int main(void)
{
int64 t0,t1,t2,t3;
d();
s=(int64*)calloc(q,sizeof(int64));
gw(2,0,1000);
gw(3,0,1500000);
sa(gr(3,0));
gw(tm(gr(3,0),gr(2,0)),(td(gr(3,0),gr(2,0)))+3,0);
_1:
sa(sr()-1);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa((sp()!=0)?0:1);
if(sp()!=0)goto _3;else goto _2;
_2:
sa(sr());
sa(0);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(tm(sr(),gr(2,0)));
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(td(sp(),gr(2,0)));
sa(sp()+3LL);
{int64 v0=sp();int64 v1=sp();gw(v1,v0,sp());}
goto _1;
_3:
gw(6,0,0);
gw(8,0,1);
sp();
_4:
if(((gr(8,0)*gr(8,0)*4)+(gr(8,0)*6)+2)>gr(3,0))goto _20;else goto _5;
_5:
sa(gr(8,0)+1);
gw(9,0,gr(8,0)+1);
_6:
sa(sr());
t0=sr()*2;
sa(sp()*t0);
t1=sp();
sa(sp()*gr(8,0)*2);
sa(t1);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(sp()+sp());
t0=sp();
t0=t0>gr(3,0)?1:0;
if((t0)!=0)goto _19;else goto _7;
_7:
t0=(gr(9,0)*gr(9,0))-(gr(8,0)*gr(8,0));
gw(2,1,(gr(9,0)*gr(9,0))-(gr(8,0)*gr(8,0)));
t1=gr(8,0)*gr(9,0)*2;
gw(3,1,gr(8,0)*gr(9,0)*2);
t2=(gr(9,0)*gr(9,0))+(gr(8,0)*gr(8,0));
gw(4,1,(gr(9,0)*gr(9,0))+(gr(8,0)*gr(8,0)));
t3=t1+t2;
t1=t0+t3;
gw(6,1,t1);
if(gr(2,1)>gr(3,1))goto _18;else goto _8;
_8:
sa(1);
sa(gr(6,1)>gr(3,0)?1:0);
_9:
if(sp()!=0)goto _17;else goto _10;
_10:
t0=sr()*((((gr(2,1)*7)+gr(3,1))*5)+gr(4,1));
gw(8,1,t0);
sa(sr()*gr(6,1));
sa(tm(sr(),gr(2,0)));
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(td(sp(),gr(2,0)));
sa(sp()+3LL);
{int64 v0=sp();sa(gr(sp(),v0));}
sa(sr());
if(sp()!=0)goto _13;else goto _11;
_11:
sp();
sa(sr()*gr(6,1));
sa(gr(8,1));
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(tm(sr(),gr(2,0)));
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(td(sp(),gr(2,0)));
sa(sp()+3LL);
{int64 v0=sp();int64 v1=sp();gw(v1,v0,sp());}
gw(6,0,gr(6,0)+1);
_12:
sa(sp()+1LL);
sa((sr()*gr(6,1))>gr(3,0)?1:0);
goto _9;
_13:
if(sr()!=gr(8,1))goto _14;else goto _16;
_14:
sa((sp()<0)?1:0);
if(sp()!=0)goto _12;else goto _15;
_15:
sa(sr()*gr(6,1));
sa(-1);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(tm(sr(),gr(2,0)));
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(td(sp(),gr(2,0)));
sa(sp()+3LL);
{int64 v0=sp();int64 v1=sp();gw(v1,v0,sp());}
gw(6,0,gr(6,0)-1);
goto _12;
_16:
sp();
goto _12;
_17:
sp();
sa(gr(9,0)+1);
gw(9,0,gr(9,0)+1);
goto _6;
_18:
t0=gr(2,1);
gw(2,1,gr(3,1));
gw(3,1,t0);
goto _8;
_19:
gw(8,0,gr(8,0)+1);
goto _4;
_20:
printf("%lld", gr(6,0));
return 0;
}
int main(void)
{
int64 t0,t1;
d();
s=(int64*)calloc(q,sizeof(int64));
gw(10,10,1);
sa(9);
_1:
sa(sr());
sa(1);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(sr());
{int64 v0=sp();int64 v1=sp();gw(v1,v0,sp());}
sa(sp()-1LL);
sa(sr());
if(sp()!=0)goto _1;else goto _3;
_3:
gw(3,0,5);
gw(2,0,48);
sp();
sa(49);
_4:
sa(0);
sa(gr(gr(2,0),gr(3,0))-48);
gw(5,0,gr(gr(2,0),gr(3,0))-48);
sa(sp()+12LL);
sa(7);
{int64 v0=sp();int64 v1=sp();gw(v1,v0,sp());}
sa(0);
sa(gr(gr(2,0)+1,gr(3,0))-48);
gw(6,0,gr(gr(2,0)+1,gr(3,0))-48);
sa(sp()+12LL);
sa(7);
{int64 v0=sp();int64 v1=sp();gw(v1,v0,sp());}
sa(0);
sa(gr(gr(2,0)+2,gr(3,0))-48);
gw(7,0,gr(gr(2,0)+2,gr(3,0))-48);
sa(sp()+12LL);
sa(7);
{int64 v0=sp();int64 v1=sp();gw(v1,v0,sp());}
gw(gr(5,0)+1,gr(6,0)+1,2);
gw(gr(5,0)+1,gr(7,0)+1,2);
gw(gr(6,0)+1,gr(7,0)+1,2);
gw(gr(7,0)+1,gr(5,0)+1,0);
gw(gr(7,0)+1,gr(6,0)+1,0);
gw(gr(6,0)+1,gr(5,0)+1,0);
sa(sr()-1);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
if(sp()!=0)goto _18;else goto _5;
_5:
gw(9,0,0);
sp();
sa(9);
sa(gr(21,7));
_6:
if(sp()!=0)goto _7;else goto _17;
_7:
sa(sr()-1);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa((sp()!=0)?0:1);
if(sp()!=0)goto _9;else goto _8;
_8:
sa(sr()+12);
sa(7);
{int64 v0=sp();sa(gr(sp(),v0));}
goto _6;
_9:
sa(sp()+1LL);
_10:
if(sr()-gr(9,0)==0)goto _13;else goto _11;
_11:
sa(sr());
sa(sr());
sa(sr()+12);
sa(9);
{int64 v0=sp();sa(gr(sp(),v0));}
sa(sp()+1LL);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(sp()+11LL);
sa(9);
{int64 v0=sp();sa(gr(sp(),v0));}
sa(sp()+1LL);
{int64 v0=sp();t0=gr(sp(),v0);}
sa(sp()*t0);
t1=sp();
t1=(t1!=0)?0:1;
if((t1)!=0)goto _9;else goto _12;
_12:
sa(sr());
sa(sr());
sa(sr()+12);
sa(9);
{int64 v0=sp();t0=gr(sp(),v0);}
gw(2,0,t0);
sa(sp()+11LL);
sa(9);
{int64 v0=sp();sa(gr(sp(),v0));}
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(sp()+12LL);
sa(9);
{int64 v0=sp();int64 v1=sp();gw(v1,v0,sp());}
sa(sp()-1LL);
sa(sr());
sa(gr(2,0));
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(sp()+12LL);
sa(9);
{int64 v0=sp();int64 v1=sp();gw(v1,v0,sp());}
goto _10;
_13:
printf("%lld", gr(12,9));
sp();
sa(1);
sa((1-gr(9,0)!=0)?0:1);
_14:
if(sp()!=0)goto _15;else goto _16;
_15:
sp();
return 0;
_16:
sa(sr()+12);
sa(9);
{int64 v0=sp();t0=gr(sp(),v0);}
printf("%lld", t0);
sa(sp()+1LL);
sa((sr()-gr(9,0)!=0)?0:1);
goto _14;
_17:
sa(sr());
sa(gr(9,0));
gw(9,0,gr(9,0)+1);
sa(sp()+12LL);
sa(9);
{int64 v0=sp();int64 v1=sp();gw(v1,v0,sp());}
goto _7;
_18:
t0=(td(sr(),10))+1;
gw(3,0,t0);
t0=((tm(sr(),10))*4)+12;
gw(2,0,t0);
goto _4;
}
bool SKCommandHandler::handle(char *s)
{
string sr(s);
return handle(sr);
}
// Test CpG sites in this read for methylation
void calculate_methylation_for_read(const ModelMap& model_map,
const Fast5Map& name_map,
const faidx_t* fai,
const bam_hdr_t* hdr,
const bam1_t* record,
size_t read_idx,
const OutputHandles& handles)
{
// Load a squiggle read for the mapped read
std::string read_name = bam_get_qname(record);
std::string fast5_path = name_map.get_path(read_name);
SquiggleRead sr(read_name, fast5_path);
// An output map from reference positions to scored CpG sites
std::map<int, ScoredSite> site_score_map;
for(size_t strand_idx = 0; strand_idx < NUM_STRANDS; ++strand_idx) {
std::vector<double> site_scores;
std::vector<int> site_starts;
std::vector<int> site_ends;
std::vector<int> site_count;
// replace the baked-in pore model with the methylation model
// (including unmethylated kmers) for this strand
std::string curr_model = sr.pore_model[strand_idx].name;
std::string methyl_model = curr_model + ".ecoli_er2925.pcr_MSssI.timp.021216.alphabet_cpg.model";
auto model_iter = model_map.find(methyl_model);
if(model_iter != model_map.end()) {
sr.pore_model[strand_idx].update_states( model_iter->second );
} else {
fprintf(stderr, "Error, methylated model %s not found\n", methyl_model.c_str());
exit(EXIT_FAILURE);
}
size_t k = sr.pore_model[strand_idx].k;
// Align in event space using the new model
EventAlignmentParameters params;
params.sr = &sr;
params.fai = fai;
params.hdr = hdr;
params.record = record;
params.strand_idx = strand_idx;
params.read_idx = read_idx;
params.alphabet = mtest_alphabet;
std::vector<EventAlignment> alignment_output = align_read_to_ref(params);
if(alignment_output.empty())
continue;
std::string contig = alignment_output.front().ref_name.c_str();
// Convert the EventAlignment to a map between reference positions and events
std::vector<AlignedPair> event_aligned_pairs;
for(size_t i = 0; i < alignment_output.size(); ++i) {
AlignedPair ap = { alignment_output[i].ref_position,
alignment_output[i].event_idx };
event_aligned_pairs.push_back(ap);
}
int ref_start_pos = event_aligned_pairs.front().ref_pos;
int ref_end_pos = event_aligned_pairs.back().ref_pos;
// Extract the reference sequence for this region
int fetched_len = 0;
assert(ref_end_pos >= ref_start_pos);
std::string ref_seq = get_reference_region_ts(params.fai, contig.c_str(), ref_start_pos,
ref_end_pos, &fetched_len);
// Remove non-ACGT bases from this reference segment
ref_seq = gDNAAlphabet.disambiguate(ref_seq);
// Scan the sequence for CpGs
std::vector<int> cpg_sites;
assert(ref_seq.size() != 0);
for(size_t i = 0; i < ref_seq.size() - 1; ++i) {
if(ref_seq[i] == 'C' && ref_seq[i+1] == 'G') {
cpg_sites.push_back(i);
}
}
// Batch the CpGs together into groups that are separated by some minimum distance
int min_separation = 10;
size_t curr_idx = 0;
while(curr_idx < cpg_sites.size()) {
// Find the endpoint of this group of sites
size_t end_idx = curr_idx + 1;
while(end_idx < cpg_sites.size()) {
if(cpg_sites[end_idx] - cpg_sites[end_idx - 1] > min_separation)
break;
end_idx += 1;
}
// the coordinates on the reference substring for this group of sites
int sub_start_pos = cpg_sites[curr_idx] - min_separation;
int sub_end_pos = cpg_sites[end_idx - 1] + min_separation;
if(sub_start_pos > min_separation && cpg_sites[end_idx - 1] - cpg_sites[curr_idx] < 200) {
std::string subseq = ref_seq.substr(sub_start_pos, sub_end_pos - sub_start_pos + 1);
std::string rc_subseq = mtest_alphabet->reverse_complement(subseq);
// using the reference-to-event map, look up the event indices for this segment
AlignedPairRefLBComp lb_comp;
AlignedPairConstIter start_iter = std::lower_bound(event_aligned_pairs.begin(), event_aligned_pairs.end(),
sub_start_pos + ref_start_pos, lb_comp);
AlignedPairConstIter stop_iter = std::lower_bound(event_aligned_pairs.begin(), event_aligned_pairs.end(),
sub_end_pos + ref_start_pos, lb_comp);
// Only process this region if the the read is aligned within the boundaries
// and the span between the start/end is not unusually short
if(start_iter != event_aligned_pairs.end() && stop_iter != event_aligned_pairs.end() &&
abs(start_iter->read_pos - stop_iter->read_pos) > 10)
{
uint32_t hmm_flags = HAF_ALLOW_PRE_CLIP | HAF_ALLOW_POST_CLIP;
// Set up event data
HMMInputData data;
data.read = &sr;
data.anchor_index = -1; // unused
data.strand = strand_idx;
data.rc = alignment_output.front().rc;
data.event_start_idx = start_iter->read_pos;
data.event_stop_idx = stop_iter->read_pos;
data.event_stride = data.event_start_idx <= data.event_stop_idx ? 1 : -1;
// Calculate the likelihood of the unmethylated sequence
HMMInputSequence unmethylated(subseq, rc_subseq, mtest_alphabet);
double unmethylated_score = profile_hmm_score(unmethylated, data, hmm_flags);
// Methylate all CpGs in the sequence and score again
std::string mcpg_subseq = mtest_alphabet->methylate(subseq);
std::string rc_mcpg_subseq = mtest_alphabet->reverse_complement(mcpg_subseq);
// Calculate the likelihood of the methylated sequence
HMMInputSequence methylated(mcpg_subseq, rc_mcpg_subseq, mtest_alphabet);
double methylated_score = profile_hmm_score(methylated, data, hmm_flags);
// Aggregate score
int start_position = cpg_sites[curr_idx] + ref_start_pos;
auto iter = site_score_map.find(start_position);
if(iter == site_score_map.end()) {
// insert new score into the map
ScoredSite ss;
ss.chromosome = contig;
ss.start_position = start_position;
ss.end_position = cpg_sites[end_idx - 1] + ref_start_pos;
ss.n_cpg = end_idx - curr_idx;
// extract the CpG site(s) with a k-mers worth of surrounding context
size_t site_output_start = cpg_sites[curr_idx] - k + 1;
size_t site_output_end = cpg_sites[end_idx - 1] + k;
ss.sequence = ref_seq.substr(site_output_start, site_output_end - site_output_start);
// insert into the map
iter = site_score_map.insert(std::make_pair(start_position, ss)).first;
}
// set strand-specific score
// upon output below the strand scores will be summed
iter->second.ll_unmethylated[strand_idx] = unmethylated_score;
iter->second.ll_methylated[strand_idx] = methylated_score;
}
}
curr_idx = end_idx;
}
} // for strands
#pragma omp critical(methyltest_write)
{
// these variables are sums over all sites within a read
double ll_ratio_sum_strand[2] = { 0.0f, 0.0f };
double ll_ratio_sum_both = 0;
size_t num_positive = 0;
// write all sites for this read
for(auto iter = site_score_map.begin(); iter != site_score_map.end(); ++iter) {
const ScoredSite& ss = iter->second;
double sum_ll_m = ss.ll_methylated[0] + ss.ll_methylated[1];
double sum_ll_u = ss.ll_unmethylated[0] + ss.ll_unmethylated[1];
double diff = sum_ll_m - sum_ll_u;
num_positive += diff > 0;
fprintf(handles.site_writer, "%s\t%d\t%d\t", ss.chromosome.c_str(), ss.start_position, ss.end_position);
fprintf(handles.site_writer, "ReadIdx=%zu;", read_idx);
fprintf(handles.site_writer, "LogLikMeth=%.2lf;LogLikUnmeth=%.2lf;LogLikRatio=%.2lf;", sum_ll_m, sum_ll_u, diff);
fprintf(handles.site_writer, "LogLikMethByStrand=%.2lf,%.2lf;", ss.ll_methylated[0], ss.ll_methylated[1]);
fprintf(handles.site_writer, "LogLikUnmethByStrand=%.2lf,%.2lf;", ss.ll_unmethylated[0], ss.ll_unmethylated[1]);
fprintf(handles.site_writer, "NumCpGs=%d;Sequence=%s\n", ss.n_cpg, ss.sequence.c_str());
ll_ratio_sum_strand[0] += ss.ll_methylated[0] - ss.ll_unmethylated[0];
ll_ratio_sum_strand[1] += ss.ll_methylated[1] - ss.ll_unmethylated[1];
ll_ratio_sum_both += diff;
}
std::string complement_model = sr.pore_model[C_IDX].name;
fprintf(handles.read_writer, "%s\t%.2lf\t%zu\t%s\tNumPositive=%zu\n", fast5_path.c_str(), ll_ratio_sum_both, site_score_map.size(), complement_model.c_str(), num_positive);
for(size_t si = 0; si < NUM_STRANDS; ++si) {
std::string model = sr.pore_model[si].name;
fprintf(handles.strand_writer, "%s\t%.2lf\t%zu\t%s\n", fast5_path.c_str(), ll_ratio_sum_strand[si], site_score_map.size(), model.c_str());
}
}
}
double nb_0(double q_tot, double sz, double emit_n, double E, double n_p_cgs, double m_ion_amu)
{
double _sr = sr(emit_n, E, n_p_cgs, m_ion_amu);
return nb_0(q_tot, sz, _sr);
}
int main(void)
{
int64 t0,t1;
d();
s=(int64*)calloc(q,sizeof(int64));
gw(0,2,99);
_1:
if(gr(0,2)!=1000)goto _2;else goto _47;
_2:
t0=gr(0,2)+1;
t1=gr(0,2)+1;
gw(0,2,gr(0,2)+1);
t1%=2;
t1=(t1!=0)?0:1;
if((t1)!=0)goto _1;else goto _3;
_3:
t0%=5;
t0=(t0!=0)?0:1;
if((t0)!=0)goto _1;else goto _4;
_4:
gw(1,2,3);
_5:
t0=gr(1,2)+1;
gw(1,2,gr(1,2)+1);
t0-=14;
t0=(t0!=0)?0:1;
if((t0)!=0)goto _1;else goto _6;
_6:
gw(2,2,0);
if(((gr(0,gr(1,2))-48)+gr(2,2))!=0)goto _8;else goto _7;
_7:
t0=gr(2,2)+1;
gw(2,2,gr(2,2)+1);
t0-=3;
t0=(t0!=0)?0:1;
if((t0)!=0)goto _5;else goto _8;
_8:
gw(4,2,gr(0,2));
sa(5);
sa(gr(5,gr(1,2))-48);
_9:
if(sp()!=0)goto _10;else goto _46;
_10:
sa(sr());
sa((tm(gr(4,2),10))+48);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(sp()+7LL);
sa(gr(1,2));
{int64 v0=sp();int64 v1=sp();gw(v1,v0,sp());}
gw(4,2,td(gr(4,2),10));
_11:
sa(sr());
sa((sp()!=0)?0:1);
if(sp()!=0)goto _12;else goto _45;
_12:
sp();
sa(gr(12,gr(1,2))-48);
sa(4);
_13:
sa(sr()+7);
sa(gr(1,2));
{int64 v0=sp();sa(gr(sp(),v0));}
sa(sp()-48LL);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(sr());
if(sp()!=0)goto _44;else goto _14;
_14:
sp();
sa(sp()*10LL);
sa(sp()+sp());
sa(sp()*10LL);
sa(sp()+sp());
sa(sp()*10LL);
sa(sp()+sp());
sa(sp()*10LL);
sa(sp()+sp());
sa(sp()*10LL);
sa(sp()+sp());
sa(sr());
gw(7,2,sp());
if(tm(sr(),2)!=0)goto _16;else goto _15;
_15:
sp();
goto _7;
_16:
if(tm(sr(),3)!=0)goto _17;else goto _15;
_17:
gw(5,2,sp());
sa(7);
sa(tm(gr(5,2),7));
_18:
if(sp()!=0)goto _19;else goto _15;
_19:
if(sr()>(td(gr(5,2),2)))goto _22;else goto _20;
_20:
sa(sr()-2);
sa(gr(5,2));
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
{int64 v0=sp();sa(tm(sp(),v0));}
sa((sp()!=0)?0:1);
if(sp()!=0)goto _15;else goto _21;
_21:
sa(sp()+6LL);
sa(sr());
sa(gr(5,2));
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
{int64 v0=sp();sa(tm(sp(),v0));}
goto _18;
_22:
gw(8,2,1);
gw(9,2,gr(2,2));
gw(9,2,gr(9,2)+1);
gw(4,2,gr(0,2));
sp();
_23:
sa(5);
sa(gr(5,gr(1,2))-48);
_24:
if(sp()!=0)goto _25;else goto _43;
_25:
sa(sr());
sa((tm(gr(4,2),10))+48);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(sp()+7LL);
sa(gr(9,2)+4);
{int64 v0=sp();int64 v1=sp();gw(v1,v0,sp());}
gw(4,2,td(gr(4,2),10));
_26:
sa(sr());
if(sp()!=0)goto _42;else goto _27;
_27:
sp();
sa(gr(12,gr(9,2)+4)-48);
sa(4);
_28:
sa(sr()+7);
sa(gr(9,2)+4);
{int64 v0=sp();sa(gr(sp(),v0));}
sa(sp()-48LL);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(sr());
if(sp()!=0)goto _41;else goto _29;
_29:
sp();
sa(sp()*10LL);
sa(sp()+sp());
sa(sp()*10LL);
sa(sp()+sp());
sa(sp()*10LL);
sa(sp()+sp());
sa(sp()*10LL);
sa(sp()+sp());
sa(sp()*10LL);
sa(sp()+sp());
if(tm(sr(),2)!=0)goto _34;else goto _30;
_30:
sp();
if(gr(9,2)!=9)goto _31;else goto _32;
_31:
gw(9,2,gr(9,2)+1);
gw(4,2,gr(0,2));
goto _23;
_32:
if(gr(8,2)!=8)goto _7;else goto _33;
_33:
printf("%lld", gr(7,2));
return 0;
_34:
if(tm(sr(),3)!=0)goto _35;else goto _30;
_35:
gw(5,2,sp());
sa(7);
sa(tm(gr(5,2),7));
_36:
if(sp()!=0)goto _37;else goto _30;
_37:
if(sr()>(td(gr(5,2),2)))goto _40;else goto _38;
_38:
sa(sr()-2);
sa(gr(5,2));
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
{int64 v0=sp();sa(tm(sp(),v0));}
sa((sp()!=0)?0:1);
if(sp()!=0)goto _30;else goto _39;
_39:
sa(sp()+6LL);
sa(sr());
sa(gr(5,2));
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
{int64 v0=sp();sa(tm(sp(),v0));}
goto _36;
_40:
gw(8,2,gr(8,2)+1);
goto _30;
_41:
sa(sp()-1LL);
goto _28;
_42:
sa(sp()-1LL);
sa(sr());
sa(gr(1,2));
{int64 v0=sp();sa(gr(sp(),v0));}
sa(sp()-48LL);
goto _24;
_43:
sa(sr());
sa(gr(9,2)+48);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(sp()+7LL);
sa(gr(9,2)+4);
{int64 v0=sp();int64 v1=sp();gw(v1,v0,sp());}
goto _26;
_44:
sa(sp()-1LL);
goto _13;
_45:
sa(sp()-1LL);
sa(sr());
sa(gr(1,2));
{int64 v0=sp();sa(gr(sp(),v0));}
sa(sp()-48LL);
goto _9;
_46:
sa(sr());
sa(gr(2,2)+48);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(sp()+7LL);
sa(gr(1,2));
{int64 v0=sp();int64 v1=sp();gw(v1,v0,sp());}
goto _11;
_47:
return 0;
}
StatusWith<std::tuple<bool, std::string>> SaslSCRAMServerMechanism<Policy>::_firstStep(
OperationContext* opCtx, StringData inputData) {
const auto badCount = [](int got) {
return Status(ErrorCodes::BadValue,
str::stream()
<< "Incorrect number of arguments for first SCRAM client message, got "
<< got
<< " expected at least 3");
};
/**
* gs2-cbind-flag := ("p=" cb-name) / 'y' / 'n'
* gs2-header := gs2-cbind-flag ',' [ authzid ] ','
* reserved-mext := "m=" 1*(value-char)
* client-first-message-bare := [reserved-mext ','] username ',' nonce [',' extensions]
* client-first-message := gs2-header client-first-message-bare
*/
const auto gs2_cbind_comma = inputData.find(',');
if (gs2_cbind_comma == std::string::npos) {
return badCount(1);
}
const auto gs2_cbind_flag = inputData.substr(0, gs2_cbind_comma);
if (gs2_cbind_flag.startsWith("p=")) {
return Status(ErrorCodes::BadValue, "Server does not support channel binding");
}
if ((gs2_cbind_flag != "y") && (gs2_cbind_flag != "n")) {
return Status(ErrorCodes::BadValue,
str::stream() << "Incorrect SCRAM client message prefix: " << gs2_cbind_flag);
}
const auto gs2_header_comma = inputData.find(',', gs2_cbind_comma + 1);
if (gs2_header_comma == std::string::npos) {
return badCount(2);
}
auto authzId = inputData.substr(gs2_cbind_comma + 1, gs2_header_comma - (gs2_cbind_comma + 1));
if (authzId.size()) {
if (authzId.startsWith("a=")) {
authzId = authzId.substr(2);
} else {
return Status(ErrorCodes::BadValue,
str::stream() << "Incorrect SCRAM authzid: " << authzId);
}
}
const auto client_first_message_bare = inputData.substr(gs2_header_comma + 1);
if (client_first_message_bare.startsWith("m=")) {
return Status(ErrorCodes::BadValue, "SCRAM mandatory extensions are not supported");
}
/* StringSplitter::split() will ignore consecutive delimiters.
* e.g. "foo,,bar" => {"foo","bar"}
* This makes our implementation of SCRAM *slightly* more generous
* in what it will accept than the standard calls for.
*
* This does not impact _authMessage, as it's composed from the raw
* string input, rather than the output of the split operation.
*/
const auto input = StringSplitter::split(client_first_message_bare.toString(), ",");
if (input.size() < 2) {
// gs2-header is not included in this count, so add it back in.
return badCount(input.size() + 2);
}
if (!str::startsWith(input[0], "n=") || input[0].size() < 3) {
return Status(ErrorCodes::BadValue,
str::stream() << "Invalid SCRAM user name: " << input[0]);
}
ServerMechanismBase::_principalName = input[0].substr(2);
decodeSCRAMUsername(ServerMechanismBase::_principalName);
if (!authzId.empty() && ServerMechanismBase::_principalName != authzId) {
return Status(ErrorCodes::BadValue,
str::stream() << "SCRAM user name " << ServerMechanismBase::_principalName
<< " does not match authzid "
<< authzId);
}
if (!str::startsWith(input[1], "r=") || input[1].size() < 6) {
return Status(ErrorCodes::BadValue,
str::stream() << "Invalid SCRAM client nonce: " << input[1]);
}
const auto clientNonce = input[1].substr(2);
// SERVER-16534, SCRAM-SHA-1 must be enabled for authenticating the internal user, so that
// cluster members may communicate with each other. Hence ignore disabled auth mechanism
// for the internal user.
UserName user(ServerMechanismBase::ServerMechanismBase::_principalName,
ServerMechanismBase::getAuthenticationDatabase());
if (!sequenceContains(saslGlobalParams.authenticationMechanisms, "SCRAM-SHA-1") &&
user != internalSecurity.user->getName()) {
return Status(ErrorCodes::BadValue, "SCRAM-SHA-1 authentication is disabled");
}
// The authentication database is also the source database for the user.
User* userObj;
auto authManager = AuthorizationManager::get(opCtx->getServiceContext());
Status status = authManager->acquireUser(opCtx, user, &userObj);
if (!status.isOK()) {
return status;
}
User::CredentialData credentials = userObj->getCredentials();
UserName userName = userObj->getName();
authManager->releaseUser(userObj);
_scramCredentials = credentials.scram<HashBlock>();
if (!_scramCredentials.isValid()) {
// Check for authentication attempts of the __system user on
// systems started without a keyfile.
if (userName == internalSecurity.user->getName()) {
return Status(ErrorCodes::AuthenticationFailed,
"It is not possible to authenticate as the __system user "
"on servers started without a --keyFile parameter");
} else {
return Status(ErrorCodes::AuthenticationFailed,
"Unable to perform SCRAM authentication for a user with missing "
"or invalid SCRAM credentials");
}
}
_secrets = scram::Secrets<HashBlock>("",
base64::decode(_scramCredentials.storedKey),
base64::decode(_scramCredentials.serverKey));
// Generate server-first-message
// Create text-based nonce as base64 encoding of a binary blob of length multiple of 3
const int nonceLenQWords = 3;
uint64_t binaryNonce[nonceLenQWords];
std::unique_ptr<SecureRandom> sr(SecureRandom::create());
binaryNonce[0] = sr->nextInt64();
binaryNonce[1] = sr->nextInt64();
binaryNonce[2] = sr->nextInt64();
_nonce =
clientNonce + base64::encode(reinterpret_cast<char*>(binaryNonce), sizeof(binaryNonce));
StringBuilder sb;
sb << "r=" << _nonce << ",s=" << _scramCredentials.salt
<< ",i=" << _scramCredentials.iterationCount;
std::string outputData = sb.str();
// add client-first-message-bare and server-first-message to _authMessage
_authMessage = client_first_message_bare.toString() + "," + outputData;
return std::make_tuple(false, std::move(outputData));
}
// Update the training data with aligned events from a read
void add_aligned_events(const Fast5Map& name_map,
const faidx_t* fai,
const bam_hdr_t* hdr,
const bam1_t* record,
size_t read_idx,
int region_start,
int region_end,
size_t round,
ModelTrainingMap& training)
{
// Load a squiggle read for the mapped read
std::string read_name = bam_get_qname(record);
std::string fast5_path = name_map.get_path(read_name);
// load read
SquiggleRead sr(read_name, fast5_path);
// replace the models that are built into the read with the current trained model
sr.replace_models(opt::trained_model_type);
for(size_t strand_idx = 0; strand_idx < NUM_STRANDS; ++strand_idx) {
// skip if 1D reads and this is the wrong strand
if(!sr.has_events_for_strand(strand_idx)) {
continue;
}
// set k
uint32_t k = sr.pore_model[strand_idx].k;
// Align to the new model
EventAlignmentParameters params;
params.sr = &sr;
params.fai = fai;
params.hdr = hdr;
params.record = record;
params.strand_idx = strand_idx;
params.alphabet = mtrain_alphabet;
params.read_idx = read_idx;
params.region_start = region_start;
params.region_end = region_end;
std::vector<EventAlignment> alignment_output = align_read_to_ref(params);
if (alignment_output.size() == 0)
return;
// Update pore model based on alignment
std::string curr_model = sr.pore_model[strand_idx].metadata.get_short_name();
double orig_score = -INFINITY;
if (opt::output_scores) {
orig_score = model_score(sr, strand_idx, fai, alignment_output, 500, NULL);
#pragma omp critical(print)
std::cout << round << " " << curr_model << " " << read_idx << " " << strand_idx << " Original " << orig_score << std::endl;
}
if ( opt::calibrate ) {
double resid = 0.;
recalibrate_model(sr, strand_idx, alignment_output, mtrain_alphabet, resid, true);
if (opt::output_scores) {
double rescaled_score = model_score(sr, strand_idx, fai, alignment_output, 500, NULL);
#pragma omp critical(print)
{
std::cout << round << " " << curr_model << " " << read_idx << " " << strand_idx << " Rescaled " << rescaled_score << std::endl;
std::cout << round << " " << curr_model << " " << read_idx << " " << strand_idx << " Delta " << rescaled_score-orig_score << std::endl;
}
}
}
// Get the training data for this model
auto& emission_map = training[curr_model];
for(size_t i = 0; i < alignment_output.size(); ++i) {
const EventAlignment& ea = alignment_output[i];
std::string model_kmer = ea.model_kmer;
// Grab the previous/next model kmer from the alignment_output table.
// If the read is from the same strand as the reference
// the next kmer comes from the next alignment_output (and vice-versa)
// other the indices are swapped
int next_stride = ea.rc ? -1 : 1;
std::string prev_kmer = "";
std::string next_kmer = "";
if(i > 0 && i < alignment_output.size() - 1) {
// check that the event indices are correct for the next expected position
assert(alignment_output[i + next_stride].event_idx - ea.event_idx == 1);
assert(alignment_output[i - next_stride].event_idx - ea.event_idx == -1);
// only set the previous/next when there was exactly one base of movement along the referenc
if( std::abs(alignment_output[i + next_stride].ref_position - ea.ref_position) == 1) {
next_kmer = alignment_output[i + next_stride].model_kmer;
}
if( std::abs(alignment_output[i - next_stride].ref_position - ea.ref_position) == 1) {
prev_kmer = alignment_output[i - next_stride].model_kmer;
}
}
// Get the rank of the kmer that we aligned to (on the sequencing strand, = model_kmer)
uint32_t rank = mtrain_alphabet->kmer_rank(model_kmer.c_str(), k);
assert(rank < emission_map.size());
auto& kmer_summary = emission_map[rank];
// We only use this event for training if its not at the end of the alignment
// (to avoid bad alignments around the read edges) and if its not too short (to
// avoid bad measurements from effecting the levels too much)
bool use_for_training = i > opt::min_distance_from_alignment_end &&
i + opt::min_distance_from_alignment_end < alignment_output.size() &&
alignment_output[i].hmm_state == 'M' &&
sr.get_duration( alignment_output[i].event_idx, strand_idx) >= opt::min_event_duration &&
sr.get_fully_scaled_level(alignment_output[i].event_idx, strand_idx) >= 1.0;
if(use_for_training) {
StateTrainingData std(sr, ea, rank, prev_kmer, next_kmer);
#pragma omp critical(kmer)
kmer_summary.events.push_back(std);
}
if(ea.hmm_state == 'M') {
#pragma omp atomic
kmer_summary.num_matches += 1;
} else if(ea.hmm_state == 'E') {
#pragma omp atomic
kmer_summary.num_stays += 1;
}
}
} // for strands
}
int main(void)
{
int64 t0,t1,t2;
d();
s=(int64*)calloc(q,sizeof(int64));
gw(1,0,150);
gw(2,0,35);
gw(4,0,5250);
gw(3,0,2);
gw(1,1,2000);
gw(2,1,5000);
gw(2,2,0);
gw(1,2,1);
gw(3,1,10000000);
_1:
gw(0,3,32);
gw(1,3,32);
gw(8,0,1073741824);
gw(tm(gr(3,0),gr(1,0)),(td(gr(3,0),gr(1,0)))+3,88);
sa(gr(3,0)+gr(3,0));
sa((gr(3,0)+gr(3,0))<gr(4,0)?1:0);
_2:
if(sp()!=0)goto _38;else goto _3;
_3:
sp();
_4:
sa(gr(3,0)+1);
gw(3,0,gr(3,0)+1);
sa(tm(sr(),gr(1,0)));
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(td(sp(),gr(1,0)));
sa(sp()+3LL);
{int64 v0=sp();t0=gr(sp(),v0);}
t0-=32;
if((t0)!=0)goto _6;else goto _4;
_6:
if(gr(4,0)>gr(3,0))goto _1;else goto _7;
_7:
gw(3,0,0);
sa(gr(1,1));
gw(4,2,gr(1,1));
_8:
sa(sr());
sa(tm(sr(),gr(1,0)));
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(td(sp(),gr(1,0)));
sa(sp()+3LL);
{int64 v0=sp();t0=gr(sp(),v0);}
t0-=88;
if((t0)!=0)goto _9;else goto _12;
_9:
sa(sp()+1LL);
if(sr()!=gr(2,1))goto _10;else goto _11;
_10:
sa(sr());
gw(4,2,sp());
goto _8;
_11:
printf("%lld", gr(1,2));
sp();
return 0;
_12:
sa(sr()+1);
_13:
sa(sr());
gw(5,2,sp());
sa(sr());
sa(tm(sr(),gr(1,0)));
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(td(sp(),gr(1,0)));
sa(sp()+3LL);
{int64 v0=sp();t0=gr(sp(),v0);}
t0-=88;
if((t0)!=0)goto _16;else goto _14;
_14:
t0=gr(4,2)*gr(5,2);
gw(7,2,gr(4,2)*gr(5,2));
t0=t0>gr(3,1)?1:0;
if((t0)!=0)goto _17;else goto _15;
_15:
t0=gr(7,2)*gr(2,2);
t1=(gr(4,2)-1)*(gr(5,2)-1);
gw(8,2,(gr(4,2)-1)*(gr(5,2)-1));
t1*=gr(1,2);
t2=t0>t1?1:0;
if((t2)!=0)goto _16;else goto _18;
_16:
sa(sp()+1LL);
if(sr()!=gr(2,1))goto _13;else goto _17;
_17:
sp();
goto _9;
_18:
sa(0);
sa(tm(gr(7,2),10));
sa(gr(7,2));
sa(gr(7,2));
_19:
if(sp()!=0)goto _20;else goto _24;
_20:
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(9);
_21:
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(sr());
if(sp()!=0)goto _23;else goto _22;
_22:
sp();
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(td(sp(),10));
sa(tm(sr(),10));
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(sr());
goto _19;
_23:
sa(sp()-1LL);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(sp()*9LL);
goto _21;
_24:
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sp();
sp();
_25:
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(sr());
if(sp()!=0)goto _26;else goto _27;
_26:
sa(sp()+sp());
goto _25;
_27:
sa(sp()+sp());
sa(0);
sa(tm(gr(8,2),10));
sa(gr(8,2));
sa(gr(8,2));
_28:
if(sp()!=0)goto _29;else goto _33;
_29:
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(9);
_30:
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(sr());
if(sp()!=0)goto _32;else goto _31;
_31:
sp();
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(td(sp(),10));
sa(tm(sr(),10));
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(sr());
goto _28;
_32:
sa(sp()-1LL);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(sp()*9LL);
goto _30;
_33:
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sp();
sp();
_34:
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(sr());
if(sp()!=0)goto _37;else goto _35;
_35:
sa(sp()+sp());
t0=sp();
sa(sp()-t0);
t1=sp();
if((t1)!=0)goto _16;else goto _36;
_36:
gw(1,2,gr(7,2));
gw(2,2,gr(8,2));
goto _16;
_37:
sa(sp()+sp());
goto _34;
_38:
sa(sr());
sa(32);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(tm(sr(),gr(1,0)));
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(td(sp(),gr(1,0)));
sa(sp()+3LL);
{int64 v0=sp();int64 v1=sp();gw(v1,v0,sp());}
sa(sp()+gr(3,0));
sa(sr()<gr(4,0)?1:0);
goto _2;
}
void SearchManager::onData(const uint8_t* buf, size_t aLen, const string& remoteIp) {
string x((char*)buf, aLen);
if(x.compare(0, 4, "$SR ") == 0) {
string::size_type i, j;
// Directories: $SR <nick><0x20><directory><0x20><free slots>/<total slots><0x05><Hubname><0x20>(<Hubip:port>)
// Files: $SR <nick><0x20><filename><0x05><filesize><0x20><free slots>/<total slots><0x05><Hubname><0x20>(<Hubip:port>)
i = 4;
if( (j = x.find(' ', i)) == string::npos) {
return;
}
string nick = x.substr(i, j-i);
i = j + 1;
// A file has 2 0x05, a directory only one
size_t cnt = count(x.begin() + j, x.end(), 0x05);
SearchResult::Types type = SearchResult::TYPE_FILE;
string file;
int64_t size = 0;
if(cnt == 1) {
// We have a directory...find the first space beyond the first 0x05 from the back
// (dirs might contain spaces as well...clever protocol, eh?)
type = SearchResult::TYPE_DIRECTORY;
// Get past the hubname that might contain spaces
if((j = x.rfind(0x05)) == string::npos) {
return;
}
// Find the end of the directory info
if((j = x.rfind(' ', j-1)) == string::npos) {
return;
}
if(j < i + 1) {
return;
}
file = x.substr(i, j-i) + '\\';
} else if(cnt == 2) {
if( (j = x.find((char)5, i)) == string::npos) {
return;
}
file = x.substr(i, j-i);
i = j + 1;
if( (j = x.find(' ', i)) == string::npos) {
return;
}
size = Util::toInt64(x.substr(i, j-i));
}
i = j + 1;
if( (j = x.find('/', i)) == string::npos) {
return;
}
int freeSlots = Util::toInt(x.substr(i, j-i));
i = j + 1;
if( (j = x.find((char)5, i)) == string::npos) {
return;
}
int slots = Util::toInt(x.substr(i, j-i));
i = j + 1;
if( (j = x.rfind(" (")) == string::npos) {
return;
}
string hubName = x.substr(i, j-i);
i = j + 2;
if( (j = x.rfind(')')) == string::npos) {
return;
}
string hubIpPort = x.substr(i, j-i);
string url = ClientManager::getInstance()->findHub(hubIpPort);
string encoding = ClientManager::getInstance()->findHubEncoding(url);
nick = Text::toUtf8(nick, encoding);
file = Text::toUtf8(file, encoding);
hubName = Text::toUtf8(hubName, encoding);
UserPtr user = ClientManager::getInstance()->findUser(nick, url);
if(!user) {
// Could happen if hub has multiple URLs / IPs
user = ClientManager::getInstance()->findLegacyUser(nick);
if(!user)
return;
}
string tth;
if(hubName.compare(0, 4, "TTH:") == 0) {
tth = hubName.substr(4);
StringList names = ClientManager::getInstance()->getHubNames(user->getCID());
hubName = names.empty() ? _("Offline") : Util::toString(names);
}
if(tth.empty() && type == SearchResult::TYPE_FILE) {
return;
}
SearchResultPtr sr(new SearchResult(user, type, slots, freeSlots, size,
file, hubName, url, remoteIp, TTHValue(tth), Util::emptyString));
fire(SearchManagerListener::SR(), sr);
} else if(x.compare(1, 4, "RES ") == 0 && x[x.length() - 1] == 0x0a) {
AdcCommand c(x.substr(0, x.length()-1));
if(c.getParameters().empty())
return;
string cid = c.getParam(0);
if(cid.size() != 39)
return;
UserPtr user = ClientManager::getInstance()->findUser(CID(cid));
if(!user)
return;
// This should be handled by AdcCommand really...
c.getParameters().erase(c.getParameters().begin());
onRES(c, user, remoteIp);
} /*else if(x.compare(1, 4, "SCH ") == 0 && x[x.length() - 1] == 0x0a) {
try {
respond(AdcCommand(x.substr(0, x.length()-1)));
} catch(ParseException& ) {
}
}*/ // Needs further DoS investigation
}
int main(void)
{
int64 t0,t1,t2;
d();
s=(int64*)calloc(q,sizeof(int64));
gw(1,0,400);
gw(0,0,10000);
sa(gr(0,0)-1);
sa(0);
sa((gr(0,0)-1)/2);
sa((gr(0,0)-1)/2);
gw(2,0,gr(0,0)-1);
_1:
if(sp()!=0)goto _2;else goto _15;
_2:
t0=gr(2,0);
sa(sr());
sa(t0);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
{int64 v0=sp();sa(tm(sp(),v0));}
t1=sp();
if((t1)!=0)goto _14;else goto _3;
_3:
sa(sr());
gw(3,0,sp());
sa(sp()+sp());
sa(gr(3,0)-1);
sa(gr(3,0)-1);
_4:
if(sp()!=0)goto _2;else goto _5;
_5:
sp();
gw(tm(gr(2,0),gr(1,0)),(td(gr(2,0),gr(1,0)))+1,sp());
_6:
sa(sr());
if(sp()!=0)goto _13;else goto _7;
_7:
gw(0,1,0);
gw(2,0,gr(0,0)-1);
gw(9,0,0);
sp();
sp();
_8:
gw(4,0,gr(tm(gr(2,0),gr(1,0)),(td(gr(2,0),gr(1,0)))+1));
gw(5,0,gr(tm(gr(4,0),gr(1,0)),(td(gr(4,0),gr(1,0)))+1));
if((gr(2,0)-gr(5,0))!=0)goto _9;else goto _11;
_9:
t2=gr(2,0);
gw(2,0,gr(2,0)-1);
if((t2)!=0)goto _8;else goto _10;
_10:
printf("%lld ", gr(9,0));
return 0;
_11:
if(gr(2,0)>gr(4,0))goto _12;else goto _9;
_12:
printf("%lld ", gr(2,0));
printf(" - ");
printf("%lld ", gr(4,0));
printf("\n");
gw(9,0,gr(9,0)+gr(2,0)+gr(4,0));
goto _9;
_13:
sa(sp()-1LL);
sa(sr());
sa(sr());
gw(2,0,sp());
sa(0);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(sp()/2LL);
sa(sr());
goto _1;
_14:
sa(sp()-1LL);
sa(sr());
goto _4;
_15:
gw(tm(gr(2,0),gr(1,0)),(td(gr(2,0),gr(1,0)))+1,1);
goto _6;
}
void CCSMainView::SearchL()
{
iContainer->SaveDataL();
iContainer->DisableEditorIndicators();
// if GPS or Cell Info data is available
if ( iSavedData.iUseFromGps && IsGpsConnectedOrCellidAvailable() && /*iWayfinderAppUi->GetCellCountry() == */iSavedData.iCountryId == -1) {
// user has selected to search from GPS
TInt32 lat, lon;
TUint cellRadius = 0;
TInt heading, speed, alt;
iWayfinderAppUi->GetDataHolder()->GetInputData(lat,lon,
heading, speed, alt);
// if there is no lat and long from GPS check for cell pos values
if (lat == MAX_INT32 || lon == MAX_INT32) {
Nav2Coordinate navCoOrd(MAX_INT32,MAX_INT32);
if ( iWayfinderAppUi->GetCellPosIfAvailable(navCoOrd, cellRadius) ) {
lat = navCoOrd.nav2lat;
lon = navCoOrd.nav2lon;
}
}
if (lat == MAX_INT32 || lon == MAX_INT32) {
// user wants to search from gps but the gps haven't reported any
// valid coords yet
iWayfinderAppUi->ShowErrorDialogL(0x0200, R_WAYFINDER_NO_GPS_POS_MSG);
} else {
// got valid coords from the gps so perfrom the search based on this
if (iSavedData.iWhat.Length() > 0) {
char* searchString = WFTextUtil::newTDesDupL(iSavedData.iWhat);
char* categoryId = WFTextUtil::newTDesDupL(iSavedData.iCategoryId);
SearchRecord sr(MAX_UINT32, "", "", searchString,
categoryId, lat, lon);
iSearchRecord = sr;
delete[] categoryId;
delete[] searchString;
iWayfinderAppUi->HandleCommandL(EWayFinderCmdCSNewSearch);
} else {
// The user still needs to specify what to search for.
WFDialog::ShowInformationL( R_WAYFINDER_NOHITS_MSG );
}
}
} else {
// user has entered searchfields to search from (not from GPS)
if (iSavedData.iCountry.Length() > 0 &&
(iSavedData.iWhat.Length() > 0 || iSavedData.iWhere.Length() > 0)) {
TInt countryId = iSavedData.iCountryId;
char* areaName = WFTextUtil::newTDesDupL(iSavedData.iWhere);
char* searchString = WFTextUtil::newTDesDupL(iSavedData.iWhat);
char* categoryId = WFTextUtil::newTDesDupL(iSavedData.iCategoryId);
char* countryName = WFTextUtil::newTDesDupL(iSavedData.iCountry);
char* charCountryId = WFTextUtil::uint32AsStringL(iSavedData.iCountryId);
iWayfinderAppUi->GetCSDispatcher()->
getCombinedSearchDataHolder().addSearchHistoryItem(searchString,
areaName,
countryName,
charCountryId,
categoryId);
SearchRecord sr(countryId, "", areaName, searchString, categoryId);
iSearchRecord = sr;
delete[] areaName;
delete[] searchString;
delete[] categoryId;
delete[] countryName;
delete[] charCountryId;
iWayfinderAppUi->HandleSaveSearchHistoryL();
iWayfinderAppUi->HandleCommandL(EWayFinderCmdCSNewSearch);
} else {
// The user has not given enough information to search for.
// Display a dialog about this.
WFDialog::ShowInformationL( R_WAYFINDER_NOHITS_MSG );
iContainer->EnableEditorIndicators();
}
}
}
int scorereads_main(int argc, char** argv)
{
parse_scorereads_options(argc, argv);
omp_set_num_threads(opt::num_threads);
Fast5Map name_map(opt::reads_file);
ModelMap models;
if (!opt::models_fofn.empty())
models = read_models_fofn(opt::models_fofn);
// Open the BAM and iterate over reads
// load bam file
htsFile* bam_fh = sam_open(opt::bam_file.c_str(), "r");
assert(bam_fh != NULL);
// load bam index file
std::string index_filename = opt::bam_file + ".bai";
hts_idx_t* bam_idx = bam_index_load(index_filename.c_str());
assert(bam_idx != NULL);
// read the bam header
bam_hdr_t* hdr = sam_hdr_read(bam_fh);
// load reference fai file
faidx_t *fai = fai_load(opt::genome_file.c_str());
hts_itr_t* itr;
// If processing a region of the genome, only emit events aligned to this window
int clip_start = -1;
int clip_end = -1;
if(opt::region.empty()) {
// TODO: is this valid?
itr = sam_itr_queryi(bam_idx, HTS_IDX_START, 0, 0);
} else {
fprintf(stderr, "Region: %s\n", opt::region.c_str());
itr = sam_itr_querys(bam_idx, hdr, opt::region.c_str());
hts_parse_reg(opt::region.c_str(), &clip_start, &clip_end);
}
#ifndef H5_HAVE_THREADSAFE
if(opt::num_threads > 1) {
fprintf(stderr, "You enabled multi-threading but you do not have a threadsafe HDF5\n");
fprintf(stderr, "Please recompile nanopolish's built-in libhdf5 or run with -t 1\n");
exit(1);
}
#endif
// Initialize iteration
std::vector<bam1_t*> records(opt::batch_size, NULL);
for(size_t i = 0; i < records.size(); ++i) {
records[i] = bam_init1();
}
int result;
size_t num_reads_realigned = 0;
size_t num_records_buffered = 0;
do {
assert(num_records_buffered < records.size());
// read a record into the next slot in the buffer
result = sam_itr_next(bam_fh, itr, records[num_records_buffered]);
num_records_buffered += result >= 0;
// realign if we've hit the max buffer size or reached the end of file
if(num_records_buffered == records.size() || result < 0) {
#pragma omp parallel for schedule(dynamic)
for(size_t i = 0; i < num_records_buffered; ++i) {
bam1_t* record = records[i];
size_t read_idx = num_reads_realigned + i;
if( (record->core.flag & BAM_FUNMAP) == 0) {
//load read
std::string read_name = bam_get_qname(record);
std::string fast5_path = name_map.get_path(read_name);
SquiggleRead sr(read_name, fast5_path);
// TODO: early exit when have processed all of the reads in readnames
if (!opt::readnames.empty() &&
std::find(opt::readnames.begin(), opt::readnames.end(), read_name) == opt::readnames.end() )
continue;
for(size_t strand_idx = 0; strand_idx < NUM_STRANDS; ++strand_idx) {
std::vector<EventAlignment> ao = alignment_from_read(sr, strand_idx, read_idx,
models, fai, hdr,
record, clip_start, clip_end);
if (ao.size() == 0)
continue;
// Update pore model based on alignment
if ( opt::calibrate )
recalibrate_model(sr, strand_idx, ao, false);
double score = model_score(sr, strand_idx, fai, ao, 500);
if (score > 0)
continue;
#pragma omp critical(print)
std::cout << read_name << " " << ( strand_idx ? "complement" : "template" )
<< " " << sr.pore_model[strand_idx].name << " " << score << std::endl;
}
}
}
num_reads_realigned += num_records_buffered;
num_records_buffered = 0;
}
} while(result >= 0);
// cleanup records
for(size_t i = 0; i < records.size(); ++i) {
bam_destroy1(records[i]);
}
// cleanup
sam_itr_destroy(itr);
bam_hdr_destroy(hdr);
fai_destroy(fai);
sam_close(bam_fh);
hts_idx_destroy(bam_idx);
return 0;
}
int main(void)
{
int64 t0;
d();
s=(int64*)calloc(q,sizeof(int64));
gw(3,3,29);
gw(2,0,0);
gw(17,0,0);
sa(8);
_1:
sa(sp()-1LL);
sa(sr());
sa(0);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(sp()+9LL);
sa(0);
{int64 v0=sp();int64 v1=sp();gw(v1,v0,sp());}
sa(sr());
if(sp()!=0)goto _1;else goto _3;
_3:
gw(2,1,0);
gw(2,2,0);
gw(13,1,0);
gw(13,2,0);
sp();
sa(8);
_4:
sa(sr());
sa(0);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(sp()+4LL);
sa(1);
{int64 v0=sp();int64 v1=sp();gw(v1,v0,sp());}
sa(sr());
sa(0);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(sp()+4LL);
sa(2);
{int64 v0=sp();int64 v1=sp();gw(v1,v0,sp());}
sa(sr());
if(sp()!=0)goto _92;else goto _5;
_5:
sp();
sa(9);
_6:
sa(sr());
sa(sr()+8);
sa(0);
{int64 v0=sp();t0=gr(sp(),v0);}
if((t0)!=0)goto _89;else goto _7;
_7:
sa(sr());
sa(sr());
sa(sp()*sp());
sa(td(sp(),10));
sa(sr()+4);
sa(2);
{int64 v0=sp();t0=gr(sp(),v0);}
t0=(t0!=0)?0:1;
t0+=gr(2,2);
gw(2,2,t0);
sa(1);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(sp()+4LL);
sa(2);
{int64 v0=sp();int64 v1=sp();gw(v1,v0,sp());}
sa(sr());
sa(sp()*sp());
sa(tm(sp(),10));
if(sr()!=9)goto _88;else goto _8;
_8:
gw(2,1,(((gr(10,1))!=0)?0:1)+gr(2,1));
gw(10,1,1);
sp();
_9:
sa(sp()-1LL);
sa(sr());
if(sp()!=0)goto _6;else goto _10;
_10:
sp();
if((gr(2,1)>6?1:0)+(gr(2,2)>6?1LL:0LL)==0)goto _17;else goto _11;
_11:
gw(17,0,((gr(17,0))!=0)?0:1);
sa(8);
sa(8);
sa(gr(17,0));
_12:
if(sp()!=0)goto _16;else goto _13;
_13:
sa((sp()!=0)?0:1);
if(sp()!=0)goto _14;else goto _15;
_14:
printf("%lld", gr(2,0));
sp();
return 0;
_15:
sa(sp()-1LL);
sa(sr());
sa(sr());
sa(sr());
sa(sr()+9);
sa(0);
{int64 v0=sp();sa(gr(sp(),v0));}
sa((sp()!=0)?0:1);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(sp()+9LL);
sa(0);
{int64 v0=sp();int64 v1=sp();gw(v1,v0,sp());}
sa(sp()+9LL);
sa(0);
{int64 v0=sp();sa(gr(sp(),v0));}
goto _12;
_16:
sp();
sp();
sa(0);
goto _3;
_17:
if(6!=gr(2,1))goto _87;else goto _18;
_18:
sa(2);
_19:
if(gr(2,2)!=6)goto _20;else goto _86;
_20:
sa(9);
sa(gr(13,2));
_21:
if(sp()!=0)goto _22;else goto _45;
_22:
sa(sr()-1);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
if(sp()!=0)goto _23;else goto _24;
_23:
sa(sr()+4);
sa(2);
{int64 v0=sp();sa(gr(sp(),v0));}
goto _21;
_24:
sp();
sa(sr());
sa((sp()!=0)?0:1);
if(sp()!=0)goto _44;else goto _26;
_26:
sa(sp()-1LL);
sa(sr());
sa((sp()!=0)?0:1);
if(sp()!=0)goto _31;else goto _27;
_27:
sa(sp()-1LL);
sa(sr());
sa((sp()!=0)?0:1);
if(sp()!=0)goto _28;else goto _30;
_28:
gw(17,0,((gr(17,0))!=0)?0:1);
sp();
sa(8);
sa(8);
sa(gr(17,0));
goto _12;
_30:
return 0;
_31:
sp();
sa(sr());
sa(0);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(sp()+4LL);
sa(1);
{int64 v0=sp();int64 v1=sp();gw(v1,v0,sp());}
sa(sr()-1);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
_33:
if(sp()!=0)goto _34;else goto _28;
_34:
sa(sr()+4);
sa(1);
{int64 v0=sp();sa(gr(sp(),v0));}
_35:
if(sp()!=0)goto _43;else goto _36;
_36:
sa(sr());
sa(1);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(sp()+4LL);
sa(1);
{int64 v0=sp();int64 v1=sp();gw(v1,v0,sp());}
if(5!=gr(2,1))goto _38;else goto _37;
_37:
sa(1);
goto _19;
_38:
sa(9);
sa(gr(13,1));
_39:
if(sp()!=0)goto _40;else goto _42;
_40:
sa(sr()-1);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
if(sp()!=0)goto _41;else goto _31;
_41:
sa(sr()+4);
sa(1);
{int64 v0=sp();sa(gr(sp(),v0));}
goto _39;
_42:
sa(sr());
sa(1);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(sp()+4LL);
sa(1);
{int64 v0=sp();int64 v1=sp();gw(v1,v0,sp());}
sa(0);
goto _19;
_43:
sa(sr()-1);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
goto _33;
_44:
sp();
sa(sr());
sa(0);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(sp()+4LL);
sa(1);
{int64 v0=sp();int64 v1=sp();gw(v1,v0,sp());}
goto _40;
_45:
sa(sr());
sa(1);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(sp()+4LL);
sa(2);
{int64 v0=sp();int64 v1=sp();gw(v1,v0,sp());}
if(5!=gr(2,2))goto _46;else goto _85;
_46:
sa(9);
sa(gr(13,2));
_47:
if(sp()!=0)goto _48;else goto _52;
_48:
sa(sr()-1);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
if(sp()!=0)goto _51;else goto _49;
_49:
sp();
sa(sr());
sa(0);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(sp()+4LL);
sa(2);
{int64 v0=sp();int64 v1=sp();gw(v1,v0,sp());}
sa(sr()-1);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
if(sp()!=0)goto _23;else goto _24;
_51:
sa(sr()+4);
sa(2);
{int64 v0=sp();sa(gr(sp(),v0));}
goto _47;
_52:
sa(sr());
sa(1);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(sp()+4LL);
sa(2);
{int64 v0=sp();int64 v1=sp();gw(v1,v0,sp());}
gw(4,0,(((gr(10,1))!=0)?0:1)+gr(13,1));
gw(5,0,(((gr(10,2))!=0)?0:1)+gr(13,2));
gw(6,0,0);
gw(7,0,0);
gw(6,0,gr(13,1)+(gr(6,0)*2));
sa(0);
_53:
sa(0);
_54:
sa(8);
_55:
sa(sr()+4);
sa(1);
{int64 v0=sp();t0=gr(sp(),v0);}
t0+=gr(6,0)*2;
gw(6,0,t0);
sa(sr()-1);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
if(sp()!=0)goto _55;else goto _57;
_57:
gw(7,0,gr(13,2)+(gr(7,0)*2));
sp();
sa(8);
_58:
sa(sr()+4);
sa(2);
{int64 v0=sp();t0=gr(sp(),v0);}
t0+=gr(7,0)*2;
gw(7,0,t0);
sa(sr()-1);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
if(sp()!=0)goto _58;else goto _60;
_60:
sp();
sa(gr(7,0));
sa(gr(6,0));
if(gr(6,0)>gr(7,0))goto _61;else goto _62;
_61:
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
_62:
sa(sp()*1024LL);
sa(sp()+sp());
t0=sp();
gw(3,0,t0);
sa(1279);
sa(gr(79,15+gr(3,3)));
sa(gr(79,15+gr(3,3))-gr(3,0));
_63:
if(sp()!=0)goto _64;else goto _84;
_64:
sa(sp()-35LL);
sa((sp()!=0)?0:1);
if(sp()!=0)goto _65;else goto _83;
_65:
sa(gr(3,0));
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(tm(sr(),80));
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(td(sp(),80));
sa(sp()+gr(3,3));
{int64 v0=sp();int64 v1=sp();gw(v1,v0,sp());}
gw(2,0,gr(2,0)+1);
_66:
sa(sp()+1LL);
sa(sr());
sa((sp()!=0)?0:1);
if(sp()!=0)goto _82;else goto _67;
_67:
sa(sp()-1LL);
sa(sr());
sa((sp()!=0)?0:1);
if(sp()!=0)goto _80;else goto _68;
_68:
sa(sp()-1LL);
sa(sr());
sa((sp()!=0)?0:1);
if(sp()!=0)goto _79;else goto _69;
_69:
sa(sp()-1LL);
sa(sr());
sa((sp()!=0)?0:1);
if(sp()!=0)goto _70;else goto _30;
_70:
gw(10,1,1);
gw(13,1,0);
gw(10,2,1);
gw(13,2,0);
sp();
_71:
if((gr(4,0))==0)goto _72;else goto _73;
_72:
gw(10,1,0);
gw(13,1,1);
gw(6,0,0);
gw(7,0,0);
gw(6,0,gr(13,1)+(gr(6,0)*2));
sa(1);
goto _54;
_73:
if((gr(5,0))==0)goto _78;else goto _74;
_74:
sa(sr());
sa((sp()!=0)?0:1);
if(sp()!=0)goto _77;else goto _75;
_75:
sa(sp()-1LL);
sa(sr());
sa((sp()!=0)?0:1);
if(sp()!=0)goto _49;else goto _76;
_76:
sa(sp()-1LL);
sa(sr());
sa((sp()!=0)?0:1);
if(sp()!=0)goto _24;else goto _30;
_77:
sp();
sa(sr());
sa(0);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(sp()+4LL);
sa(2);
{int64 v0=sp();int64 v1=sp();gw(v1,v0,sp());}
goto _48;
_78:
gw(10,2,0);
gw(13,2,1);
gw(6,0,0);
gw(7,0,0);
gw(6,0,gr(13,1)+(gr(6,0)*2));
sa(-1);
goto _54;
_79:
gw(10,1,1);
gw(13,1,0);
sp();
goto _73;
_80:
sp();
if((gr(4,0)+gr(5,0))!=0)goto _71;else goto _81;
_81:
gw(10,1,0);
gw(13,1,1);
gw(10,2,0);
gw(13,2,1);
gw(6,0,0);
gw(7,0,0);
gw(6,0,gr(13,1)+(gr(6,0)*2));
sa(2);
goto _54;
_82:
gw(10,2,1);
gw(13,2,0);
sp();
goto _74;
_83:
sa(sp()-1LL);
sa(sr());
sa(tm(sr(),80));
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(td(sp(),80));
sa(sp()+gr(3,3));
{int64 v0=sp();sa(gr(sp(),v0));}
sa(sr()-gr(3,0));
goto _63;
_84:
sp();
sp();
goto _66;
_85:
gw(4,0,(((gr(10,1))!=0)?0:1)+gr(13,1));
gw(5,0,(((gr(10,2))!=0)?0:1)+gr(13,2));
gw(6,0,0);
gw(7,0,0);
gw(6,0,gr(13,1)+(gr(6,0)*2));
sa(1);
goto _53;
_86:
gw(4,0,(((gr(10,1))!=0)?0:1)+gr(13,1));
gw(5,0,(((gr(10,2))!=0)?0:1)+gr(13,2));
gw(6,0,0);
gw(7,0,0);
gw(6,0,gr(13,1)+(gr(6,0)*2));
sa(2);
goto _53;
_87:
sa(9);
sa(gr(13,1));
goto _35;
_88:
sa(sr()+4);
sa(1);
{int64 v0=sp();t0=gr(sp(),v0);}
t0=(t0!=0)?0:1;
t0+=gr(2,1);
gw(2,1,t0);
sa(1);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(sp()+4LL);
sa(1);
{int64 v0=sp();int64 v1=sp();gw(v1,v0,sp());}
goto _9;
_89:
sa(sr());
sa(sr());
sa(sp()*sp());
sa(td(sp(),10));
sa(sr()+4);
sa(1);
{int64 v0=sp();t0=gr(sp(),v0);}
t0=(t0!=0)?0:1;
t0+=gr(2,1);
gw(2,1,t0);
sa(1);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(sp()+4LL);
sa(1);
{int64 v0=sp();int64 v1=sp();gw(v1,v0,sp());}
sa(sr());
sa(sp()*sp());
sa(tm(sp(),10));
if(sr()!=9)goto _91;else goto _90;
_90:
gw(2,2,(((gr(10,2))!=0)?0:1)+gr(2,2));
gw(10,2,1);
sp();
goto _9;
_91:
sa(sr()+4);
sa(2);
{int64 v0=sp();t0=gr(sp(),v0);}
t0=(t0!=0)?0:1;
t0+=gr(2,2);
gw(2,2,t0);
sa(1);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(sp()+4LL);
sa(2);
{int64 v0=sp();int64 v1=sp();gw(v1,v0,sp());}
goto _9;
_92:
sa(sp()-1LL);
goto _4;
}
int main(void)
{
int64 t0;
d();
s=(int64*)calloc(q,sizeof(int64));
gw(1,0,600);
gw(2,0,150);
gw(9,0,90000);
gw(3,0,2);
gw(4,0,1000);
gw(3,1,0);
_1:
gw(tm(gr(3,0),gr(1,0)),(td(gr(3,0),gr(1,0)))+3,88);
sa(gr(3,0)+gr(3,0));
sa((gr(3,0)+gr(3,0))<gr(9,0)?1:0);
_2:
if(sp()!=0)goto _21;else goto _3;
_3:
sp();
_4:
sa(gr(3,0)+1);
gw(3,0,gr(3,0)+1);
sa(tm(sr(),gr(1,0)));
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(td(sp(),gr(1,0)));
sa(sp()+3LL);
{int64 v0=sp();t0=gr(sp(),v0);}
t0-=32;
if((t0)!=0)goto _6;else goto _4;
_6:
if(gr(9,0)>gr(3,0))goto _1;else goto _7;
_7:
gw(0,3,32);
gw(1,3,32);
gw(5,0,1-gr(4,0));
gw(6,0,2);
_8:
gw(7,0,0);
sa((gr(5,0)*gr(7,0))+gr(6,0));
sa(((gr(5,0)*gr(7,0))+gr(6,0))>1?1:0);
_9:
if(sp()!=0)goto _10;else goto _20;
_10:
sa(tm(sr(),gr(1,0)));
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(td(sp(),gr(1,0)));
sa(sp()+3LL);
{int64 v0=sp();t0=gr(sp(),v0);}
t0-=32;
if((t0)!=0)goto _19;else goto _11;
_11:
t0=gr(7,0);
if(gr(7,0)>gr(3,1))goto _18;else goto _12;
_12:
t0=gr(5,0)+2;
gw(5,0,gr(5,0)+2);
t0=t0>gr(4,0)?1:0;
t0=(t0!=0)?0:1;
if((t0)!=0)goto _8;else goto _13;
_13:
gw(5,0,1-gr(4,0));
_14:
sa(gr(6,0)+1);
gw(6,0,gr(6,0)+1);
sa(tm(sr(),gr(1,0)));
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(td(sp(),gr(1,0)));
sa(sp()+3LL);
{int64 v0=sp();t0=gr(sp(),v0);}
t0-=32;
t0=(t0!=0)?0:1;
if((t0)!=0)goto _14;else goto _16;
_16:
if(gr(6,0)<=gr(4,0))goto _8;else goto _17;
_17:
printf("%lld", gr(1,1)*gr(2,1));
return 0;
_18:
gw(3,1,t0);
gw(1,1,gr(5,0));
gw(2,1,gr(6,0));
goto _12;
_19:
sa(gr(7,0)+1);
gw(7,0,gr(7,0)+1);
sa(sr());
sa(sp()*sp());
sa(sp()+(gr(5,0)*gr(7,0))+gr(6,0));
sa(sr()>1?1:0);
goto _9;
_20:
sp();
goto _11;
_21:
sa(sr());
sa(32);
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(tm(sr(),gr(1,0)));
{int64 v0=sp();int64 v1=sp();sa(v0);sa(v1);}
sa(td(sp(),gr(1,0)));
sa(sp()+3LL);
{int64 v0=sp();int64 v1=sp();gw(v1,v0,sp());}
sa(sp()+gr(3,0));
sa(sr()<gr(9,0)?1:0);
goto _2;
}
unsigned getCCRandomSeed() {
scoped_ptr<SecureRandom> sr( SecureRandom::create() );
return sr->nextInt64();
}
void
TListItem::DrawItem(BView *owner, BRect r, bool /* complete */)
{
if (IsSelected()) {
owner->SetHighColor(180, 180, 180);
owner->SetLowColor(180, 180, 180);
} else {
owner->SetHighColor(255, 255, 255);
owner->SetLowColor(255, 255, 255);
}
owner->FillRect(r);
owner->SetHighColor(0, 0, 0);
BFont font = *be_plain_font;
font.SetSize(font.Size() * kPlainFontSizeScale);
owner->SetFont(&font);
owner->MovePenTo(r.left + 24, r.bottom - 4);
if (fComponent) {
// if it's already a mail component, we don't have an icon to
// draw, and the entry_ref is invalid
BMailAttachment *attachment = dynamic_cast<BMailAttachment *>(fComponent);
char name[B_FILE_NAME_LENGTH * 2];
if ((attachment == NULL) || (attachment->FileName(name) < B_OK))
strcpy(name, "unnamed");
BMimeType type;
if (fComponent->MIMEType(&type) == B_OK)
sprintf(name + strlen(name), ", Type: %s", type.Type());
owner->DrawString(name);
BRect iconRect(0, 0, B_MINI_ICON - 1, B_MINI_ICON - 1);
BBitmap bitmap(iconRect, B_COLOR_8_BIT);
if (GetTrackerIcon(type, &bitmap, B_MINI_ICON) == B_NO_ERROR) {
BRect rect(r.left + 4, r.top + 1, r.left + 4 + 15, r.top + 1 + 15);
owner->SetDrawingMode(B_OP_OVER);
owner->DrawBitmap(&bitmap, iconRect, rect);
owner->SetDrawingMode(B_OP_COPY);
} else {
// ToDo: find some nicer image for this :-)
owner->SetHighColor(150, 150, 150);
owner->FillEllipse(BRect(r.left + 8, r.top + 4, r.left + 16, r.top + 13));
}
return;
}
BFile file(&fRef, O_RDONLY);
BEntry entry(&fRef);
BPath path;
if (entry.GetPath(&path) == B_OK && file.InitCheck() == B_OK) {
owner->DrawString(path.Path());
BNodeInfo info(&file);
BRect sr(0, 0, B_MINI_ICON - 1, B_MINI_ICON - 1);
BBitmap bitmap(sr, B_COLOR_8_BIT);
if (info.GetTrackerIcon(&bitmap, B_MINI_ICON) == B_NO_ERROR) {
BRect dr(r.left + 4, r.top + 1, r.left + 4 + 15, r.top + 1 + 15);
owner->SetDrawingMode(B_OP_OVER);
owner->DrawBitmap(&bitmap, sr, dr);
owner->SetDrawingMode(B_OP_COPY);
}
} else
owner->DrawString("<missing attachment>");
}
void SubRectAllocator::GetRect(CRect& rect, const Subtitle* s, const Align& align, int tlb, int brb)
{
SubRect sr(rect, s->m_layer);
sr.rect.InflateRect(tlb, tlb, brb, brb);
StringMapW<SubRect>::CPair* pPair = Lookup(s->m_name);
if(pPair && pPair->m_value.rect != sr.rect)
{
RemoveKey(s->m_name);
pPair = NULL;
}
if(!pPair)
{
bool vertical = s->m_direction.primary == _T("down") || s->m_direction.primary == _T("up");
bool fOK = false;
while(!fOK)
{
fOK = true;
POSITION pos = GetStartPosition();
while(pos)
{
const SubRect& sr2 = GetNextValue(pos);
if(sr.layer == sr2.layer && !(sr.rect & sr2.rect).IsRectEmpty())
{
if(vertical)
{
if(align.h < 0.5)
{
sr.rect.right = sr2.rect.right + sr.rect.Width();
sr.rect.left = sr2.rect.right;
}
else
{
sr.rect.left = sr2.rect.left - sr.rect.Width();
sr.rect.right = sr2.rect.left;
}
}
else
{
if(align.v < 0.5)
{
sr.rect.bottom = sr2.rect.bottom + sr.rect.Height();
sr.rect.top = sr2.rect.bottom;
}
else
{
sr.rect.top = sr2.rect.top - sr.rect.Height();
sr.rect.bottom = sr2.rect.top;
}
}
fOK = false;
}
}
}
SetAt(s->m_name, sr);
rect = sr.rect;
rect.DeflateRect(tlb, tlb, brb, brb);
}
}
int main(void)
{
int64 t0,t1,t2,t3;
int64 x0=1000;
int64 x1=2;
int64 x2=34;
int64 x3=53;
s=(int64*)calloc(q,sizeof(int64));
_1:
x2=1;
_2:
sa((x2*x2)+(x1*x1));
x3=(x2*x2)+(x1*x1);
sa(0);
sa(0-x3);
_3:
if(sp()!=0)goto _4;else goto _10;
_4:
sa(sp()+1LL);
if(sr()!=x0)goto _9;else goto _5;
_5:
sp();
sp();
_6:
t0=x2+1;
x2++;
t0-=x1;
if((t0)!=0)goto _2;else goto _7;
_7:
t0=x1+1;
x1++;
t0-=x0;
if((t0)!=0)goto _1;else goto _8;
_8:
return 0;
_9:
sa(sr());
sa(sr());
sa(sp()*sp());
sa(sp()-x3);
goto _3;
_10:
x3=sr();
sa(sp()+x2+x1);
sa(sp()-x0);
if(sp()!=0)goto _11;else goto _12;
_11:
sp();
goto _6;
_12:
t0=x2;
printf("%lld", x2);
printf(" ");
t1=x1;
printf("%lld", x1);
printf(" ");
t2=x3;
printf("%lld", x3);
printf("=");
t3=t1*t2;
t1=t0*t3;
printf("%lld", t1);
return 0;
}
static void testschurproblem(const ap::real_2d_array& a,
int n,
double& materr,
double& orterr,
bool& errstruct,
bool& wfailed)
{
ap::real_2d_array s;
ap::real_2d_array t;
ap::real_1d_array sr;
ap::real_1d_array astc;
ap::real_1d_array sastc;
int i;
int j;
int k;
double v;
double locerr;
sr.setbounds(0, n-1);
astc.setbounds(0, n-1);
sastc.setbounds(0, n-1);
//
// Schur decomposition, convergence test
//
t.setbounds(0, n-1, 0, n-1);
for(i = 0; i <= n-1; i++)
{
for(j = 0; j <= n-1; j++)
{
t(i,j) = a(i,j);
}
}
if( !rmatrixschur(t, n, s) )
{
wfailed = true;
return;
}
//
// decomposition error
//
locerr = 0;
for(j = 0; j <= n-1; j++)
{
ap::vmove(&sr(0), &s(j, 0), ap::vlen(0,n-1));
for(k = 0; k <= n-1; k++)
{
v = ap::vdotproduct(&t(k, 0), &sr(0), ap::vlen(0,n-1));
astc(k) = v;
}
for(k = 0; k <= n-1; k++)
{
v = ap::vdotproduct(&s(k, 0), &astc(0), ap::vlen(0,n-1));
sastc(k) = v;
}
for(k = 0; k <= n-1; k++)
{
locerr = ap::maxreal(locerr, fabs(sastc(k)-a(k,j)));
}
}
materr = ap::maxreal(materr, locerr);
//
// orthogonality error
//
locerr = 0;
for(i = 0; i <= n-1; i++)
{
for(j = 0; j <= n-1; j++)
{
v = ap::vdotproduct(s.getcolumn(i, 0, n-1), s.getcolumn(j, 0, n-1));
if( i!=j )
{
locerr = ap::maxreal(locerr, fabs(v));
}
else
{
locerr = ap::maxreal(locerr, fabs(v-1));
}
}
}
orterr = ap::maxreal(orterr, locerr);
//
// T matrix structure
//
for(j = 0; j <= n-1; j++)
{
for(i = j+2; i <= n-1; i++)
{
if( t(i,j)!=0 )
{
errstruct = true;
}
}
}
}
/* the function called by each thread is "mainLoop" */
void*
mainLoop(void* arg)
{
loopArg *loopA = (loopArg*)arg;
istream* testSStream = loopA->inpt;
ostream* pstatStream = loopA->outpt;
int id = loopA->id;
double log600 = log2(600.0);
PrintStack printStack;
for( ; ; )
{
InputTree correct;
InputTree* cuse;
/* first lock to read in the material */
pthread_mutex_lock(&readlock);
if( !*testSStream ) {
pthread_mutex_unlock(&readlock);
break;
}
*testSStream >> correct;
if( !*testSStream ){
pthread_mutex_unlock(&readlock);
break;
}
totWords += correct.length()+1;
int locCount = sentenceCount++;
list<ECString> wtList;
correct.make(wtList);
SentRep sr( wtList ); // used in precision calc
ExtPos extPos;
if(params.extPosIfstream)
extPos.read(params.extPosIfstream,sr);
pthread_mutex_unlock(&readlock);
cuse = &correct;
int len = correct.length();
if(len > params.maxSentLen) continue;
//cerr << "Len = " << len << endl;
/*
if( !params.field().in(sentenceCount) )
{
sentenceCount++;
continue;
}
if(sentenceCount < -1)
{
sentenceCount++;
continue;
}
sentenceCount++;
*/
vector<ECString> poslist;
correct.makePosList(poslist);
ScoreTree sc;
sc.setEquivInts(poslist);
MeChart* chart = new MeChart( sr,extPos,id );
chart->parse( );
Item* topS = chart->topS();
if(!topS)
{
cerr << "Parse failed" << endl;
cerr << correct << endl;
error(" could not parse ");
delete chart;
continue;
}
// compute the outside probabilities on the items so that we can
// skip doing detailed computations on the really bad ones
chart->set_Alphas();
Bst& bst = chart->findMapParse();
if( bst.empty()) error( "mapProbs did not return answer");
float bestF = -1;
int i;
int numVersions = 0;
Link diffs(0);
//cerr << "Need num diff: " << Bchart::Nth << endl;
printStruct printS;
printS.sentenceCount = locCount;
printS.numDiff = 0;
for(numVersions = 0 ; ; numVersions++)
{
short pos = 0;
Val* val = bst.next(numVersions);
if(!val)
{
//cerr << "Breaking" << endl;
break;
}
InputTree* mapparse = inputTreeFromBsts(val,pos,sr);
bool isU;
int dummy = 0;
diffs.is_unique(mapparse, isU, dummy);
// cerr << "V " << isU << " " << numVersions << *mapparse << endl;
if(isU)
{
printS.probs.push_back(val->prob());
printS.trees.push_back(mapparse);
printS.numDiff++;
}
else
{
delete mapparse;
}
if(printS.numDiff >= Bchart::Nth) break;
if(numVersions > 20000) break;
}
ParseStats* locPst = new ParseStats[Bchart::Nth];
ParseStats bestPs;
for(i = 0 ; i <printS.numDiff ; i++)
{
InputTree *mapparse = printS.trees[i];
assert(mapparse);
sc.trips.clear();
ParseStats pSt;
sc.recordGold(cuse,pSt);
sc.precisionRecall(mapparse,pSt);
float newF = pSt.fMeasure();
cerr << printS.sentenceCount << "\t" << newF << endl;
if(newF > bestF)
{
bestF = newF;
bestPs = pSt;
}
if(histPoints[i])
{
locPst[i] += bestPs;
}
}
if(printS.numDiff < Bchart::Nth)
{
for(i = printS.numDiff ; i < Bchart::Nth ; i++)
{
if(histPoints[i]) locPst[i] += bestPs;
}
}
pthread_mutex_lock(&scorelock);
for(i = 0 ; i < Bchart::Nth ; i++) totPst[i]+=locPst[i];
pthread_mutex_unlock(&scorelock);
int numPrinted;
/* put the sentence with which we just finished at the end of the printStack*/
printStack.push_back(printS);
PrintStack::iterator psi = printStack.begin();
/* now look at each item from the front of the print stack
to see if it should be printed now */
pthread_mutex_lock(&writelock);
for( numPrinted =0; psi != printStack.end(); numPrinted++ )
{
printStruct& pstr=(*psi);
if(pstr.sentenceCount != printCount) break;
*pstatStream << pstr.sentenceCount << "\t" << pstr.numDiff << "\n";
printCount++;
for(i = 0 ; i < pstr.numDiff ; i++)
{
InputTree* mapparse = pstr.trees[i];
assert(mapparse);
double logP =log2(pstr.probs[i]);
logP -= (sr.length()*log600);
*pstatStream << logP << "\n";
if(Bchart::prettyPrint) *pstatStream << *mapparse << "\n\n";
else
{
mapparse->printproper(*pstatStream);
*pstatStream << "\n";
}
delete mapparse;
}
*pstatStream << endl;
psi++;
}
pthread_mutex_unlock(&writelock);
for(i = 0 ; i < numPrinted ; i++) printStack.pop_front();
if(Feature::isLM)
{
double lgram = log2(bst.sum());
lgram -= (sr.length()*log600);
double pgram = pow(2,lgram);
double iptri = chart->triGram();;
double ltri = (log2(iptri)-sr.length()*log600);
double ptri = pow(2.0,ltri);
double pcomb1 = (0.667 * pgram)+(0.333 * ptri);
double lcom1 = log2(pcomb1);
totGram -= lgram;
totTri -= ltri;
totMix -= lcom1;
if(locCount%10 == 9)
{
cerr << locCount << "\t";
cerr << pow(2.0,totGram/(double)totWords);
cerr <<"\t" << pow(2.0,totTri/(double)totWords);
cerr << "\t" << pow(2.0,totMix/(double)(totWords));
cerr << endl;
}
}
if(locCount%50 == 1)
{
cerr << sentenceCount << "\t";
for(int i = 0 ; i < Bchart::Nth ; i++)
if(histPoints[i])
{
cerr << i << " " << totPst[i].fMeasure() << "\t";
}
cerr << endl;
}
delete chart;
delete [] locPst;
}
return 0;
}
int a3_getLeptonPrediction(int pdgId, double metCut, double jetptCut, double ptCut, double iasCut, bool doEcaloCut, double ecaloCut, TString region){
gDirectory->Delete();
cout<<endl<<"Get leptonic bkg prediction in "<<region<<"."<<endl;
// %%%%%%%%%%%%%%%%%%% Get correct scaling factors %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
TFile *in = new TFile(Form("templates/leptonScalingFactors_pdgId_%i_metCut_%.f_jetptCut_%.0f_ptCut_%.0f",pdgId,metCut,jetptCut,ptCut) + region + ".root","READ");
TGraphAsymmErrors *GScalingFactors = 0;
TString name = Form("%.0f_%.0f",ptCut,ecaloCut);
in -> GetObject(name,GScalingFactors);
if(GScalingFactors==0){
cout<<"No Graph available!"<<endl;
return 1;
}
double aux;
double scalingFactor;
GScalingFactors->GetPoint(0,aux,scalingFactor);
double scalingFactorErrorUp = GScalingFactors->GetErrorYhigh(0);
double scalingFactorErrorLow = GScalingFactors->GetErrorYlow(0);
cout.precision(3);
cout<<"scaling factor = "<<scientific<<scalingFactor<<" + "<<scalingFactorErrorUp<<" - "<<scalingFactorErrorLow<<endl;
// %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
// %%%%%%%%%%%%%%%%%%% Get number of Events in CR_lepton from data %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
sample data("data");
sample sr("data");
sr.getTree(fileSR);
if(pdgId==211) data.getTree(filePionCS);
else if(pdgId==11) data.getTree(fileElectronCS);
else if(pdgId==13) data.getTree(fileMuonCS);
data.getTreeVariables();
sr.getTreeVariables();
data.histo = new TH1D("data","data",1,0,1);
data.histo->Sumw2();
sr.histo = new TH1D("sr","sr",1,0,1);
sr.histo->Sumw2();
//data.Selection(0, pdgId, metCut, jetptCut, ptCut, iasCut, doEcaloCut, ecaloCut, 0, region);
//sr.Selection( 0, pdgId, metCut, jetptCut, ptCut, iasCut, 1, ecaloCut, 0, region);
data.Selection(0, pdgId, metCut, jetptCut, ptCut, 0.0 , doEcaloCut, ecaloCut, 1, region);
sr.Selection( 0, pdgId, metCut, jetptCut, ptCut, iasCut, 1 , ecaloCut, 0, region);
double nSRInclusive = data.histo->Integral(1,data.histo->GetNbinsX()+1);
double nSRErrorUpInclusive = nSRInclusive;
double nSRErrorLowInclusive = nSRInclusive;
cout<<"Data Yield (CR) = "<<fixed<<nSRInclusive<<endl;
if(nSRInclusive==0){
/*
nSR = getOneSidedUpperLimit(nSR , 0.6827) - nSR;
nSRErrorUp = 0;
nSRErrorLow = 0;
*/
nSRInclusive = 0;
nSRErrorUpInclusive = getOneSidedUpperLimit(nSRInclusive , 0.6827);
nSRErrorLowInclusive = getOneSidedLowerLimit(nSRInclusive , 0.6827);
}
nSRInclusive = nSRInclusive * scalingFactor;
nSRErrorUpInclusive = nSRErrorUpInclusive * scalingFactorErrorUp;
nSRErrorLowInclusive = nSRErrorLowInclusive * scalingFactorErrorLow;
// %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
//%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
cout<<"nSRInclusive ("<<pdgId<<") = "<<nSRInclusive<<" + "<<nSRErrorUpInclusive<<" - "<<nSRErrorLowInclusive<<endl;
//cout<<"Data Yield (CR) = "<<sr.histo->Integral()<<endl;
//%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
//%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Get Ias template from MC %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
TString filename = Form("templates/IasTemplate_METGt%.0f_JetPtGt%.0f_trackPtGt%0.f_ECaloEq%.0f_pdgId%i.root",metCut,jetptCut,ptCut,ecaloCut,pdgId);
cout<<"Ias template from : "<<filename<<endl;
TFile *inIas = new TFile(filename,"READ");
TH1D* histoIas = 0;
TString histoName = Form("lepton_bkg_data_Iascut_0p%02.0f",iasCut*100);
cout<<"histogram = "<<histoName<<endl;
inIas -> GetObject(histoName,histoIas);
double Ias = 0;
double IasErr = 0;
if(region=="SR" || region=="CR1"){
Ias = histoIas->GetBinContent(2);
IasErr = histoIas->GetBinError(2);
}
else if(region=="CR2" || region=="CR3"){
Ias = histoIas->GetBinContent(1);
IasErr = histoIas->GetBinError(1);
}
cout<<"histoIas->GetBinContent(1) = "<<histoIas->GetBinContent(1)<<endl;
cout<<"histoIas->GetBinContent(2) = "<<histoIas->GetBinContent(2)<<endl;
int nEntries = histoIas->GetEntries();
cout<<"nEntries = "<<nEntries<<endl;
double a = nEntries/(histoIas->Integral());
double IasErrUp = (getOneSidedUpperLimit(a*Ias , 0.6827) - a*Ias)/a;
double IasErrLow = (a*Ias - getOneSidedLowerLimit(a*Ias , 0.6827))/a;
if(Ias==0){
double up = getOneSidedUpperLimit(0 , 0.6827);
double low = getOneSidedLowerLimit(0 , 0.6827);
cout<<"Upper limit = "<<up<<endl;
IasErrUp = up/nEntries;
IasErrLow = low/nEntries;
cout<<"IasErrUp = "<<IasErrUp<<endl;
}
cout<<"Ias = "<<Ias<<" +/- "<<IasErr<<endl;
double nSR = nSRInclusive*Ias;
double nSRErrorUp = sqrt( pow( Ias*nSRErrorUpInclusive ,2) + pow( nSRInclusive*IasErrUp ,2) );
double nSRErrorLow = sqrt( pow( Ias*nSRErrorLowInclusive ,2) + pow( nSRInclusive*IasErrLow ,2) );
cout<<"###########################################################################"<<endl;
cout.precision(2);
cout<<"Statisitcs for "<<pdgId<<" : "<<"pt="<<ptCut<<" ECalo="<<ecaloCut<<endl;
cout<<"NEntries in Ias histo = "<<histoIas->Integral()*a<<endl;
cout<<"NEntries in high Ias = "<<Ias*a<<" +/- "<<IasErr<<endl;
//cout<<"scaling factor = "<<scientific<<scalingFactor<<" + "<<scalingFactorErrorUp<<" - "<<scalingFactorErrorLow<<endl;
cout<<"###########################################################################"<<endl;
cout<<"nSR ("<<pdgId<<") = "<<nSR<<" + "<<nSRErrorUp<<" - "<<nSRErrorLow<<endl;
//%%%%%%%%%%%%%%%%%%%% Write output %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
filename = Form("results/Bkg%i_metCutEq%.0f_ptCutEq%.0f_ECaloCutEq%.0f_IasCutEq0p%02.0f_",pdgId,metCut,ptCut,ecaloCut,iasCut*100) + region + ".root";
TFile *out = new TFile(filename,"RECREATE");
if(pdgId==11) name = "electrons";
else if(pdgId==13) name = "muons";
else if(pdgId==211) name = "pions";
double x[1] = {0.5};
double xLow[1] = {0};
double xUp[1] = {0};
double y[1] = {nSR};
double yLow[1] = {nSRErrorLow};
double yUp[1] = {nSRErrorUp};
TGraphAsymmErrors* GnSR = new TGraphAsymmErrors(1,x,y,xLow,xUp,yLow,yUp);
GnSR -> SetMarkerStyle(20);
GnSR -> Write(name);
out->Close();
if(pdgId==211){
filename = Form("results/DataYield_metCutEq%.0f_ptCutEq%.0f_ECaloCutEq%.0f_IasCutEq0p%02.0f_",metCut,ptCut,ecaloCut,iasCut*100) + region + ".root";
TFile *outData = new TFile(filename,"RECREATE");
name="data";
TH1D *histoData = new TH1D(name,name,1,0,1);
histoData->Fill("CR1",0);
histoData->Fill("CR2",0);
histoData->Fill("CR3",0);
histoData->Fill("SR",0);
int bin = histoData->GetXaxis()->FindBin("SR");
histoData->SetBinContent(bin,sr.histo->Integral());
histoData->SetBinError(bin,sqrt(sr.histo->Integral()));
histoData->Write();
outData->Close();
delete outData;
}
return 0;
}
bool LevellerDataset::write_header()
{
char szHeader[5];
strcpy(szHeader, "trrn");
szHeader[4] = 7; // TER v7 introduced w/ Lev 2.6.
if(1 != VSIFWriteL(szHeader, 5, 1, m_fp)
|| !this->write_tag("hf_w", (size_t)nRasterXSize)
|| !this->write_tag("hf_b", (size_t)nRasterYSize))
{
CPLError( CE_Failure, CPLE_FileIO, "Could not write header" );
return false;
}
m_dElevBase = 0.0;
m_dElevScale = 1.0;
if(m_pszProjection == NULL || m_pszProjection[0] == 0)
{
this->write_tag("csclass", LEV_COORDSYS_RASTER);
}
else
{
this->write_tag("coordsys_wkt", m_pszProjection);
const UNITLABEL units_elev = this->id_to_code(m_szElevUnits);
const int bHasECS =
(units_elev != UNITLABEL_PIXEL && units_elev != UNITLABEL_UNKNOWN);
this->write_tag("coordsys_haselevm", bHasECS);
OGRSpatialReference sr(m_pszProjection);
if(bHasECS)
{
if(!this->compute_elev_scaling(sr))
return false;
// Raw-to-real units scaling.
this->write_tag("coordsys_em_scale", m_dElevScale);
//elev offset, in real units.
this->write_tag("coordsys_em_base", m_dElevBase);
this->write_tag("coordsys_em_units", units_elev);
}
if(sr.IsLocal())
{
this->write_tag("csclass", LEV_COORDSYS_LOCAL);
const double dfLinear = sr.GetLinearUnits();
const int n = this->meter_measure_to_code(dfLinear);
this->write_tag("coordsys_units", n);
}
else
{
this->write_tag("csclass", LEV_COORDSYS_GEO);
}
if( m_adfTransform[2] != 0.0 || m_adfTransform[4] != 0.0)
{
CPLError( CE_Failure, CPLE_IllegalArg,
"Cannot handle rotated geotransform" );
return false;
}
// todo: GDAL gridpost spacing is based on extent / rastersize
// instead of extent / (rastersize-1) like Leveller.
// We need to look into this and adjust accordingly.
// Write north-south digital axis.
this->write_tag("coordsys_da0_style", LEV_DA_PIXEL_SIZED);
this->write_tag("coordsys_da0_fixedend", 0);
this->write_tag("coordsys_da0_v0", m_adfTransform[3]);
this->write_tag("coordsys_da0_v1", m_adfTransform[5]);
// Write east-west digital axis.
this->write_tag("coordsys_da1_style", LEV_DA_PIXEL_SIZED);
this->write_tag("coordsys_da1_fixedend", 0);
this->write_tag("coordsys_da1_v0", m_adfTransform[0]);
this->write_tag("coordsys_da1_v1", m_adfTransform[1]);
}
this->write_tag_start("hf_data",
sizeof(float) * nRasterXSize * nRasterYSize);
return true;
}
int main()
{
{
Juncture * j = new Juncture(0, "1", 1);
delete j;
}
{
Juncture * j = new Juncture(0, "1", 1);
OpVector res;
Operation op;
j->operation(op, res);
delete j;
}
{
Juncture * j = new Juncture(0, "1", 1);
OpVector res;
Atlas::Objects::Operation::Login op;
j->operation(op, res);
delete j;
}
// Login op, no args
{
Juncture * j = new Juncture(0, "1", 1);
OpVector res;
Operation op;
j->LoginOperation(op, res);
delete j;
}
// Login op, empty arg
{
Juncture * j = new Juncture(0, "1", 1);
OpVector res;
Operation op;
Atlas::Objects::Root arg;
op->setArgs1(arg);
j->LoginOperation(op, res);
delete j;
}
// Login op, username in arg
{
Juncture * j = new Juncture(0, "1", 1);
OpVector res;
Operation op;
Atlas::Objects::Root arg;
arg->setAttr("username", "69e362c6-03a4-11e0-9608-001ec93e7c08");
op->setArgs1(arg);
j->LoginOperation(op, res);
delete j;
}
// Login op, bad username in arg
{
Juncture * j = new Juncture(0, "1", 1);
OpVector res;
Operation op;
Atlas::Objects::Root arg;
arg->setAttr("username", 0x69e362c6);
op->setArgs1(arg);
j->LoginOperation(op, res);
delete j;
}
// Login op, username & password in arg
{
Juncture * j = new Juncture(0, "1", 1);
OpVector res;
Operation op;
Atlas::Objects::Root arg;
arg->setAttr("username", "69e362c6-03a4-11e0-9608-001ec93e7c08");
arg->setAttr("password", "a12a2f3a-03a4-11e0-8379-001ec93e7c08");
op->setArgs1(arg);
j->LoginOperation(op, res);
delete j;
}
// Login op, username & bad password in arg
{
Juncture * j = new Juncture(0, "1", 1);
OpVector res;
Operation op;
Atlas::Objects::Root arg;
arg->setAttr("username", "69e362c6-03a4-11e0-9608-001ec93e7c08");
arg->setAttr("password", 0x12a2f3aL);
op->setArgs1(arg);
j->LoginOperation(op, res);
delete j;
}
// Login op, username & password in arg, connected
{
ServerRouting sr(*(BaseWorld*)0, "", "", "2", 2, "3", 3);
TestJuncture * j = new TestJuncture(0);
boost::asio::io_service io_service;
CommPeer * cp = new CommPeer("", io_service);
j->test_addPeer(new Peer(*cp, sr, "", 6767, "4", 4));
OpVector res;
Operation op;
Atlas::Objects::Root arg;
arg->setAttr("username", "69e362c6-03a4-11e0-9608-001ec93e7c08");
arg->setAttr("password", "a12a2f3a-03a4-11e0-8379-001ec93e7c08");
op->setArgs1(arg);
j->LoginOperation(op, res);
delete j;
}
// Login op, username & password in arg, connected already authenticating
{
ServerRouting sr(*(BaseWorld*)0, "", "", "2", 2, "3", 3);
TestJuncture * j = new TestJuncture(0);
boost::asio::io_service io_service;
CommPeer * cp = new CommPeer("", io_service);
Peer * p = new Peer(*cp, sr, "", 6767, "4", 4);
j->test_addPeer(p);
p->setAuthState(PEER_AUTHENTICATING);
OpVector res;
Operation op;
Atlas::Objects::Root arg;
arg->setAttr("username", "69e362c6-03a4-11e0-9608-001ec93e7c08");
arg->setAttr("password", "a12a2f3a-03a4-11e0-8379-001ec93e7c08");
op->setArgs1(arg);
j->LoginOperation(op, res);
delete j;
}
// Login op, username & password in arg, connected, with serialno
{
ServerRouting sr(*(BaseWorld*)0, "", "", "2", 2, "3", 3);
TestJuncture * j = new TestJuncture(0);
boost::asio::io_service io_service;
CommPeer * cp = new CommPeer("", io_service);
j->test_addPeer(new Peer(*cp, sr, "", 6767, "4", 4));
OpVector res;
Operation op;
Atlas::Objects::Root arg;
arg->setAttr("username", "69e362c6-03a4-11e0-9608-001ec93e7c08");
arg->setAttr("password", "a12a2f3a-03a4-11e0-8379-001ec93e7c08");
op->setArgs1(arg);
op->setSerialno(0x6dc5b5eaL);
j->LoginOperation(op, res);
delete j;
}
{
Juncture * j = new Juncture(0, "1", 1);
OpVector res;
Operation op;
j->OtherOperation(op, res);
delete j;
}
{
Juncture * j = new Juncture(0, "1", 1);
OpVector res;
Atlas::Objects::Operation::Connect op;
j->OtherOperation(op, res);
delete j;
}
// Connect op, no args
{
Juncture * j = new Juncture(0, "1", 1);
OpVector res;
Operation op;
j->customConnectOperation(op, res);
delete j;
}
// Connect op, no args, already connected
{
TestJuncture * j = new TestJuncture(0);
j->test_addPeer(new Peer(*(CommPeer*)0, *(ServerRouting*)0, "", 6767, "4", 4));
OpVector res;
Operation op;
j->customConnectOperation(op, res);
delete j;
}
// Connect op, hostname in arg
{
Juncture * j = new Juncture(0, "1", 1);
OpVector res;
Operation op;
Atlas::Objects::Root arg;
arg->setAttr("hostname", "3752ca4a-03a9-11e0-bd8a-001ec93e7c08");
op->setArgs1(arg);
j->customConnectOperation(op, res);
delete j;
}
// Connect op, bad hostname in arg
{
Juncture * j = new Juncture(0, "1", 1);
OpVector res;
Operation op;
Atlas::Objects::Root arg;
arg->setAttr("hostname", 0x3752ca4aL);
op->setArgs1(arg);
j->customConnectOperation(op, res);
delete j;
}
// Connect op, hostname and port in arg, connected this end
{
ServerRouting sr(*(BaseWorld*)0, "", "", "2", 2, "3", 3);
boost::asio::io_service io_service;
CommSocket * cc = new StubSocket(io_service);
Connection * c = new Connection(*cc, sr, "", "4", 4);
Juncture * j = new Juncture(c, "1", 1);
OpVector res;
Operation op;
Atlas::Objects::Root arg;
arg->setAttr("hostname", "3752ca4a-03a9-11e0-bd8a-001ec93e7c08");
arg->setAttr("port", 0x03a9);
op->setArgs1(arg);
j->customConnectOperation(op, res);
delete j;
}
// Connect op, hostname and port in arg, connected this end, connect fails
{
stub_CommPeer_connect_return = -1;
ServerRouting sr(*(BaseWorld*)0, "", "", "2", 2, "3", 3);
boost::asio::io_service io_service;
CommSocket * cc = new StubSocket(io_service);
Connection * c = new Connection(*cc, sr, "", "4", 4);
Juncture * j = new Juncture(c, "1", 1);
OpVector res;
Operation op;
Atlas::Objects::Root arg;
arg->setAttr("hostname", "3752ca4a-03a9-11e0-bd8a-001ec93e7c08");
arg->setAttr("port", 0x03a9);
op->setArgs1(arg);
j->customConnectOperation(op, res);
stub_CommPeer_connect_return = 0;
delete j;
}
// Teleport unconnected
{
TestJuncture * j = new TestJuncture(0);
j->teleportEntity(0);
delete j;
}
// Teleport connected
{
TestJuncture * j = new TestJuncture(0);
j->test_addPeer(new Peer(*(CommPeer*)0, *(ServerRouting*)0, "", 6767, "4", 4));
j->teleportEntity(0);
delete j;
}
{
TestJuncture * j = new TestJuncture(0);
j->test_onPeerLost();
delete j;
}
// Peer replied, unconnected this end
{
TestJuncture * j = new TestJuncture(0);
Operation op;
j->test_onPeerReplied(op);
delete j;
}
// Peer replied, connected this end
{
Connection * c = new Connection(*(CommSocket*)0,
*(ServerRouting*)0, "", "4", 4);
TestJuncture * j = new TestJuncture(c);
Operation op;
j->test_onPeerReplied(op);
delete j;
}
return 0;
}
