Description: Do not build the canonical_gfa tool
 It requires handlegraph/algorithms/canonical_gfa.hpp, which was added to
 libhandlegraph after the 2024-11-22 snapshot packaged in Debian.
Author: Andreas Tille <tille@debian.org>
Last-Update: 2026-10-25

diff --git a/Makefile b/Makefile
index cbe568e..761d6aa 100644
--- a/Makefile
+++ b/Makefile
@@ -58,7 +58,7 @@ LIBRARY=$(BUILD_LIB)/libgbwtgraph.a
 LIBRARY_SONAME=libgbwtgraph.so.1
 LIBRARY_SHARED=$(BUILD_LIB)/libgbwtgraph.so.1.5
 
-PROGRAMS=$(addprefix $(BUILD_BIN)/,canonical_gfa chunk_gbz gfa2gbwt gbz_extract gbz_find gbz_stats kmer_freq subgraph_query)
+PROGRAMS=$(addprefix $(BUILD_BIN)/,chunk_gbz gfa2gbwt gbz_extract gbz_find gbz_stats kmer_freq subgraph_query)
 OBSOLETE=gfa2gbwt
 
 .PHONY: all clean directories test
diff --git a/tests/test_gfa.cpp b/tests/test_gfa.cpp
index 308fede..591739d 100644
--- a/tests/test_gfa.cpp
+++ b/tests/test_gfa.cpp
@@ -4,8 +4,6 @@
 #include <gbwtgraph/gfa.h>
 #include <gbwtgraph/internal.h>
 
-#include <handlegraph/algorithms/canonical_gfa.hpp>
-
 #include <sstream>
 
 #include "shared.h"
@@ -762,27 +760,6 @@ TEST_F(GFAExtraction, Translation)
   }
 }
 
-TEST_F(GFAExtraction, CanonicalGFA)
-{
-  std::vector<std::string> inputs = { "gfas/components_walks.gfa", "gfas/example_walks.gfa", "gfas/example_chopping.gfa" };
-
-  for(const std::string& input : inputs)
-  {
-    auto gfa_parse = gfa_to_gbwt(input);
-    GBZ gbz(gfa_parse.first, gfa_parse.second);
-
-    std::stringstream truth_stream;
-    handlegraph::algorithms::canonical_gfa(gbz.graph, truth_stream, true);
-    std::string truth = truth_stream.str();
-
-    std::stringstream output_stream;
-    gbwt_to_canonical_gfa(gbz.graph, output_stream);
-    std::string output = output_stream.str();
-
-    ASSERT_EQ(output, truth) << "Canonical GFA mismatch for " << input;
-  }
-}
-
 //------------------------------------------------------------------------------
 
 class GBWTMetadata : public ::testing::Test
