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Make vg inject use AlignmentEmitter and support GAF #4319

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merged 1 commit into from
Jul 1, 2024
Merged

Make vg inject use AlignmentEmitter and support GAF #4319

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36 changes: 27 additions & 9 deletions src/subcommand/inject_main.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@
#include "../alignment.hpp"
#include "../vg.hpp"
#include "../xg.hpp"
#include "../hts_alignment_emitter.hpp"
#include <vg/io/stream.hpp>
#include <vg/io/vpkg.hpp>
#include <bdsg/overlays/overlay_helper.hpp>
Expand All @@ -23,10 +24,11 @@ using namespace vg;
using namespace vg::subcommand;

void help_inject(char** argv) {
cerr << "usage: " << argv[0] << " inject [options] input.[bam|sam|cram] >output.gam" << endl
cerr << "usage: " << argv[0] << " inject -x graph.xg [options] input.[bam|sam|cram] >output.gam" << endl
<< endl
<< "options:" << endl
<< " -x, --xg-name FILE use this graph or xg index (required, non-XG formats also accepted)" << endl
<< " -o, --output-format NAME output the alignments in NAME format (gam / gaf / json) [gam]" << endl
<< " -t, --threads N number of threads to use" << endl;
}

Expand All @@ -37,6 +39,8 @@ int main_inject(int argc, char** argv) {
}

string xg_name;
string output_format = "GAM";
std::set<std::string> output_formats = { "GAM", "GAF", "JSON" };
int threads = get_thread_count();

int c;
Expand All @@ -46,12 +50,13 @@ int main_inject(int argc, char** argv) {
{
{"help", no_argument, 0, 'h'},
{"xg-name", required_argument, 0, 'x'},
{"output-format", required_argument, 0, 'o'},
{"threads", required_argument, 0, 't'},
{0, 0, 0, 0}
};

int option_index = 0;
c = getopt_long (argc, argv, "hx:t:",
c = getopt_long (argc, argv, "hx:o:t:",
long_options, &option_index);

// Detect the end of the options.
Expand All @@ -63,6 +68,19 @@ int main_inject(int argc, char** argv) {
case 'x':
xg_name = optarg;
break;

case 'o':
{
output_format = optarg;
for (char& c : output_format) {
c = std::toupper(c);
}
if (output_formats.find(output_format) == output_formats.end()) {
std::cerr << "error: [vg inject] Invalid output format: " << optarg << std::endl;
std::exit(1);
}
}
break;

case 't':
threads = parse<int>(optarg);
Expand Down Expand Up @@ -90,14 +108,14 @@ int main_inject(int argc, char** argv) {
}
unique_ptr<PathHandleGraph> path_handle_graph = vg::io::VPKG::load_one<PathHandleGraph>(xg_name);
bdsg::PathPositionOverlayHelper overlay_helper;
PathPositionHandleGraph* xgidx = overlay_helper.apply(path_handle_graph.get());
PathPositionHandleGraph* xgidx = overlay_helper.apply(path_handle_graph.get());

vg::io::ProtobufEmitter<Alignment> buf(cout);
function<void(Alignment&)> lambda = [&buf](Alignment& aln) {
#pragma omp critical (buf)
{
buf.write(std::move(aln));
}
// We don't do HTS output formats but we do need an empty paths collection to make an alignment emitter
vector<tuple<path_handle_t, size_t, size_t>> paths;
unique_ptr<vg::io::AlignmentEmitter> alignment_emitter = get_alignment_emitter("-", output_format, paths, threads, xgidx);

function<void(Alignment&)> lambda = [&](Alignment& aln) {
alignment_emitter->emit_mapped_single({std::move(aln)});
};
if (threads > 1) {
hts_for_each_parallel(file_name, lambda, xgidx);
Expand Down
4 changes: 3 additions & 1 deletion test/t/39_vg_inject.t
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Expand Up @@ -6,7 +6,7 @@ BASH_TAP_ROOT=../deps/bash-tap
PATH=../bin:$PATH # for vg


plan tests 12
plan tests 13

vg construct -r small/x.fa > j.vg
vg index -x j.xg j.vg
Expand Down Expand Up @@ -52,5 +52,7 @@ cat <(samtools view -H small/x.bam) <(printf "name\t4\t*\t0\t0\t*\t*\t0\t0\tACGT
is "$(vg inject -x x.xg unmapped.sam | vg view -aj - | grep "path" | wc -l)" 0 "vg inject does not make an alignment for an umapped read"
is "$(echo $?)" 0 "vg inject does not crash on an unmapped read"

is $(vg inject -x x.xg small/x.bam -o GAF | wc -l) \
1000 "vg inject supports GAF output"

rm j.vg j.xg x.vg x.gcsa x.gcsa.lcp x.xg unmapped.sam
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