[misc] deactivate BIFM by default

Author: h-2

.github/workflows/ci_linux.yml

@@ -21,6 +21,13 @@ jobs:
       fail-fast: false
       matrix:
         include:
+          - name: "gcc12 bifm"
+            install: "g++-12"
+            cxx: "g++-12"
+            cmake_flags: "-DLAMBDA_WITH_BIFM=1"
+            cc: "gcc-12"
+            build_type: Release
+
           - name: "gcc12"
             install: "g++-12"
             cxx: "g++-12"
@@ -94,7 +101,7 @@ jobs:
         run: |
           mkdir build
           cd build
-          cmake ../lambda -DLAMBDA_COMPILE_THREADS=2 -DLAMBDA_NATIVE_BUILD=OFF -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }}" -DCMAKE_CXX_COMPILER_LAUNCHER=ccache -DCMAKE_C_COMPILER_LAUNCHER=ccache
+          cmake ../lambda -DLAMBDA_COMPILE_THREADS=2 -DLAMBDA_NATIVE_BUILD=OFF ${{ matrix.cmake_flags }} -DCMAKE_CXX_COMPILER_LAUNCHER=ccache -DCMAKE_C_COMPILER_LAUNCHER=ccache
 
       - name: Build tests
         if: matrix.name != 'clang_format'

CMakeLists.txt

@@ -22,6 +22,16 @@ if (NOT CMAKE_BUILD_TYPE)
          FORCE)
 endif ()
 
+# ----------------------------------------------------------------------------
+# Options
+# ----------------------------------------------------------------------------
+
+option (LAMBDA_WITH_BIFM "Include codepaths for bidirectional indexes." OFF)
+
+if (LAMBDA_WITH_BIFM)
+    add_definitions (-DLAMBDA_WITH_BIFM=1)
+endif ()
+
 # ----------------------------------------------------------------------------
 # Begin of dependency detection
 # ----------------------------------------------------------------------------

src/CMakeLists.txt

@@ -30,6 +30,7 @@ message ("\n${ColourBold}Build configuration${ColourReset}")
 message (STATUS "LAMBDA version is: ${SEQAN_APP_VERSION}")
 
 option (LAMBDA_STATIC_BUILD "Include all libraries in the binaries." OFF)
+option (LAMBDA_WITH_BIFM "Include codepaths for bidirectional indexes." OFF)
 
 if (LAMBDA_STATIC_BUILD)
     add_definitions (-DLAMBDA_STATIC_BUILD=1)
@@ -47,9 +48,13 @@ if (LAMBDA_STATIC_BUILD)
     endif (CMAKE_SYSTEM_NAME MATCHES "Linux")
 endif (LAMBDA_STATIC_BUILD)
 
+if (LAMBDA_WITH_BIFM)
+    add_definitions (-DLAMBDA_WITH_BIFM=1)
+endif ()
 
 message(STATUS "The following options are selected for the build:")
 message(   "     LAMBDA_STATIC_BUILD             ${LAMBDA_STATIC_BUILD}")
+message(   "     LAMBDA_WITH_BIFM                ${LAMBDA_WITH_BIFM}")
 message(STATUS "Run 'cmake -LH' to get a comment on each option.")
 message(STATUS "Remove CMakeCache.txt and re-run cmake with -DOPTIONNAME=ON|OFF to change an option.")
 

src/mkindex.cpp

@@ -103,7 +103,12 @@ void argConv0(LambdaIndexerOptions & options)
         case DbIndexType::FM_INDEX:
             return argConv1<DbIndexType::FM_INDEX>(options);
         case DbIndexType::BI_FM_INDEX:
+#if LAMBDA_WITH_BIFM
             return argConv1<DbIndexType::BI_FM_INDEX>(options);
+#else
+            throw std::runtime_error{
+              "To create bidirectional indexes, you need to rebuild lambda with LAMBDA_WITH_BIFM=1 ."};
+#endif
         default:
             throw 42;
     }

src/search.cpp

@@ -248,7 +248,12 @@ void argConv0(LambdaOptions & options)
         case DbIndexType::FM_INDEX:
             return argConv1<DbIndexType::FM_INDEX>(options);
         case DbIndexType::BI_FM_INDEX:
+#if LAMBDA_WITH_BIFM
             return argConv1<DbIndexType::BI_FM_INDEX>(options);
+#else
+            throw std::runtime_error{
+              "To open bidirectional indexes, you need to rebuild lambda with LAMBDA_WITH_BIFM=1 ."};
+#endif
         default:
             throw 52;
     }

src/shared_definitions.hpp

@@ -51,6 +51,10 @@
 #include "view_duplicate.hpp"
 #include "view_reduce_to_bisulfite.hpp"
 
+#ifndef LAMBDA_WITH_BIFM
+#    define LAMBDA_WITH_BIFM 0
+#endif
+
 // ==========================================================================
 //  DbIndexType
 // ==========================================================================

test/cli/index_test.cpp

@@ -135,44 +135,48 @@ TEST_F(index_test, nucl_fm)
     run_index_test("mkindexn", "db_nucl.fasta.gz", "db_nucl_fm_test.fasta.gz.lba", "fm", "", "db_nucl_fm.fasta.gz.lba");
 }
 
-TEST_F(index_test, nucl_bifm)
-{
-    run_index_test("mkindexn", "db_nucl.fasta.gz", "db_nucl_bifm_test.fasta.gz.lba", "bifm", "",
-                   "db_nucl_bifm.fasta.gz.lba");
-}
-
 TEST_F(index_test, nucl_bs_fm)
 {
     run_index_test("mkindexbs", "db_nucl_bs.fasta.gz", "db_nucl_bs_fm_test.fasta.gz.lba", "fm", "",
                    "db_nucl_bs_fm.fasta.gz.lba");
 }
 
-TEST_F(index_test, nucl_bs_bifm)
-{
-    run_index_test("mkindexbs", "db_nucl_bs.fasta.gz", "db_nucl_bs_bifm_test.fasta.gz.lba", "bifm", "",
-                   "db_nucl_bs_bifm.fasta.gz.lba");
-}
-
 TEST_F(index_test, prot_fm)
 {
     run_index_test("mkindexp", "db_prot.fasta.gz", "db_prot_fm_test.fasta.gz.lba", "fm", "li10",
                    "db_prot_fm.fasta.gz.lba");
 }
 
-TEST_F(index_test, prot_bifm)
-{
-    run_index_test("mkindexp", "db_prot.fasta.gz", "db_prot_bifm_test.fasta.gz.lba", "bifm", "li10",
-                   "db_prot_bifm.fasta.gz.lba");
-}
-
 TEST_F(index_test, trans_fm)
 {
     run_index_test("mkindexp", "db_nucl.fasta.gz", "db_trans_fm_test.fasta.gz.lba", "fm", "li10",
                    "db_trans_fm.fasta.gz.lba");
 }
 
+#if LAMBDA_WITH_BIFM
+
+TEST_F(index_test, nucl_bifm)
+{
+    run_index_test("mkindexn", "db_nucl.fasta.gz", "db_nucl_bifm_test.fasta.gz.lba", "bifm", "",
+                   "db_nucl_bifm.fasta.gz.lba");
+}
+
+TEST_F(index_test, nucl_bs_bifm)
+{
+    run_index_test("mkindexbs", "db_nucl_bs.fasta.gz", "db_nucl_bs_bifm_test.fasta.gz.lba", "bifm", "",
+                   "db_nucl_bs_bifm.fasta.gz.lba");
+}
+
+TEST_F(index_test, prot_bifm)
+{
+    run_index_test("mkindexp", "db_prot.fasta.gz", "db_prot_bifm_test.fasta.gz.lba", "bifm", "li10",
+                   "db_prot_bifm.fasta.gz.lba");
+}
+
 TEST_F(index_test, trans_bifm)
 {
     run_index_test("mkindexp", "db_nucl.fasta.gz", "db_trans_bifm_test.fasta.gz.lba", "bifm", "li10",
                    "db_trans_bifm.fasta.gz.lba");
 }
+
+#endif

test/cli/search_test.cpp

@@ -395,6 +395,8 @@ TEST_F(search_test, tblastx_fm_bam)
 
 // Search with bi-directional index
 
+#if LAMBDA_WITH_BIFM
+
 // TEST_F(search_test, blastn_bifm_m8)
 // {
 //     run_search_test("mkindexn", "db_nucl.fasta.gz", "db_nucl_bifm.fasta.gz.lba", "bifm", "", "searchn",
@@ -467,6 +469,8 @@ TEST_F(search_test, tblastx_bifm_sam)
                     "queries_nucl.fasta.gz", "none", "output_tblastx_bifm_test.sam", "sam", "output_tblastx_fm.sam");
 }
 
+#endif
+
 // Fast mode
 
 TEST_F(search_test, blastn_fm_fast_m8)