Merge pull request #4079 from vgteam/no-translation

Convert GBWTGraph to GFA without using translation
vgteam · Sep 8, 2023 · 01ecaa3 · 01ecaa3
2 parents bcd5712 + 699a1de
commit 01ecaa3
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Showing 3 changed files with 36 additions and 9 deletions.
diff --git a/deps/gbwtgraph b/deps/gbwtgraph
diff --git a/src/subcommand/convert_main.cpp b/src/subcommand/convert_main.cpp
@@ -64,7 +64,10 @@ int main_convert(int argc, char** argv) {
     bool rgfa_pline = false;
     bool wline = true;
     algorithm_type gfa_output_algorithm = ALGORITHM_DEFAULT;
-    int num_threads = omp_get_max_threads(); // For GBWTGraph to GFA.
+
+    // For GBWTGraph to GFA.
+    int num_threads = omp_get_max_threads();
+    bool use_translation = true;
 
     if (argc == 2) {
         help_convert(argv);
@@ -74,6 +77,7 @@ int main_convert(int argc, char** argv) {
     constexpr int OPT_REF_SAMPLE = 1000;
     constexpr int OPT_GBWTGRAPH_ALGORITHM = 1001;
     constexpr int OPT_VG_ALGORITHM = 1002;
+    constexpr int OPT_NO_TRANSLATION = 1003;
 
     int c;
     optind = 2; // force optind past command positional argument
@@ -98,6 +102,7 @@ int main_convert(int argc, char** argv) {
             {"no-wline", no_argument, 0, 'W'},
             {"gbwtgraph-algorithm", no_argument, 0, OPT_GBWTGRAPH_ALGORITHM},
             {"vg-algorithm", no_argument, 0, OPT_VG_ALGORITHM},
+            {"no-translation", no_argument, 0, OPT_NO_TRANSLATION},
             {"gam-to-gaf", required_argument, 0, 'G'},
             {"gaf-to-gam", required_argument, 0, 'F'},
             {"threads", required_argument, 0, 't'},
@@ -173,6 +178,9 @@ int main_convert(int argc, char** argv) {
         case OPT_VG_ALGORITHM:
             gfa_output_algorithm = algorithm_vg;
             break;
+        case OPT_NO_TRANSLATION:
+            use_translation = false;
+            break;
         case 'G':
             no_multiple_inputs(input);
             input = input_gam;
@@ -411,6 +419,7 @@ int main_convert(int argc, char** argv) {
 
             gbwtgraph::GFAExtractionParameters parameters;
             parameters.num_threads = num_threads;
+            parameters.use_translation = use_translation;
             gbwtgraph::gbwt_to_gfa(*gbwt_graph, std::cout, parameters);
         } else if (gfa_output_algorithm == algorithm_vg) {
             // Use HandleGraph GFA conversion code
@@ -468,14 +477,22 @@ void help_convert(char** argv) {
          << "    -p, --packed-out       output in PackedGraph format [default]" << endl
          << "    -x, --xg-out           output in XG format" << endl
          << "    -f, --gfa-out          output in GFA format" << endl
-         << "    -H, --drop-haplotypes  do not include haplotype paths in the output (useful with GBWTGraph / GBZ inputs)" << endl
+         << "    -H, --drop-haplotypes  do not include haplotype paths in the output" << endl
+         << "                           (useful with GBWTGraph / GBZ inputs)" << endl
          << "gfa output options (use with -f):" << endl
-         << "    -P, --rgfa-path STR    write given path as rGFA tags instead of lines (multiple allowed, only rank-0 supported)" << endl
-         << "    -Q, --rgfa-prefix STR  write paths with given prefix as rGFA tags instead of lines (multiple allowed, only rank-0 supported)" << endl
+         << "    -P, --rgfa-path STR    write given path as rGFA tags instead of lines" << endl
+         << "                           (multiple allowed, only rank-0 supported)" << endl
+         << "    -Q, --rgfa-prefix STR  write paths with given prefix as rGFA tags instead of lines" << endl
+         << "                           (multiple allowed, only rank-0 supported)" << endl
          << "    -B, --rgfa-pline       paths written as rGFA tags also written as lines" << endl
-         << "    -W, --no-wline         write all paths as GFA P-lines instead of W-lines. Allows handling multiple phase blocks and subranges used together." << endl
-         << "    --gbwtgraph-algorithm  Always use the GBWTGraph library GFA algorithm. Not compatible with other GBWT output options or non-GBWT graphs." << endl
-         << "    --vg-algorithm         Always use the VG GFA algorithm. Works with all options and graph types, but can't preserve original GFA coordinates." << endl
+         << "    -W, --no-wline         Write all paths as GFA P-lines instead of W-lines." << endl
+         << "                           Allows handling multiple phase blocks and subranges used together." << endl
+         << "    --gbwtgraph-algorithm  Always use the GBWTGraph library GFA algorithm." << endl
+         << "                           Not compatible with other GFA output options or non-GBWT graphs." << endl
+         << "    --vg-algorithm         Always use the VG GFA algorithm. Works with all options and graph types," << endl
+         << "                           but can't preserve original GFA coordinates." << endl
+         << "    --no-translation       When using the GBWTGraph algorith, convert the graph directly to GFA." << endl
+         << "                           Do not use the translation to preserve original coordinates." << endl
          << "alignment options:" << endl
          << "    -G, --gam-to-gaf FILE  convert GAM FILE to GAF" << endl
          << "    -F, --gaf-to-gam FILE  convert GAF FILE to GAM" << endl

diff --git a/test/t/48_vg_convert.t b/test/t/48_vg_convert.t
@@ -7,7 +7,7 @@ PATH=../bin:$PATH # for vg
 
 export LC_ALL="C" # force a consistent sort order
 
-plan tests 102
+plan tests 106
 
 vg construct -r complex/c.fa -v complex/c.vcf.gz > c.vg
 cat <(vg view c.vg | grep ^S | sort) <(vg view c.vg | grep L | uniq | wc -l) <(vg paths -v c.vg -E) > c.info
@@ -361,13 +361,23 @@ vg convert -f components.gbz | sort > sorted.gfa
 cmp sorted.gfa correct.gfa
 is $? 0 "GBZ to GFA conversion works with multiple threads"
 
+# GFA extraction from GBZ with/without translation.
+vg gbwt --gbz-format -g chopping.gbz --max-node 2 -G graphs/chopping_walks.gfa
+vg convert -f -t 1 chopping.gbz > with-translation.gfa
+is $? 0 "GBZ to GFA with translation"
+is "$(grep -c "^S" with-translation.gfa)" "8" "8 segments"
+vg convert -f -t 1 --no-translation chopping.gbz > no-translation.gfa
+is $? 0 "GBZ to GFA without translation"
+is "$(grep -c "^S" no-translation.gfa)" "9" "9 segments"
+
 rm -f components.gbwt components.gg components.gbz
 rm -f direct.hg correct_paths.gaf correct_haplotypes.gaf
 rm -f components.hg hg_paths.gaf hg_haplotypes.gaf gbz_hg_paths.gaf gbz_hg_haplotypes.gaf
 rm -f components.xg xg_paths.gaf xg_haplotypes.gaf gbz_xg_paths.gaf gbz_xg_haplotypes.gaf
 rm -f no_haplotypes.xg no_haplotypes.hg
 rm -f extracted.gfa gbz.gfa extracted.hg
 rm -f sorted.gfa correct.gfa
+rm -f chopping.gbz with-translation.gfa no-translation.gfa
 
 #####
 # Reference path conversion
+3 −0		include/gbwtgraph/gfa.h
+4 −0		src/algorithms.cpp
+5 −4		src/gfa.cpp
+11 −1		src/gfa2gbwt.cpp
+21 −0		tests/gfas/example_chopped.gfa
+19 −0		tests/gfas/example_from_chopping.gfa