void
mrb_gc_mark_hash(mrb_state *mrb, struct RHash *hash)
{
khiter_t k;
khash_t(ht) *h = hash->ht;
if (!h) return;
for (k = kh_begin(h); k != kh_end(h); k++) {
if (kh_exist(h, k)) {
mrb_value key = kh_key(h, k);
mrb_value val = kh_value(h, k);
mrb_gc_mark_value(mrb, key);
mrb_gc_mark_value(mrb, val);
}
}
}
static int
rbk_finish(strm_stream* strm, strm_value data)
{
struct rbk_data *d = strm->data;
khiter_t i;
for (i=kh_begin(d->tbl); i!=kh_end(d->tbl); i++) {
if (kh_exist(d->tbl, i)) {
strm_value values[2];
values[0] = kh_key(d->tbl, i);
values[1] = kh_value(d->tbl, i);
strm_emit(strm, strm_ary_new(values, 2), NULL);
}
}
return STRM_OK;
}
static mrb_value
mrb_hash_values(mrb_state *mrb, mrb_value hash)
{
khash_t(ht) *h = RHASH_TBL(hash);
khiter_t k;
mrb_value ary;
if (!h) return mrb_ary_new(mrb);
ary = mrb_ary_new_capa(mrb, kh_size(h));
for (k = kh_begin(h); k != kh_end(h); k++) {
if (kh_exist(h, k)){
mrb_value v = kh_value(h,k);
mrb_ary_push(mrb, ary, v);
}
}
return ary;
}
static bam_header_t *hash2header(const kh_ref_t *hash)
{
bam_header_t *header;
khiter_t k;
header = bam_header_init();
header->n_targets = kh_size(hash);
header->target_name = (char**)calloc(kh_size(hash), sizeof(char*));
header->target_len = (uint32_t*)calloc(kh_size(hash), 4);
for (k = kh_begin(hash); k != kh_end(hash); ++k) {
if (kh_exist(hash, k)) {
int i = (int)kh_value(hash, k);
header->target_name[i] = (char*)kh_key(hash, k);
header->target_len[i] = kh_value(hash, k)>>32;
}
}
bam_init_header_hash(header);
return header;
}
static mrb_value
mrb_hash_values(mrb_state *mrb, mrb_value hash)
{
khash_t(ht) *h = RHASH_TBL(hash);
khiter_t k;
mrb_value ary = mrb_ary_new(mrb);
if (!h) return ary;
for (k = kh_begin(h); k != kh_end(h); k++) {
if (kh_exist(h, k)){
mrb_value v = kh_value(h,k);
if ( !mrb_special_const_p(v) )
v = mrb_obj_dup(mrb, v);
mrb_ary_push(mrb, ary, v);
}
}
return ary;
}
void cram_stats_dump(cram_stats *st) {
int i;
fprintf(stderr, "cram_stats:\n");
for (i = 0; i < MAX_STAT_VAL; i++) {
if (!st->freqs[i])
continue;
fprintf(stderr, "\t%d\t%d\n", i, st->freqs[i]);
}
if (st->h) {
khint_t k;
for (k = kh_begin(st->h); k != kh_end(st->h); k++) {
if (!kh_exist(st->h, k))
continue;
fprintf(stderr, "\t%d\t%d\n", kh_key(st->h, k), kh_val(st->h, k));
}
}
}
static mrb_value
mrb_hash_has_valueWithvalue(mrb_state *mrb, mrb_value hash, mrb_value value)
{
khash_t(ht) *h = RHASH_TBL(hash);
khiter_t k;
if (h) {
for (k = kh_begin(h); k != kh_end(h); k++) {
if (!kh_exist(h, k)) continue;
if (mrb_equal(mrb, kh_value(h,k), value)) {
return mrb_true_value();
}
}
}
return mrb_false_value();
}
// Called when the manager sends a complete message
void messageArrivedFromManager() {
printf ("Message arrived: >%s< for >%s<\r\n", commandMessage, commandClientId);
// See if the client is connected, if so immediately forward
khiter_t k = kh_get(clientStatuses, clientStatuses, (char*)commandClientId); // Find it in the hash
if (k != kh_end(clientStatuses)) { // Was it in the hash?
clientStatus* status = kh_value(clientStatuses, k); // Grab the clientStatus from the hash
snprintf(httpResponse, HTTP_RESPONSE_SIZE, HTTP_TEMPLATE, commandMessageLen, commandMessage); // Compose the response message
write(status->io.fd, httpResponse, strlen(httpResponse)); // Send it
closeConnection((ev_io*)status); // Close the conn
return;
}
// If not, add to a queue
khiter_t q = kh_get(queue, queue, (char*)commandClientId); // See if this client is already in the queue
if (q == kh_end(queue)) {
printf("Creating queue for %s\r\n", commandClientId);
// This client needs to be added to the queue
// First make a new list
klist_t(messages) *newMessageList = kl_init(messages);
*kl_pushp(messages, newMessageList) = strdup((char*)commandMessage); // Add the message to the list
// Now make a new hash entry pointing to this new list
int ret;
q = kh_put(queue, queue, strdup((char*)commandClientId), &ret);
kh_value(queue, q) = newMessageList;
} else {
printf("Adding to the queue for %s\r\n", commandClientId);
// This client is in the queue already eg it has a hash entry
// Pushp puts this message at the end of the queue, so that shift will grab the oldest first (like a FIFO)
*kl_pushp(messages, kh_value(queue, q)) = strdup((char*)commandMessage);
}
// Now do a printout of the hash list
for (khiter_t qi = kh_begin(queue); qi < kh_end(queue); qi++) {
if (kh_exist(queue, qi)) {
printf("Queue for %s\n", kh_key(queue,qi));
klist_t(messages) *list = kh_value(queue, qi);
kliter_t(messages) *li;
for (li = kl_begin(list); li != kl_end(list); li = kl_next(li))
printf("%s\n", kl_val(li));
printf("----\n");
}
}
}
void bcf_hdr_destroy(bcf_hdr_t *h)
{
int i;
khint_t k;
for (i = 0; i < 3; ++i) {
vdict_t *d = (vdict_t*)h->dict[i];
if (d == 0) continue;
for (k = kh_begin(d); k != kh_end(d); ++k)
if (kh_exist(d, k)) free((char*)kh_key(d, k));
kh_destroy(vdict, d);
free(h->id[i]);
}
for (i=0; i<h->nhrec; i++)
bcf_hrec_destroy(h->hrec[i]);
if (h->nhrec) free(h->hrec);
if (h->samples) free(h->samples);
free(h->mem.s); free(h->text);
free(h);
}
/* lenp must be a pointer to a size_t variable */
const char*
mrb_sym2name_len(mrb_state *mrb, mrb_sym sym, size_t *lenp)
{
khash_t(n2s) *h = mrb->name2sym;
khiter_t k;
symbol_name sname;
for (k = kh_begin(h); k != kh_end(h); k++) {
if (kh_exist(h, k)) {
if (kh_value(h, k) == sym) {
sname = kh_key(h, k);
*lenp = sname.len;
return sname.name;
}
}
}
*lenp = 0;
return NULL; /* missing */
}
int merge_interval(kh_pos_t* positions_read, char *max_chromosome_merged, unsigned long max_position_merged,
char **chromosome_order, int num_chromosomes, vcf_file_t **files,
shared_options_data_t *shared_options_data, merge_options_data_t *options_data, list_t *output_list) {
int num_entries = 0;
#pragma omp parallel for num_threads(shared_options_data->num_threads) reduction(+:num_entries)
for (int k = kh_begin(positions_read); k < kh_end(positions_read); k++) {
if (kh_exist(positions_read, k)) {
array_list_t *records_in_position = kh_value(positions_read, k);
assert(records_in_position);
vcf_record_t *record = ((vcf_record_file_link*) array_list_get(0, records_in_position))->record;
vcf_record_file_link **links = NULL;
int num_links = 0;
// Remove positions prior to the last chromosome:position to merge
int cmp_chrom = compare_chromosomes(record->chromosome, max_chromosome_merged, chromosome_order, num_chromosomes);
if (cmp_chrom < 0 || (cmp_chrom == 0 && compare_positions(record->position, max_position_merged) <= 0)) {
links = records_in_position->items;
num_links = records_in_position->size;
}
// Launch merge
if (num_links > 0) {
// printf("links[0] = %s:%ld in file %s\n", links[0]->record->chromosome, links[0]->record->position, links[0]->file->filename);
int err_code = 0;
vcf_record_t *merged = merge_position(links, num_links, files, options_data->num_files, options_data, &err_code);
if (!err_code) {
list_item_t *item = list_item_new(k, MERGED_RECORD, merged);
list_insert_item(item, output_list);
num_entries += 1;
}
// Free empty nodes (lists of records in the same position)
array_list_free(records_in_position, vcf_record_file_link_free);
kh_del(pos, positions_read, k);
}
} // End kh_exist
}
return num_entries;
}
void
int_htable_destroy(int_htable *ht)
{
khiter_t k;
if (!ht) {
return;
}
for (k = kh_begin(sh->htable); k != kh_end(ht->htable); ++k) {
if (kh_exist(ht->htable, k)) {
if (ht->free_value_fn) {
ht->free_value_fn(kh_value(ht->htable,k));
}
}
}
kh_destroy(int, ht->htable);
free(ht);
}
static pic_value
pic_dict_dictionary_for_each(pic_state *pic)
{
struct pic_proc *proc;
struct pic_dict *dict;
khiter_t it;
khash_t(dict) *kh;
pic_get_args(pic, "ld", &proc, &dict);
kh = &dict->hash;
for (it = kh_begin(kh); it != kh_end(kh); ++it) {
if (kh_exist(kh, it)) {
pic_apply1(pic, proc, pic_obj_value(kh_key(kh, it)));
}
}
return pic_undef_value();
}
static mrb_bool
iv_foreach(mrb_state *mrb, iv_tbl *t, iv_foreach_func *func, void *p)
{
khash_t(iv) *h = &t->h;
khiter_t k;
int n;
if (h) {
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, h, k);
}
}
}
}
return TRUE;
}
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(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) {
if (!h2) return mrb_true_value();
return mrb_false_value();
}
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, 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();
}
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
mrb_hash_has_value(mrb_state *mrb, mrb_value hash)
{
mrb_value val;
khash_t(ht) *h;
khiter_t k;
mrb_get_args(mrb, "o", &val);
h = RHASH_TBL(hash);
if (h) {
for (k = kh_begin(h); k != kh_end(h); k++) {
if (!kh_exist(h, k)) continue;
if (mrb_equal(mrb, kh_value(h, k).v, val)) {
return mrb_true_value();
}
}
}
return mrb_false_value();
}
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;
}
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_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;
}
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);
}
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;
}
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;
}
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 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;
}
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;
}
/*
* 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 cache_iter_t
cachessess_begin_cb(void)
{
return kh_begin(srcsessmap);
}
static cache_iter_t
cachefkcrt_begin_cb(void)
{
return kh_begin(certmap);
}
