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Option to mark a GBZ as a subgraph of another #4897

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Merged
jltsiren merged 2 commits into from
May 7, 2026
+43 −8
Merged

Option to mark a GBZ as a subgraph of another #4897

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7a86737
Mark a graph as a subgraph of another
jltsiren May 6, 2026
39fdeb3
Merge branch 'master' of https://github.com/vgteam/vg
jltsiren May 6, 2026
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2 changes: 1 addition & 1 deletion deps/gbwtgraph
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Submodule gbwtgraph updated 5 files
+3 −0 include/gbwtgraph/gbz.h
+102 −0 include/gbwtgraph/minimizer.h
+19 −0 src/gbz.cpp
+6 −2 src/index.cpp
+12 −0 tests/test_gbz.cpp
35 changes: 31 additions & 4 deletions src/subcommand/gbwt_main.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -55,6 +55,7 @@ struct GBWTConfig {

// GBZ construction.
bool set_pggname = false;
std::string supergraph_filename;
bool unset_pggname = false;
bool gbz_v1 = false;

Expand Down Expand Up @@ -307,6 +308,7 @@ void help_gbwt(char** argv) {
std::cerr << " --translation FILE write the segment to node translation table to FILE" << std::endl;
std::cerr << " -Z, --gbz-input use GBZ as input GBWT and input graph (one input arg)" << std::endl;
std::cerr << " --set-pggname compute the pggname for the GBZ if not already present" << std::endl;
std::cerr << " --subgraph-of FILE mark the GBZ as a subgraph of the other GBZ in FILE" << std::endl;
std::cerr << " --unset-pggname clear the stored pggname for the GBZ if present" << std::endl;
std::cerr << " -E, --index-paths index the embedded non-alt paths in the graph" << std::endl;
std::cerr << " (requires -x, no input args)" << std::endl;
Expand Down Expand Up @@ -443,8 +445,9 @@ GBWTConfig parse_gbwt_config(int argc, char** argv) {
constexpr int OPT_PATH_FIELDS = 1116;
constexpr int OPT_TRANSLATION = 1117;
constexpr int OPT_SET_PGGNAME = 1118;
constexpr int OPT_UNSET_PGGNAME = 1119;
constexpr int OPT_GAM_FORMAT = 1120;
constexpr int OPT_SUBGRAPH_OF = 1119;
constexpr int OPT_UNSET_PGGNAME = 1120;
constexpr int OPT_GAM_FORMAT = 1121;
constexpr int OPT_CHUNK_SIZE = 1200;
constexpr int OPT_POS_BUFFER = 1201;
constexpr int OPT_THREAD_BUFFER = 1202;
Expand Down Expand Up @@ -512,6 +515,7 @@ GBWTConfig parse_gbwt_config(int argc, char** argv) {
// Input GBWT construction: GBZ
{ "gbz-input", no_argument, 0, 'Z' },
{ "set-pggname", no_argument, 0, OPT_SET_PGGNAME },
{ "subgraph-of", required_argument, 0, OPT_SUBGRAPH_OF },
{ "unset-pggname", no_argument, 0, OPT_UNSET_PGGNAME },

// Input GBWT construction: paths
Expand Down Expand Up @@ -724,6 +728,9 @@ GBWTConfig parse_gbwt_config(int argc, char** argv) {
case OPT_SET_PGGNAME:
config.set_pggname = true;
break;
case OPT_SUBGRAPH_OF:
config.supergraph_filename = require_exists(config.logger, optarg);
break;
case OPT_UNSET_PGGNAME:
config.unset_pggname = true;
break;
Expand Down Expand Up @@ -951,7 +958,7 @@ GBWTConfig parse_gbwt_config(int argc, char** argv) {
//----------------------------------------------------------------------------

void validate_gbwt_config(GBWTConfig& config) {
// We can either write GBWT in SDSL format to a separate file or as part of a GBZ graph.
// We can either write GBWT to a separate file or as part of a GBZ graph.
// However, `--parse-only` uses `gbwt_output` for other purposes.
bool has_gbwt_output =
(!config.gbwt_output.empty() || (!config.graph_output.empty() && !config.parse_only));
Expand Down Expand Up @@ -1351,7 +1358,7 @@ void step_1_build_gbwts(GBWTHandler& gbwts, GraphHandler& graphs, GBWTConfig& co
config.logger.info() << "Input type: GBZ" << std::endl;
}
graphs.load_gbz(gbwts, config);
if (config.set_pggname) {
if (config.set_pggname || !config.supergraph_filename.empty()) {
std::string pggname = graphs.gbz_graph->pggname();
if (pggname.empty()) {
if (config.show_progress) {
Expand All @@ -1363,6 +1370,26 @@ void step_1_build_gbwts(GBWTHandler& gbwts, GraphHandler& graphs, GBWTConfig& co
if (config.show_progress) {
config.logger.info() << "Graph name: " << pggname << std::endl;
}
if (!config.supergraph_filename.empty()) {
gbwtgraph::GraphName supergraph;
try {
gbwt::Tags tags = gbwtgraph::GBZ::simple_sds_load_tags(config.supergraph_filename);
supergraph = gbwtgraph::GraphName(tags);
} catch (const std::runtime_error& e) {
config.logger.error() << "Failed to load supergraph tags from " << config.supergraph_filename << ": " << e.what() << std::endl;
}
if (supergraph.name().empty()) {
config.logger.warn() << "Supergraph " << config.supergraph_filename << " does not have a pggname" << std::endl;
} else {
if (config.show_progress) {
config.logger.info() << "Supergraph name: " << supergraph.name() << std::endl;
}
gbwtgraph::GraphName subgraph = graphs.gbz_graph->graph_name();
subgraph.add_subgraph(subgraph.name(), supergraph.name());
subgraph.add_relationships(supergraph);
subgraph.set_tags(graphs.gbz_graph->tags);
}
}
}
if (config.unset_pggname) {
gbwtgraph::GraphName empty;
Expand Down
14 changes: 11 additions & 3 deletions test/t/37_vg_gbwt.t
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ BASH_TAP_ROOT=../deps/bash-tap

PATH=../bin:$PATH # for vg

plan tests 164
plan tests 168


# Build vg graphs for two chromosomes
Expand Down Expand Up @@ -240,6 +240,16 @@ vg gbwt --set-pggname -Z x.gbz -g x.gbz
is $? 0 "Graph name can be set"
is "$(vg describe x.gbz | grep -c 'pggname =')" 1 "GBZ contains graph name after setting"

# Set graph name and a subgraph relationship
vg gbwt -g supergraph.gbz -G graphs/components_walks.gfa
is $? 0 "GBZ construction for supergraph"
vg chunk --gbz --contig A -x supergraph.gbz
is $? 0 "Graph component extraction"
vg gbwt --subgraph-of supergraph.gbz -g subgraph.gbz -Z chunk_0_component_0.gbz
is $? 0 "Subgraph relationship can be set"
is "$(vg describe subgraph.gbz | grep -c 'subgraph =')" 1 "GBZ contains subgraph relationship"
rm -f supergraph.gbz chunk_0_component_0.gbz subgraph.gbz

# Build and serialize GBZ from VCF
vg gbwt -x x.vg -g x2.gbz -v small/xy2.vcf.gz
is $? 0 "GBZ construction from VCF"
Expand Down Expand Up @@ -430,5 +440,3 @@ vg gbwt -g gfa.gbz -G graphs/gfa_two_part_reference.gfa
is "$(vg paths -M --reference-paths -x gfa.gbz | grep -v "^#" | cut -f4 | grep NO_HAPLOTYPE | wc -l)" "2" "GBZ can represent reference paths without haplotype numbers"

rm -f gfa.gbz


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