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YunDeng98YunDeng98
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relogic rate computation
1 parent cc48a41 commit 43e72d5

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+27
-108
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4 files changed

+27
-108
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‎SINGER/SINGER.xcodeproj/project.xcworkspace/xcuserdata/yun_deng.xcuserdatad/UserInterfaceState.xcuserstate‎

609 Bytes
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‎SINGER/SINGER.xcodeproj/xcuserdata/yun_deng.xcuserdatad/xcdebugger/Breakpoints_v2.xcbkptlist‎

Lines changed: 8 additions & 72 deletions
Original file line numberDiff line numberDiff line change
@@ -361,28 +361,12 @@
361361
filePath = "SINGER/Sampler.cpp"
362362
startingColumnNumber = "9223372036854775807"
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endingColumnNumber = "9223372036854775807"
364-
startingLineNumber = "680"
365-
endingLineNumber = "680"
364+
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365+
endingLineNumber = "683"
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landmarkName = "Sampler::debug_resume_fast_internal_sample(num_iters, spacing)"
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landmarkType = "7">
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</BreakpointContent>
369369
</BreakpointProxy>
370-
<BreakpointProxy
371-
BreakpointExtensionID = "Xcode.Breakpoint.FileBreakpoint">
372-
<BreakpointContent
373-
uuid = "3A646B35-E567-485E-86D9-7A83BE6A1903"
374-
shouldBeEnabled = "No"
375-
ignoreCount = "0"
376-
continueAfterRunningActions = "No"
377-
filePath = "SINGER/main.cpp"
378-
startingColumnNumber = "9223372036854775807"
379-
endingColumnNumber = "9223372036854775807"
380-
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381-
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382-
landmarkName = "main(argc, argv)"
383-
landmarkType = "9">
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<BreakpointProxy
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BreakpointExtensionID = "Xcode.Breakpoint.FileBreakpoint">
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<BreakpointContent
@@ -399,38 +383,6 @@
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landmarkType = "7">
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</BreakpointContent>
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</BreakpointProxy>
402-
<BreakpointProxy
403-
BreakpointExtensionID = "Xcode.Breakpoint.FileBreakpoint">
404-
<BreakpointContent
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uuid = "E8920469-0B32-4E38-A8EC-F62ABD94A831"
406-
shouldBeEnabled = "Yes"
407-
ignoreCount = "0"
408-
continueAfterRunningActions = "No"
409-
filePath = "SINGER/main.cpp"
410-
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411-
endingColumnNumber = "9223372036854775807"
412-
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413-
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landmarkName = "main(argc, argv)"
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landmarkType = "9">
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BreakpointExtensionID = "Xcode.Breakpoint.FileBreakpoint">
420-
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422-
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423-
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424-
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425-
filePath = "SINGER/main.cpp"
426-
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427-
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428-
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429-
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landmarkName = "main(argc, argv)"
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BreakpointExtensionID = "Xcode.Breakpoint.FileBreakpoint">
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<BreakpointContent
@@ -441,28 +393,12 @@
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filePath = "SINGER/Sampler.cpp"
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444-
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445-
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396+
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397+
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landmarkName = "Sampler::iterative_start()"
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landmarkType = "7">
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450-
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BreakpointExtensionID = "Xcode.Breakpoint.FileBreakpoint">
452-
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454-
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455-
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456-
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457-
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458-
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459-
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460-
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461-
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463-
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@@ -473,8 +409,8 @@
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filePath = "SINGER/Sampler.cpp"
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476-
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412+
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413+
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@@ -505,8 +441,8 @@
505441
filePath = "SINGER/Sampler.cpp"
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508-
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444+
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445+
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landmarkName = "Sampler::iterative_start()"
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</BreakpointContent>

‎SINGER/SINGER/Sampler.cpp‎

Lines changed: 15 additions & 16 deletions
Original file line numberDiff line numberDiff line change
@@ -306,8 +306,11 @@ void Sampler::build_singleton_arg() {
306306
arg = ARG(Ne, sequence_length);
307307
arg.discretize(bin_size);
308308
arg.build_singleton_arg(n);
309-
// arg.compute_rhos_thetas(recomb_rate, mut_rate);
310-
arg.compute_rhos_thetas(recomb_map, mut_map);
309+
if (mut_rate > 0 and recomb_rate > 0) {
310+
arg.compute_rhos_thetas(recomb_rate, mut_rate);
311+
} else {
312+
arg.compute_rhos_thetas(recomb_map, mut_map);
313+
}
311314
}
312315

313316
void Sampler::build_void_arg() {
@@ -777,22 +780,18 @@ void Sampler::write_cut(tuple<double, Branch, double> cut_point) {
777780
void Sampler::load_resume_arg() {
778781
arg = ARG(Ne, sequence_length);
779782
string node_file, branch_file, recomb_file, mut_file, coord_file;
780-
if (!fast_mode) {
781-
node_file = output_prefix + "_nodes_" + to_string(sample_index) + ".txt";
782-
branch_file= output_prefix + "_branches_" + to_string(sample_index) + ".txt";
783-
recomb_file = output_prefix + "_recombs_" + to_string(sample_index) + ".txt";
784-
mut_file = output_prefix + "_muts_" + to_string(sample_index) + ".txt";
785-
coord_file = output_prefix + "_coordinates.txt";
786-
} else {
787-
node_file = output_prefix + "_fast_nodes_" + to_string(sample_index) + ".txt";
788-
branch_file= output_prefix + "_fast_branches_" + to_string(sample_index) + ".txt";
789-
recomb_file = output_prefix + "_fast_recombs_" + to_string(sample_index) + ".txt";
790-
mut_file = output_prefix + "_fast_muts_" + to_string(sample_index) + ".txt";
791-
coord_file = output_prefix + "_fast_coordinates.txt";
792-
}
783+
node_file = output_prefix + "_fast_nodes_" + to_string(sample_index) + ".txt";
784+
branch_file= output_prefix + "_fast_branches_" + to_string(sample_index) + ".txt";
785+
recomb_file = output_prefix + "_fast_recombs_" + to_string(sample_index) + ".txt";
786+
mut_file = output_prefix + "_fast_muts_" + to_string(sample_index) + ".txt";
787+
coord_file = output_prefix + "_fast_coordinates.txt";
793788
arg.read(node_file, branch_file, recomb_file, mut_file);
794789
arg.read_coordinates(coord_file);
795-
arg.compute_rhos_thetas(recomb_rate, mut_rate);
790+
if (mut_rate > 0 and recomb_rate > 0) {
791+
arg.compute_rhos_thetas(recomb_rate, mut_rate);
792+
} else {
793+
arg.compute_rhos_thetas(recomb_map, mut_map);
794+
}
796795
}
797796

798797
vector<string> Sampler::read_last_line(string filename) {

‎SINGER/SINGER/main.cpp‎

Lines changed: 4 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -273,31 +273,15 @@ int main(int argc, const char * argv[]) {
273273
sampler.end = end_pos;
274274
if (resume) {
275275
sampler.sequence_length = end_pos - start_pos;
276-
if (fast) {
277-
sampler.resume_fast_internal_sample(num_iters, spacing);
278-
} else {
279-
sampler.resume_internal_sample(num_iters, spacing);
280-
}
276+
sampler.resume_internal_sample(num_iters, spacing);
281277
return 0;
282278
} else if (debug) {
283279
sampler.sequence_length = end_pos - start_pos;
284-
if (fast) {
285-
sampler.debug_resume_fast_internal_sample(num_iters, spacing);
286-
} else {
287-
sampler.debug_resume_internal_sample(num_iters, spacing);
288-
}
280+
sampler.debug_resume_internal_sample(num_iters, spacing);
289281
return 0;
290282
}
291283
sampler.load_vcf(input_filename, start_pos, end_pos);
292-
if (fast) {
293-
sampler.fast_iterative_start();
294-
} else {
295-
sampler.iterative_start();
296-
}
297-
if (fast) {
298-
sampler.fast_internal_sample(num_iters, spacing);
299-
} else {
300-
sampler.internal_sample(num_iters, spacing);
301-
}
284+
sampler.iterative_start();
285+
sampler.internal_sample(num_iters, spacing);
302286
return 0;
303287
}

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