void
processCCO(SnapConConMesg *cco) {
int *contigGapToUngap = NULL;
int contigLengthGapped = strlen(cco->consensus);
int contigLengthUngap = 0;
int i = 0, j = 0;
int isDegenerate = 0;
// By definition, a degenerate contig has one unitig and is unplaced.
// In reality, those two conditions always occur together.
//
FILE *len = ctglen;
FILE *frg = frgctg;
FILE *utg = utgctg;
FILE *var = varctg;
if ((cco->placed == AS_UNPLACED) && (cco->num_unitigs == 1)) {
isDegenerate = 1;
len = deglen;
frg = frgdeg;
utg = utgdeg;
var = vardeg;
}
contigGapToUngap = (int *)safe_calloc(contigLengthGapped + 1, sizeof(int));
contigGapToUngap[0] = 0;
for (i=0; i<contigLengthGapped; i++) {
if (cco->consensus[i] != '-')
contigLengthUngap++;
contigGapToUngap[i+1] = contigLengthUngap;
}
fprintf(len, "%s\t%d\n",
AS_UID_toString(cco->eaccession),
contigLengthUngap);
if (isDegenerate == 0)
fprintf(ctginf, "%s\t%d\t%d\t%d\t%d\n",
AS_UID_toString(cco->eaccession),
contigLengthUngap,
cco->num_unitigs,
cco->num_pieces,
cco->num_vars);
else
fprintf(deginf, "%s\t%d\t%d\t%d\t%d\t%s\t%f\t%f\n",
AS_UID_toString(cco->eaccession),
contigLengthUngap,
cco->num_unitigs,
cco->num_pieces,
cco->num_vars,
AS_UID_toString(cco->unitigs[0].eident),
covStat[cco->unitigs[0].eident],
microHet[cco->unitigs[0].eident]);
uid2iid[cco->eaccession] = cco->iaccession;
if (ctgInfoMax <= cco->iaccession) {
ctgInfoMax *= 2;
ctgInfo = (ctgInfo_t *)safe_realloc(ctgInfo, ctgInfoMax * sizeof(ctgInfo_t));
}
ctgInfo[cco->iaccession].len = contigLengthUngap;
// VAR/variants
for (i=0; i<cco->num_vars; i++) {
IntMultiVar *v = cco->vars + i;
int bgn = contigGapToUngap[v->position.bgn];
int end = contigGapToUngap[v->position.end];
fprintf(var, "%s\t%s\t%d\t%d\t%d\t%d\t%d\t%d\t%s\t%s\t%s\n",
v->enc_var_seq,
AS_UID_toString(cco->eaccession),
bgn, end,
v->num_reads,
v->num_alleles_confirmed,
v->min_anchor_size,
v->var_length,
v->enc_num_reads,
v->enc_weights,
v->enc_read_ids);
}
// Remember what fragments were placed. This is used to ignore
// some fragments when reporting unplaced surrogate fragments.
set<AS_UID> placed;
// MPS/fragments
for (i=0; i<cco->num_pieces; i++) {
int bgn = contigGapToUngap[cco->pieces[i].position.bgn];
int end = contigGapToUngap[cco->pieces[i].position.end];
char ori = ORIF;
// If bgn == end, then the fragment fell entirely within a gap.
if (cco->pieces[i].position.bgn > cco->pieces[i].position.end) {
ori = ORIR;
end = contigGapToUngap[cco->pieces[i].position.bgn];
bgn = contigGapToUngap[cco->pieces[i].position.end];
}
fprintf(frg, "%s\t%s\t%d\t%d\t%c\n",
AS_UID_toString(cco->pieces[i].eident),
AS_UID_toString(cco->eaccession),
bgn, end, ori);
if (writeUnplaced)
placed.insert(cco->pieces[i].eident);
}
// UPS/unitigs
for (i=0; i<cco->num_unitigs; i++) {
int bgn = contigGapToUngap[cco->unitigs[i].position.bgn];
int end = contigGapToUngap[cco->unitigs[i].position.end];
char ori = ORIF;
// If this is a SURROGATE UNITIG, report "fraguid unitiguid contiguid"
if (cco->unitigs[i].position.bgn > cco->unitigs[i].position.end) {
ori = ORIR;
end = contigGapToUngap[cco->unitigs[i].position.bgn];
bgn = contigGapToUngap[cco->unitigs[i].position.end];
}
if (isDegenerate == 0)
fprintf(utg, "%s\t%s\t%d\t%d\t%c\t%s\n",
AS_UID_toString(cco->unitigs[i].eident),
AS_UID_toString(cco->eaccession),
bgn, end, ori,
decodeUnitigType(cco->unitigs[i].type));
else
fprintf(utg, "%s\t%s\t%d\t%d\t%c\n",
AS_UID_toString(cco->unitigs[i].eident),
AS_UID_toString(cco->eaccession),
bgn, end, ori);
// unplaced surrogate fragments
if ((writeUnplaced) && (surrogateUnitigFrags.count(cco->unitigs[i].eident) > 0)) {
vector<surFrag_t> &frg = surrogateUnitigFrags[cco->unitigs[i].eident];
for (uint32 ii=0; ii<frg.size(); ii++) {
char const *status = "unplaced";
if (placed.count(frg[ii].id) > 0) {
// Read already placed.
//continue;
status = "resolved";
}
int32 frgbgn = frg[ii].bgn + bgn;
int32 frgend = frg[ii].end + bgn;
if (ori == ORIR) {
frgbgn = end - frg[ii].bgn;
frgend = end - frg[ii].end;
}
if (frgbgn < frgend) {
fprintf(sfgctg, "%s\t%s\t%d\t%d\t%c\t%s\t%s\n",
AS_UID_toString(frg[ii].id),
AS_UID_toString(cco->eaccession),
contigGapToUngap[frgbgn],
contigGapToUngap[frgend],
ORIF,
status,
AS_UID_toString(cco->unitigs[i].eident));
} else {
fprintf(sfgctg, "%s\t%s\t%d\t%d\t%c\t%s\t%s\n",
AS_UID_toString(frg[ii].id),
AS_UID_toString(cco->eaccession),
contigGapToUngap[frgend],
contigGapToUngap[frgbgn],
ORIR,
status,
AS_UID_toString(cco->unitigs[i].eident));
}
}
}
}
safe_free(contigGapToUngap);
}
void VmBase::refresh_most()
{
vm_ids_.clear();
stable_vmthread_id_to_vm_id_.clear();
name_.clear();
uuid_.clear();
vsocket_num_.clear();
vcore_num_.clear();
vhpthread_num_.clear();
total_mem_size_.clear();
string cmd = "ps -C " + vm_cmd_ + " -wwo etime=,pid=,args=";
time_t cur_time;
time(&cur_time);
FILE* data = popen(cmd.c_str(), "r");
string pid;
string start_timestamp;
vector<string> args;
string tmp_str;
while(fgets(buf_.get(), BUF_SIZE, data))
{
args.clear();
istringstream is(buf_.get());
is >> start_timestamp;
long long days = 0;
long long hours = 0;
long long minutes = 0;
long long seconds = 0;
time_t start_time;
if (count(start_timestamp.begin(), start_timestamp.end(), '-') > 0)
sscanf(start_timestamp.c_str(), "%lld-%lld:%lld:%lld", &days, &hours, &minutes, &seconds);
else if (count(start_timestamp.begin(), start_timestamp.end(), ':') == 2)
sscanf(start_timestamp.c_str(), "%lld:%lld:%lld", &hours, &minutes, &seconds);
else if (count(start_timestamp.begin(), start_timestamp.end(), ':') == 1)
sscanf(start_timestamp.c_str(), "%lld:%lld", &minutes, &seconds);
start_time = cur_time - (((days * 24 + hours) * 60 + minutes) * 60 + seconds);
is >> pid;
while(is)
{
is >> tmp_str;
args.push_back(tmp_str);
}
//add vm_ids
VmId vm_id(start_time, stoull(pid));
vm_ids_.insert(vm_id);
//add name
string name = "";
auto name_iter = find(args.begin(), args.end(), "-name");
if (name_iter != args.end())
{
++name_iter;
name = *name_iter;
}
else
{
//TODO throw //because of cgroup need it
}
name_[vm_id] = name;
//add uuid
string uuid = "";
auto uuid_iter = find(args.begin(), args.end(), "-uuid");
if (uuid_iter != args.end())
{
++uuid_iter;
uuid = *uuid_iter;
}
uuid_[vm_id] = uuid;
//add vsocket vcore vhpthread
auto iter = find(args.begin(), args.end(), "-smp");
if (iter != args.end())
{
++iter;
vector<string> ops;
str_tools::split(*iter, ',', ops);
for(auto& op : ops)
{
vector<string> data;
str_tools::split(op, '=', data);
if (data.size() == 2) {
if(data[0] == "sockets")
vsocket_num_[vm_id] = stoi(data[1]);
else if(data[0] == "cores")
vcore_num_[vm_id] = stoi(data[1]);
else if(data[0] == "threads")
vhpthread_num_[vm_id] = stoi(data[1]);
}
}
}
//add total_mem_size
int size = -1;
auto size_iter = find(args.begin(), args.end(), "-m");
if (size_iter != args.end())
{
++size_iter;
size = stoi(*size_iter);
}
total_mem_size_[vm_id] = size;
}
pclose(data);
}
