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Merge pull request #91 from pjotrp/main
Minor fixes for testing with vcflib
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,6 @@ | ||
| #!/bin/bash | ||
| # PROJECT: Wavefront Alignments Algorithms (Unitary Tests) | ||
| # LICENCE: MIT License | ||
| # LICENCE: MIT License | ||
| # AUTHOR(S): Santiago Marco-Sola <[email protected]> | ||
| # 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,$M2)" | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,8 +1,8 @@ | ||
| #!/bin/bash | ||
| # PROJECT: Wavefront Alignments Algorithms (Unitary Tests) | ||
| # LICENCE: MIT License | ||
| # LICENCE: MIT License | ||
| # AUTHOR(S): Santiago Marco-Sola <[email protected]> | ||
| # DESCRIPTION: WFA unitary tests (correcness) | ||
| # DESCRIPTION: WFA unitary tests (correctness) | ||
| # USAGE: ./wfa.utest.sh | ||
|
|
||
| # Config | ||
|
|
@@ -12,50 +12,55 @@ OUTPUT="$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 | ||
|
|
||
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