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remove vg paths -V #4846

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remove vg paths -V #4846

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1117bd6
deprecate vg paths -V
faithokamoto Mar 6, 2026
faa861c
error
faithokamoto Mar 6, 2026
4255afb
don't use -V in tests
faithokamoto Mar 9, 2026
18c7b65
change toil-vg version to one that doesn't use -V
faithokamoto Mar 17, 2026
32eab38
bump again
faithokamoto Mar 17, 2026
8e2a58f
bump again again
faithokamoto Mar 18, 2026
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4 changes: 2 additions & 2 deletions scripts/mcmc_Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,7 @@ $(TOIL_OS)/$(BASENAME).snarls: $(TOIL_OS)/$(BASENAME).vg

$(TOIL_OS)/$(BASENAME)_$(HAPLO_0)_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_0)_thread.merge.vg
vg paths --gbwt $(TOIL_OS)/$(BASENAME).gbwt --extract-vg -x $(TOIL_OS)/$(BASENAME).xg -Q _thread_$(SAMP)_x_$(HAPLO_0) >> $(TOIL_OS)/$(BASENAME)_$(HAPLO_0)_thread.merge.vg
vg paths --gbwt $(TOIL_OS)/$(BASENAME).gbwt --retain-paths -x $(TOIL_OS)/$(BASENAME).xg -Q _thread_$(SAMP)_x_$(HAPLO_0) >> $(TOIL_OS)/$(BASENAME)_$(HAPLO_0)_thread.merge.vg

$(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_0).vg: $(TOIL_OS)/$(BASENAME)_$(HAPLO_0)_thread.merge.vg
vg mod -N $(TOIL_OS)/$(BASENAME)_$(HAPLO_0)_thread.merge.vg > $(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_0).vg
Expand All @@ -57,7 +57,7 @@ $(TOIL_OS)/$(BASENAME)_$(HAPLO_0).gam: $(TOIL_OS)/$(BASENAME).xg $(TOIL_OS)/$(BA

$(TOIL_OS)/$(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
vg paths --gbwt $(TOIL_OS)/$(BASENAME).gbwt --extract-vg -x $(TOIL_OS)/$(BASENAME).xg -Q _thread_$(SAMP)_x_$(HAPLO_1) >> $(TOIL_OS)/$(BASENAME)_$(HAPLO_1)_thread.merge.vg
vg paths --gbwt $(TOIL_OS)/$(BASENAME).gbwt --retain-paths -x $(TOIL_OS)/$(BASENAME).xg -Q _thread_$(SAMP)_x_$(HAPLO_1) >> $(TOIL_OS)/$(BASENAME)_$(HAPLO_1)_thread.merge.vg

$(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_1).vg: $(TOIL_OS)/$(BASENAME)_$(HAPLO_1)_thread.merge.vg
vg mod -N $(TOIL_OS)/$(BASENAME)_$(HAPLO_1)_thread.merge.vg > $(TOIL_OS)/$(BASENAME)_thread_$(SAMP)_$(HAPLO_1).vg
Expand Down
17 changes: 2 additions & 15 deletions src/subcommand/paths_main.cpp
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Expand Up @@ -41,7 +41,6 @@ void help_paths(char** argv) {
<< " (graph also required for most output options;" << endl
<< " -g takes priority over -x)" << endl
<< "output graph (.vg format):" << endl
<< " -V, --extract-vg output a path-only graph covering the selected paths" << endl
<< " -d, --drop-paths output a graph with the selected paths removed" << endl
<< " -r, --retain-paths output a graph with only the selected paths retained" << endl
<< " -n, --normalize-paths output a graph where equivalent paths in a site are" << endl
Expand Down Expand Up @@ -124,7 +123,6 @@ int main_paths(int argc, char** argv) {

bool extract_as_gam = false;
bool extract_as_gaf = false;
bool extract_as_vg = false;
bool list_names = false;
bool extract_as_fasta = false;
bool drop_paths = false;
Expand Down Expand Up @@ -228,8 +226,7 @@ int main_paths(int argc, char** argv) {
break;

case 'V':
extract_as_vg = true;
output_formats++;
logger.error() << "-V/--extract-vg has been removed" << endl;
break;

case 'd':
Expand Down Expand Up @@ -399,7 +396,7 @@ int main_paths(int argc, char** argv) {
logger.error() << "at least one input format (-x, -g) must be specified" << std::endl;
}
if (!gbwt_file.empty()) {
bool need_graph = (extract_as_gam || extract_as_gaf || extract_as_vg || drop_paths
bool need_graph = (extract_as_gam || extract_as_gaf || drop_paths
|| retain_paths || extract_as_fasta || list_lengths);
if (need_graph && graph_file.empty()) {
logger.error() << "a graph is needed for extracting threads in "
Expand Down Expand Up @@ -556,15 +553,10 @@ int main_paths(int argc, char** argv) {
// We may need to emit a stream of Alignments
unique_ptr<vg::io::AlignmentEmitter> aln_emitter;

// Or we might need to emit a stream of VG Graph objects
unique_ptr<vg::io::ProtobufEmitter<Graph>> graph_emitter;
if (extract_as_gam || extract_as_gaf) {
// Open up a GAM/GAF output stream
aln_emitter = vg::io::get_non_hts_alignment_emitter("-", extract_as_gaf ? "GAF" : "GAM", {}, get_thread_count(),
graph);
} else if (extract_as_vg) {
// Open up a VG Graph chunk output stream
graph_emitter = unique_ptr<vg::io::ProtobufEmitter<Graph>>(new vg::io::ProtobufEmitter<Graph>(cout));
}

if (gbwt_index) {
Expand Down Expand Up @@ -646,9 +638,6 @@ int main_paths(int argc, char** argv) {
if (extract_as_gam || extract_as_gaf) {
// Write as an Alignment. Must contain the whole path.
aln_emitter->emit_singles({alignment_from_path(*graph, path)});
} else if (extract_as_vg) {
// Write as a Path in a VG
chunk_to_emitter(path, *graph_emitter);
} else if (extract_as_fasta) {
write_fasta_sequence(name, path_sequence(*graph, path), cout);
}
Expand Down Expand Up @@ -966,8 +955,6 @@ int main_paths(int argc, char** argv) {
Path path = path_from_path_handle(*graph, path_handle);
if (extract_as_gam || extract_as_gaf) {
aln_emitter->emit_singles({alignment_from_path(*graph, path)});
} else if (extract_as_vg) {
chunk_to_emitter(path, *graph_emitter);
} else if (extract_as_fasta) {
write_fasta_sequence(graph->get_path_name(path_handle), path_sequence(*graph, path), cout);
}
Expand Down
2 changes: 1 addition & 1 deletion vgci/vgci.sh
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Expand Up @@ -32,7 +32,7 @@ KEEP_INTERMEDIATE_FILES=0
# Should we show stdout and stderr from tests? If so, set to "-s".
SHOW_OPT=""
# What toil-vg should we install?
TOIL_VG_PACKAGE="git+https://github.com/vgteam/toil-vg.git@a56a860ad31583ce4b1616c9fa2bfb4bfe06d635"
TOIL_VG_PACKAGE="git+https://github.com/vgteam/toil-vg.git@6fffa1128cdeaefb92d41db47de9a6565dd478d8"
# What toil should we install?
# Could be something like "toil[aws,mesos]==3.20.0"
# or "toil[wdl,aws,mesos]@git+https://github.com/DataBiosphere/toil.git@52aa2979f23c24001837b2808552973e7bb263e6"
Expand Down
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