Merge pull request #91 from pjotrp/main

Minor fixes for testing with vcflib

.gitignore

@@ -1,6 +1,7 @@
 lib/
 bin/
 build/
+Testing/
 
 # Prerequisites
 *.d
@@ -39,5 +40,5 @@ build/
 tests/wfa.utest.log.correct
 tests/wfa.utest.log.mem
 tests/wfa.utest.log.time
-
+tests/*.alg
 

CMakeLists.txt

@@ -1,9 +1,9 @@
 # For Debian currently with
 #
 #   cd build
-#   cmake -DCMAKE_BUILD_TYPE=RelWithDebInfo ..
-#   make
-#   make test
+#   cmake -DCMAKE_BUILD_TYPE=RelWithDebInfo -DOPENMP=1 ..
+#   cmake --build .
+#   ctest .
 #   make install
 # See below option statements and the README for build information
 
@@ -192,16 +192,58 @@ set(wfa2lib_LIBS
 # add_dependencies(wfa2lib ${wfa2lib_DEPS})
 
 # ---- Build all
+# add_subdirectory(tools/align_benchmark)
+
+
+add_executable(align_benchmark
+  tools/align_benchmark/align_benchmark_params.c
+  tools/align_benchmark/align_benchmark.c
+  tools/align_benchmark/benchmark/benchmark_check.c
+  tools/align_benchmark/benchmark/benchmark_edit.c
+  tools/align_benchmark/benchmark/benchmark_gap_affine2p.c
+  tools/align_benchmark/benchmark/benchmark_gap_affine.c
+  tools/align_benchmark/benchmark/benchmark_gap_linear.c
+  tools/align_benchmark/benchmark/benchmark_indel.c
+  tools/align_benchmark/benchmark/benchmark_utils.c
+  system/mm_allocator.c
+  system/mm_stack.c
+  system/profiler_counter.c
+  system/profiler_timer.c
+  utils/bitmap.c
+  utils/commons.c
+  utils/dna_text.c
+  utils/heatmap.c
+  utils/sequence_buffer.c
+  utils/vector.c
+  alignment/affine2p_penalties.c
+  alignment/affine_penalties.c
+  alignment/cigar.c
+  alignment/score_matrix.c
+  tools/align_benchmark/gap_affine/affine_matrix.c
+  tools/align_benchmark/gap_affine/swg.c
+  tools/align_benchmark/gap_linear/nw.c
+  tools/align_benchmark/gap_affine2p/affine2p_dp.c
+  tools/align_benchmark/gap_affine2p/affine2p_matrix.c
+  tools/align_benchmark/edit/edit_bpm.c
+  tools/align_benchmark/edit/edit_dp.c
+  tools/align_benchmark/indel/indel_dp.c
+)
+target_include_directories(align_benchmark PUBLIC . wavefront system utils tools/align_benchmark)
+add_dependencies(align_benchmark wfa2)
+target_link_libraries(align_benchmark m)
+target_link_libraries(align_benchmark wfa2)
+if(OPENMP)
+  target_link_libraries(align_benchmark OpenMP::OpenMP_C)
+endif(OPENMP)
 
 # ---- Test
 
 enable_testing()
 
-
 function(add_wfa_test)
   add_test(
     NAME wfa2lib
-    COMMAND ./tests/wfa.utest.sh
+    COMMAND ./tests/wfa.utest.sh ${CMAKE_CURRENT_BINARY_DIR}
     WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
     )
 endfunction()

README.md

@@ -16,7 +16,7 @@ The WFA2 library implements the WFA algorithm for different distance metrics and
 
 ### 1.3 Getting started
 
-Git clone and compile the library, tools, and examples (by default, use cmake).
+Git clone and compile the library, tools, and examples (by default, use cmake for the library and benchmark build).
 
 ```
 git clone https://github.com/smarco/WFA2-lib
@@ -34,13 +34,7 @@ cmake .. -DOPENMP=TRUE
 cmake .. -DCMAKE_BUILD_TYPE=Release -DEXTRA_FLAGS="-ftree-vectorizer-verbose=5"
 ```
 
-To build a shared library (static is the default).
-
-```
-cmake -DBUILD_SHARED_LIBS=ON
-```
-
-Alternatively, the Makefile build system can be used.
+Alternatively, the simple Makefile build system can be used.
 
 ```
 $> git clone https://github.com/smarco/WFA2-lib

guix.scm

@@ -1,6 +1,6 @@
 ;; Set up build environment using GNU Guix packages
 ;;
-;; CC0 license, Pjotr Prins (c) 2022-2023
+;; CC0 license, Pjotr Prins (c) 2022-2024
 ;;
 ;; To use this file to build HEAD:
 ;;
@@ -44,6 +44,7 @@
   (gnu packages llvm)
   (gnu packages parallel)
   (gnu packages pkg-config)
+  (gnu packages time)
   (srfi srfi-1)
   (ice-9 popen)
   (ice-9 rdelim))
@@ -61,6 +62,7 @@
     (build-system cmake-build-system)
     (inputs
      `(("bash" ,bash)
+       ("time" ,time)
        ("gdb" ,gdb)))
     (native-inputs
      `(("pkg-config" ,pkg-config)))

tests/wfa.utest.clean.sh

@@ -9,5 +9,5 @@
 OUTPUT="./tests"
 
 # Clear
-rm $OUTPUT/*.alg $OUTPUT/*.log* &> /dev/null
+rm -f $OUTPUT/*.alg $OUTPUT/*.log* &> /dev/null
 

tests/wfa.utest.cmp.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 # PROJECT: Wavefront Alignments Algorithms (Unitary Tests)
-# LICENCE: MIT License 
+# LICENCE: MIT License
 # AUTHOR(S): Santiago Marco-Sola <santiagomsola@gmail.com>
 # DESCRIPTION: Compares alignments (*.alg) from two folders
 # USAGE: ./wfa.utest.cmp.sh folder_1 folder_2 [--cmp-performance]
@@ -20,6 +20,7 @@ STATUS=0
 echo "> Comparing $FOLDER1 vs $FOLDER2"
 for FILE_ALG1 in $FOLDER1/*.alg
 do
+  echo $FILE_ALG1
   FILENAME=$(basename -- "$FILE_ALG1")
   PREFIX=${FILENAME%.*}
   FILE_ALG2="$FOLDER2/$FILENAME"
@@ -34,7 +35,7 @@ do
     continue
   fi
   # Check diff
-  if [[ $(diff $FILE_ALG1 $FILE_ALG2) ]] 
+  if [[ $(diff $FILE_ALG1 $FILE_ALG2) ]]
   then
     if [[ $(diff <(awk '{if ($1<0) print -$1; else print $1}' $FILE_ALG1) <(awk '{if ($1<0) print -$1; else print $1}' $FILE_ALG2)) ]]
     then
@@ -52,7 +53,7 @@ do
   if [[ $CMP_PERF == 1 ]]
   then
     T1=$(grep -m1 "Time.Alignment" $FOLDER1/$PREFIX.log | awk '{print $3" "$4}')
-    T2=$(grep -m1 "Time.Alignment" $FOLDER2/$PREFIX.log | awk '{print $3" "$4}')  
+    T2=$(grep -m1 "Time.Alignment" $FOLDER2/$PREFIX.log | awk '{print $3" "$4}')
     M1=$(grep -m1 "Maximum resident set size" $FOLDER1/$PREFIX.log | tr -d "(:)" | awk '{print $6" "$5}')
     M2=$(grep -m1 "Maximum resident set size" $FOLDER2/$PREFIX.log | tr -d "(:)" | awk '{print $6" "$5}')
     echo -e "\tTIME($T1,$T2)\tMEM($M1,$M2)"

tests/wfa.utest.performance.sh

@@ -14,7 +14,7 @@ LOWMEMORY="--wfa-memory-mode=med"
 BIWFA="--wfa-memory-mode=ultralow"
 
 # Clear
-rm $OUTPUT/*.log $OUTPUT/*.alg
+rm -f $OUTPUT/*.log $OUTPUT/*.alg
 
 # Utest for length=100
 \time -v ./bin/align_benchmark -a $ALGORITHM -i ../data/sim.l100.n100K.e2.seq -o $OUTPUT/sim.l100.e2.W.alg               &> $OUTPUT/sim.l100.e2.W.log
@@ -41,4 +41,4 @@ rm $OUTPUT/*.log $OUTPUT/*.alg
 echo ">>> "
 echo ">>> Performance [base vs new]: "
 echo ">>> "
-./tests/wfa.utest.cmp.sh tests/wfa.utest.performance.check/ tests/ --cmp-performance
+./tests/wfa.utest.cmp.sh tests/wfa.utest.performance.check/ tests/ --cmp-performance

tests/wfa.utest.sh

@@ -1,8 +1,8 @@
 #!/bin/bash
 # PROJECT: Wavefront Alignments Algorithms (Unitary Tests)
-# LICENCE: MIT License 
+# LICENCE: MIT License
 # AUTHOR(S): Santiago Marco-Sola <santiagomsola@gmail.com>
-# DESCRIPTION: WFA unitary tests (correcness)
+# DESCRIPTION: WFA unitary tests (correctness)
 # USAGE: ./wfa.utest.sh
 
 # Config
@@ -12,50 +12,55 @@ OUTPUT="$PREFIX"
 LOG="$PREFIX/wfa.utest.log"
 
 CMP_SCORE=$(readlink -f "$PREFIX/../scripts/wfa.alg.cmp.score.sh")
-BIN=$(readlink -f "$PREFIX/../build/bin/align_benchmark")
-if [ ! -f "$BIN" ] 
+
+BIN=$1/align_benchmark
+if [ ! -f "$BIN" ]
 then
     BIN=$(readlink -f "$PREFIX/../bin/align_benchmark")
     if [ ! -f "$BIN" ]
     then
-        echo "[Error] Binaries not built. Please run cmake or make"  
-        exit -1
-    fi 
+        BIN=$(readlink -f "$PREFIX/../build/align_benchmark") # cmake
+        if [ ! -f "$BIN" ]
+        then
+            echo "[Error] Binaries not built. Please run cmake or make"
+            exit -1
+        fi
+    fi
 fi
 
 # Clear
-rm $OUTPUT/*.alg $OUTPUT/*.log* &> /dev/null
+rm -f $OUTPUT/*.alg $OUTPUT/*.log* &> /dev/null
 
 # Run tests
 for opt in "--check=correct","test" \
            "--wfa-score-only","test.score" \
            "--wfa-memory-mode=med --check=correct","test.pb" \
            "--wfa-memory-mode=ultralow --check=correct","test.biwfa" \
-           "--wfa-memory-mode=ultralow --wfa-score-only","test.biwfa.score" 
-do 
+           "--wfa-memory-mode=ultralow --wfa-score-only","test.biwfa.score"
+do
     # Config
     IFS=','; set -- $opt
     IFS=' '; MODE="$1"; NAME="$2"
     echo ">>> Testing '$NAME' ($MODE)"
-    
+
     # Testing distance functions
-    \time -v $BIN -i $INPUT -o $OUTPUT/$NAME.indel.alg    -a indel-wfa        $MODE >> $LOG 2>&1 
-    \time -v $BIN -i $INPUT -o $OUTPUT/$NAME.edit.alg     -a edit-wfa         $MODE >> $LOG 2>&1        
-    \time -v $BIN -i $INPUT -o $OUTPUT/$NAME.affine.alg   -a gap-affine-wfa   $MODE >> $LOG 2>&1    
-    \time -v $BIN -i $INPUT -o $OUTPUT/$NAME.affine2p.alg -a gap-affine2p-wfa $MODE >> $LOG 2>&1 
-    
+    \time -v $BIN -i $INPUT -o $OUTPUT/$NAME.indel.alg    -a indel-wfa        $MODE >> $LOG 2>&1
+    \time -v $BIN -i $INPUT -o $OUTPUT/$NAME.edit.alg     -a edit-wfa         $MODE >> $LOG 2>&1
+    \time -v $BIN -i $INPUT -o $OUTPUT/$NAME.affine.alg   -a gap-affine-wfa   $MODE >> $LOG 2>&1
+    \time -v $BIN -i $INPUT -o $OUTPUT/$NAME.affine2p.alg -a gap-affine2p-wfa $MODE >> $LOG 2>&1
+
     # Testing penalty-scores
-    \time -v $BIN -i $INPUT -o $OUTPUT/$NAME.affine.p0.alg -a gap-affine-wfa $MODE --affine-penalties="0,1,2,1" >> $LOG 2>&1 
-    \time -v $BIN -i $INPUT -o $OUTPUT/$NAME.affine.p1.alg -a gap-affine-wfa $MODE --affine-penalties="0,3,1,4" >> $LOG 2>&1 
-    \time -v $BIN -i $INPUT -o $OUTPUT/$NAME.affine.p2.alg -a gap-affine-wfa $MODE --affine-penalties="0,5,3,2" >> $LOG 2>&1  
-    
-    \time -v $BIN -i $INPUT -o $OUTPUT/$NAME.affine.p3.alg -a gap-affine-wfa $MODE --affine-penalties="-5,1,2,1" >> $LOG 2>&1 
-    \time -v $BIN -i $INPUT -o $OUTPUT/$NAME.affine.p4.alg -a gap-affine-wfa $MODE --affine-penalties="-2,3,1,4" >> $LOG 2>&1 
-    \time -v $BIN -i $INPUT -o $OUTPUT/$NAME.affine.p5.alg -a gap-affine-wfa $MODE --affine-penalties="-3,5,3,2" >> $LOG 2>&1 
-    
+    \time -v $BIN -i $INPUT -o $OUTPUT/$NAME.affine.p0.alg -a gap-affine-wfa $MODE --affine-penalties="0,1,2,1" >> $LOG 2>&1
+    \time -v $BIN -i $INPUT -o $OUTPUT/$NAME.affine.p1.alg -a gap-affine-wfa $MODE --affine-penalties="0,3,1,4" >> $LOG 2>&1
+    \time -v $BIN -i $INPUT -o $OUTPUT/$NAME.affine.p2.alg -a gap-affine-wfa $MODE --affine-penalties="0,5,3,2" >> $LOG 2>&1
+
+    \time -v $BIN -i $INPUT -o $OUTPUT/$NAME.affine.p3.alg -a gap-affine-wfa $MODE --affine-penalties="-5,1,2,1" >> $LOG 2>&1
+    \time -v $BIN -i $INPUT -o $OUTPUT/$NAME.affine.p4.alg -a gap-affine-wfa $MODE --affine-penalties="-2,3,1,4" >> $LOG 2>&1
+    \time -v $BIN -i $INPUT -o $OUTPUT/$NAME.affine.p5.alg -a gap-affine-wfa $MODE --affine-penalties="-3,5,3,2" >> $LOG 2>&1
+
     # Heuristics
-    \time -v $BIN -i $INPUT -o $OUTPUT/$NAME.affine.wfapt0.alg -a gap-affine-wfa $MODE --wfa-heuristic=wfa-adaptive --wfa-heuristic-parameters=10,50,1 >> $LOG 2>&1 
-    \time -v $BIN -i $INPUT -o $OUTPUT/$NAME.affine.wfapt1.alg -a gap-affine-wfa $MODE --wfa-heuristic=wfa-adaptive --wfa-heuristic-parameters=10,50,10 >> $LOG 2>&1 
+    \time -v $BIN -i $INPUT -o $OUTPUT/$NAME.affine.wfapt0.alg -a gap-affine-wfa $MODE --wfa-heuristic=wfa-adaptive --wfa-heuristic-parameters=10,50,1 >> $LOG 2>&1
+    \time -v $BIN -i $INPUT -o $OUTPUT/$NAME.affine.wfapt1.alg -a gap-affine-wfa $MODE --wfa-heuristic=wfa-adaptive --wfa-heuristic-parameters=10,50,10 >> $LOG 2>&1
 done
 
 # Intra-tests
@@ -91,9 +96,9 @@ grep "Maximum resident set size" $LOG | awk '{print $6}' | sort -n > $LOG.mem
 
 # Display performance
 echo ">>> Performance Time (s) [base vs new]: "
-paste <(tail -n 4 $OUTPUT/wfa.utest.check/wfa.utest.log.time) <(tail -n 4 $OUTPUT/wfa.utest.log.time) 
+paste <(tail -n 4 $OUTPUT/wfa.utest.check/wfa.utest.log.time) <(tail -n 4 $OUTPUT/wfa.utest.log.time)
 echo ">>> Performance Mem (KB) [base vs new]: "
-paste <(tail -n 4 $OUTPUT/wfa.utest.check/wfa.utest.log.mem) <(tail -n 4 $OUTPUT/wfa.utest.log.mem) 
+paste <(tail -n 4 $OUTPUT/wfa.utest.check/wfa.utest.log.mem) <(tail -n 4 $OUTPUT/wfa.utest.log.mem)
 
 # Display correct
 ./tests/wfa.utest.cmp.sh $OUTPUT $OUTPUT/wfa.utest.check
@@ -110,4 +115,3 @@ else
   echo -e ">>>\n>>> ERROR\n>>>"
   exit -1
 fi
-

tests/wfa.utest.valgrind.sh

@@ -12,7 +12,7 @@ OUTPUT="./tests"
 LOG="./tests/wfa.utest.log.valgrind"
 
 # Clear
-rm $OUTPUT/*.alg $LOG
+rm -f $OUTPUT/*.alg $LOG
 touch $LOG
 
 # Run tests

tools/align_benchmark/align_benchmark.c

@@ -535,9 +535,11 @@ void align_benchmark_parallel() {
     if (seqs_batch == 0) break;
     // Parallel processing of the sequences batch
     timer_start(&parameters.timer_global); // PROFILE
+#ifdef WFA_PARALLEL
     #pragma omp parallel num_threads(parameters.num_threads)
     {
       int tid = omp_get_thread_num();
+
       #pragma omp for
       for (int seq_idx=0;seq_idx<seqs_batch;++seq_idx) {
         // Configure sequence
@@ -551,6 +553,7 @@ void align_benchmark_parallel() {
         align_benchmark_run_algorithm(align_input+tid);
       }
     }
+#endif
     timer_stop(&parameters.timer_global); // PROFILE
     // Update progress
     seqs_processed += seqs_batch;