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Merge pull request #3264 from code-s-witch/min-cut-graph
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Add ensure_vg() to mcmc_main subcommand
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@adamnovak
adamnovak authored May 21, 2021
2 parents f52d3a2 + 21027b8 commit 99cbb47
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Showing 2 changed files with 28 additions and 8 deletions.
8 changes: 4 additions & 4 deletions scripts/mcmc_Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -52,8 +52,8 @@ $(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_0).vg: $(TOIL_OS)/$(BASENAME)_$(HA
$(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_0).xg: $(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_0).vg
vg index -x $(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_0).xg $(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_0).vg

$(TOIL_OS)/$(BASENAME)_$(HAPLO_0).gam: $(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_0).xg
toil-vg sim --gam --sim_opts '--sub-rate 0.1 --indel-rate 0.1 --read-length 100' --container None --out_name $(BASENAME)_$(HAPLO_0) $(TOIL_JS) $(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_0).xg $(READS) $(TOIL_OS)
$(TOIL_OS)/$(BASENAME)_$(HAPLO_0).gam: $(TOIL_OS)/$(BASENAME).xg $(TOIL_OS)/$(BASENAME).gbwt
vg sim -x $(TOIL_OS)/$(BASENAME).xg -g $(TOIL_OS)/$(BASENAME).gbwt -m $(SAMP) -n 300 --sub-rate 0.05 --indel-rate 0.05 --read-length 100 -a > $(TOIL_OS)/$(BASENAME)_$(HAPLO_0).gam

$(TOIL_OS)/$(BASENAME)_$(HAPLO_1)_thread.merge.vg: $(TOIL_OS)/$(BASENAME).vg $(TOIL_OS)/$(BASENAME).gbwt $(TOIL_OS)/$(BASENAME).xg
vg paths -d -v $(TOIL_OS)/$(BASENAME).vg > $(TOIL_OS)/$(BASENAME)_$(HAPLO_1)_thread.merge.vg
Expand All @@ -65,8 +65,8 @@ $(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_1).vg: $(TOIL_OS)/$(BASENAME)_$(HA
$(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_1).xg: $(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_1).vg
vg index -x $(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_1).xg $(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_1).vg

$(TOIL_OS)/$(BASENAME)_$(HAPLO_1).gam: $(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_1).xg
toil-vg sim --gam --sim_opts '--sub-rate 0.1 --indel-rate 0.1 --read-length 100' --container None --out_name $(BASENAME)_$(HAPLO_1) $(TOIL_JS) $(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_1).xg $(READS) $(TOIL_OS)
$(TOIL_OS)/$(BASENAME)_$(HAPLO_1).gam: $(TOIL_OS)/$(BASENAME).xg $(TOIL_OS)/$(BASENAME).gbwt
vg sim -x $(TOIL_OS)/$(BASENAME).xg -g $(TOIL_OS)/$(BASENAME).gbwt -m $(SAMP) -n 300 --sub-rate 0.05 --indel-rate 0.05 --read-length 100 -a > $(TOIL_OS)/$(BASENAME)_$(HAPLO_1).gam

$(TOIL_OS)/$(BASENAME)_merged.gam: $(TOIL_OS)/$(BASENAME)_$(HAPLO_0).gam $(TOIL_OS)/$(BASENAME)_$(HAPLO_1).gam
cat $(TOIL_OS)/$(BASENAME)_$(HAPLO_0).gam $(TOIL_OS)/$(BASENAME)_$(HAPLO_1).gam > $(TOIL_OS)/$(BASENAME)_merged.gam
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28 changes: 24 additions & 4 deletions src/subcommand/mcmc_main.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -135,16 +135,36 @@ int main_mcmc(int argc, char** argv) {
unique_ptr<SnarlManager> snarls = (vg::io::VPKG::load_one<SnarlManager>(snarls_file));

// // create a PathHandleGraph
unique_ptr<VG> vg_graph;
unique_ptr<PathHandleGraph> path_hgraph;
bdsg::PathPositionOverlayHelper overlay_helper;
vg_graph = vg::io::VPKG::load_one<VG>(graph_file);
path_hgraph = vg::io::VPKG::load_one<PathHandleGraph>(graph_file);

if(vg_graph.get() == nullptr || vg_graph.get() == 0){
// Some stuff below here needs a vg graph.
VG* vg_graph = dynamic_cast<vg::VG*>(path_hgraph.get());

// Call this to populate the vg_graph if it isn't populated.
auto ensure_vg = [&]() -> vg::VG* {
if (vg_graph == nullptr) {
// Copy instead.
vg_graph = new vg::VG();
handlealgs::copy_path_handle_graph(path_hgraph.get(), vg_graph);
// Give the unique_ptr ownership and delete the graph we loaded.
path_hgraph.reset(vg_graph);
// Make sure the paths are all synced up
vg_graph->paths.to_graph(vg_graph->graph);
}
return vg_graph;
};

//convert to VG graph if needed
ensure_vg();

if(vg_graph == nullptr || vg_graph == 0){
cerr << "Graph is NULL" <<endl;
exit(1);
}
PathPositionHandleGraph* graph = nullptr;
graph = overlay_helper.apply(vg_graph.get());
graph = overlay_helper.apply(vg_graph);


// Check our paths
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vg CI tests complete for merge to master. View the full report here.

16 tests passed, 0 tests failed and 0 tests skipped in 11369 seconds

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