;
key = kh_key(h, it);
val = kh_val(h, it);
if (is_alive(key)) {
if (pic_obj_p(pic, val) && ! is_alive((struct object *) pic_ptr(pic, val))) {
gc_mark(pic, val);
++j;
}
}
}
attr = attr->prev;
}
} while (j > 0);
/* reclaim dead weak references */
while (pic->gc_attrs != NULL) {
khash_t(attr) *h = &pic->gc_attrs->hash;
for (it = kh_begin(h); it != kh_end(h); ++it) {
if (! kh_exist(h, it))
continue;
obj = kh_key(h, it);
if (! is_alive(obj)) {
kh_del(attr, h, it);
}
}
pic->gc_attrs = pic->gc_attrs->prev;
}
for (it = kh_begin(s); it != kh_end(s); ++it) {
if (! kh_exist(s, it))
continue;
sym = kh_val(s, it);
if (sym && ! is_alive((struct object *)sym)) {
kh_del(oblist, s, it);
}
}
/* reclaim dead objects */
for (prev = &pic->gc_head, obj = prev->next; obj != &pic->gc_head; prev = obj, obj = next) {
next = obj->next;
if (is_alive(obj)) {
unmark(obj);
} else {
gc_finalize_object(pic, obj);
pic_free(pic, obj);
prev->next = next;
obj = prev;
}
}
}
ERR_VALUE kmer_freq_distribution(const PROGRAM_OPTIONS *Options, const uint32_t KMerSize, const ONE_READ *Reads, const size_t ReadCount)
{
int err;
size_t maxValue = 0;
khiter_t it;
size_t kmerCount = 0;
char *kmerString = NULL;
khash_t(kc) *table = kh_init(kc);
ERR_VALUE ret = ERR_INTERNAL_ERROR;
ret = utils_calloc(KMerSize + 1, sizeof(char), &kmerString);
if (ret == ERR_SUCCESS) {
const ONE_READ *r = Reads;
kmerString[KMerSize] = '\0';
for (size_t i = 0; i < ReadCount; ++i) {
const READ_PART *p = &r->Part;
read_split(r);
if (p->ReadSequenceLength >= KMerSize) {
for (size_t j = 0; j < p->ReadSequenceLength - KMerSize + 1; ++j) {
char *s = NULL;
memcpy(kmerString, p->ReadSequence + j, KMerSize*sizeof(char));
ret = utils_copy_string(kmerString, &s);
if (ret == ERR_SUCCESS) {
it = kh_put(kc, table, s, &err);
switch (err) {
case 0:
kh_value(table, it) += 1;
if (kh_value(table, it) > maxValue)
maxValue = kh_value(table, it);
utils_free(s);
break;
case 1:
case 2:
kh_value(table, it) = 1;
break;
default:
ret = ERR_OUT_OF_MEMORY;
break;
}
++kmerCount;
if (ret != ERR_SUCCESS)
utils_free(s);
}
if (ret != ERR_SUCCESS)
break;
}
}
if (ret != ERR_SUCCESS)
break;
++r;
}
if (ret == ERR_SUCCESS) {
size_t *freqArray = NULL;
++maxValue;
ret = utils_calloc(maxValue, sizeof(size_t), &freqArray);
if (ret == ERR_SUCCESS) {
memset(freqArray, 0, maxValue*sizeof(size_t));
for (it = kh_begin(table); it != kh_end(table); ++it) {
if (kh_exist(table, it))
++freqArray[kh_value(table, it)];
}
for (size_t i = 0; i < maxValue; ++i) {
if (freqArray[i] > 0)
fprintf(stdout, "%Iu, %Iu, %lf\n", i, freqArray[i], (double)freqArray[i]*100/ (double)kmerCount);
}
utils_free(freqArray);
}
}
utils_free(kmerString);
}
for (size_t i = kh_begin(table); i < kh_end(table); ++i) {
if (kh_exist(table, i))
utils_free(kh_key(table, i));
}
kh_destroy(kc, table);
return ret;
}
void printSegCounter() {
for (khint_t k = kh_begin(seg_counter); k != kh_end(seg_counter); ++k) // traverse
if (kh_exist(seg_counter, k)) // test if a bucket contains data
printf("%04X %*d |%s", kh_key(seg_counter, k), 6, kh_value(seg_counter, k), !(k%16) ? "\n": " ");
}
int main(int argc, char *argv[])
{
int c, i, n, ret, res;
int tid, pos, *n_plp;
cmdopt_t o;
bam_mplp_t mplp;
const bam_pileup1_t **plp;
aux_t **data;
bam_hdr_t *h = 0;
sv_t sv1;
qual_sum_t qual2;
khiter_t k_iter;
khash_t(sv_hash) *sv_h = kh_init(sv_hash);
khash_t(sv_geno) *geno_h = kh_init(sv_geno);
khash_t(colmap) *smp_cols;
khash_t(ped) *ped_h = 0;
mempool_t *mp;
char **samples;
o.min_q = 40; o.min_s = 80; o.min_len = 150; o.min_dp = 10; o.bed = 0, o.fnped = 0, o.mi_prob=0.005;
while ((c = getopt(argc, argv, "hq:s:l:d:b:p:m:")) >= 0) {
if (c == 'h') { usage(stderr, &o); return 0; }
else if (c == 'q') o.min_q = atoi(optarg);
else if (c == 's') o.min_s = atoi(optarg);
else if (c == 'l') o.min_len = atoi(optarg);
else if (c == 'd') o.min_dp = atoi(optarg);
else if (c == 'p') o.fnped = optarg;
else if (c == 'm') o.mi_prob = atof(optarg);
else if (c == 'b') {
if ((o.bed = bed_read(optarg)) == NULL) {
return -1;
}
}
}
if (o.mi_prob < 0.0000000000001 || o.mi_prob > 0.1) {
fprintf(stderr, "Error. Probability of a mendelian inconsistency must be between 0.1 and 0.0000000000001.\n");
}
if (argc - optind < 1) {
usage(stderr, &o);
return 1;
}
// Open files and initalize aux data //
n = argc - optind;
data = calloc(n, sizeof(aux_t*));
samples = (char**)malloc(n * sizeof(char*));
for (i = 0; i < n; ++i) {
data[i] = calloc(1, sizeof (aux_t));
data[i]->fp = sam_open(argv[optind + i], "r");
if (!data[i]->fp) {
fprintf(stderr, "Input file \"%s\" could not be opened.\n", argv[optind + 1]);
return 1;
}
data[i]->min_mapq = o.min_q;
data[i]->min_as = o.min_s;
data[i]->min_len = o.min_len;
data[i]->hdr = sam_hdr_read(data[i]->fp);
if (!data[i]->hdr) {
fprintf(stderr, "Could not read the header for input file \"%s\".\n", argv[optind + 1]);
return 1;
}
samples[i] = find_sample(data[i]->hdr, &res);
if (!samples[i]) {
fprintf(stderr, "Warning. No sample name detected for bam %s. Using filename\n", argv[optind + i]);
samples[i] = argv[optind + i];
}
}
h = data[0]->hdr;
smp_cols = map_samples(samples, n);
if (o.fnped) {
if ((ped_h = read_ped(o.fnped, smp_cols)) == 0) { return -1; }
}
// The core data processing loop //
mplp = bam_mplp_init(n, read_bam, (void**)data);
n_plp = calloc(n, sizeof(int)); // n_plp[i] is the number of covering reads from the i-th BAM
plp = calloc(n, sizeof(bam_pileup1_t*)); // plp[i] points to the array of covering reads in mplp
//quals = (qual_vec_t*)calloc(n, sizeof(qual_vec_t));
mp = mp_init();
while ((ret = bam_mplp_auto(mplp, &tid, &pos, n_plp, plp)) > 0) { // iterate of positions with coverage
int n_sv;
if (o.bed && tid >= 0 && !bed_overlap(o.bed, h->target_name[tid], pos, pos+1)) continue;
n_sv = plp2sv(h, tid, pos, n, n_plp, plp, sv_h);
if (n_sv > 1) { fprintf(stderr, "Warning: more than two alleles detected at %s:%d\n", h->target_name[tid], pos); }
if (n_sv) {
fprintf(stderr, "SV detected at %d:%d\n", tid, pos);
for (k_iter = kh_begin(sv_h); k_iter != kh_end(sv_h); ++k_iter) {
if (kh_exist(sv_h, k_iter)) {
sv1 = kh_value(sv_h, k_iter);
fprintf(stderr, "SV tid1=%d, tid2=%d, pos1=%d, pos2=%d, ori1=%d, ori2=%d, allele=%d\n", sv1.tid1, sv1.tid2, sv1.pos1, sv1.pos2, sv1.ori1, sv1.ori2, sv1.allele);
}
}
res = get_qual_data(h, tid, pos, n, n_plp, plp, n_sv + 1, sv_h, geno_h, mp);
if (res < 0) {
fprintf(stderr, "Error collecting quality data from reads\n");
return -1;
}
kh_clear(sv_hash, sv_h);
}
}
print_header(h, optind, n, argv);
genotype_sv(h, n, geno_h, o.min_dp, ped_h, o.mi_prob);
free(n_plp);
free(plp);
bam_mplp_destroy(mplp);
mp_destroy(mp);
if (o.bed) bed_destroy(o.bed);
for (i = 0; i < n; ++i) {
bam_hdr_destroy(data[i]->hdr);
sam_close(data[i]->fp);
free(data[i]);
free(samples[i]);
}
free(data);
free(samples);
kh_destroy(sv_hash, sv_h);
kh_destroy(sv_geno, geno_h);
kh_destroy(colmap, smp_cols);
kh_destroy(ped, ped_h);
return 0;
}
static int
cachessess_exist_cb(cache_iter_t it)
{
return kh_exist(srcsessmap, it);
}
size_t
sen_render_flush(int clear_buff)
{
// gl_check_error();
//_logfi("1");
blend_group_t* bg;
khint_t i,k,j;
size_t total = 0;
khash_t(hmsp)* tgs;
camera_t* cam = sen_camera();
tex_group_t* tg;
khash_t(hmsp)* sgs;
shader_group_t* sg;
vector_clear(zsorter);
for (k = kh_begin(g_bgs); k != kh_end(g_bgs); ++k)
{
if (!kh_exist(g_bgs,k)) continue;
bg = kh_val(g_bgs, k);
if (bg->num == 0) {
kh_del(hmip,g_bgs,k);
continue;
}
tgs = bg->tgs;
// set_blending( (blend_func) (kh_key(g_bgs, k)) );
for (i = kh_begin(tgs); i != kh_end(tgs); ++i)
{
if (!kh_exist(tgs,i)) continue;
tg = kh_val(tgs, i);
if (tg->num == 0) {
kh_del(hmsp,tgs,i);
continue;
}
/*
if (tg->tex)
sen_texture_bind(tg->tex);
else if (tg->font)
sen_font_bind(tg->font);
*/
sgs = tg->sgs;
for (j = kh_begin(sgs); j != kh_end(sgs); ++j)
{
if (!kh_exist(sgs,j)) continue;
sg = kh_val(sgs, j);
if (sg->num == 0 || !sg->buff) {
kh_del(hmsp,sgs,j);
continue;
}
if (sg->buff) {
/*
sen_shader_use(sg->program);
{
if (tg->tex || tg->font)
sen_uniform_1iN(sg->program, "u_tex0", 0);
sen_uniform_m4fN(sg->program, "u_mvp", cam->view_proj.data);
vertex_buffer_render( sg->buff, GL_TRIANGLES);
total+=vertex_buffer_size(sg->buff);
if (clear_buff)
vertex_buffer_clear( sg->buff );
//sen_shader_use(NULL);
}*/
vector_push_back( zsorter, &sg );
}
sg->num = 0;
}
tg->num = 0;
}
bg->num = 0;
}
if (zsorter->size > 0)
vector_sort(zsorter, zcmp);
for (j = 0; j < zsorter->size; j++) {
shader_group_t* sg = *(shader_group_t**)vector_get(zsorter, j);
// _logfi("%s %d",sg->name, sg->z);
set_blending( (blend_func) (sg->bg->key) );
if (sg->tg->tex)
sen_texture_bind(sg->tg->tex);
else if (sg->tg->font)
sen_font_bind(sg->tg->font);
sen_shader_use(sg->program);
{
if (sg->tg->tex || sg->tg->font)
sen_uniform_1iN(sg->program, "u_tex0", 0);
sen_uniform_m4fN(sg->program, "u_mvp", sg->z > 9500 ? cam->proj.data : cam->view_proj.data);
vertex_buffer_render( sg->buff, GL_TRIANGLES);
total+=vertex_buffer_size(sg->buff);
if (clear_buff)
vertex_buffer_clear( sg->buff );
//sen_shader_use(NULL);
}
}
// _logfi("-------------------------------------------------");
return total;
}
