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From: Michael R. Crusoe <michael.crusoe@gmail.com>
Subject: Enable and update tests for lambda2
Skip checking the md5sums as they are not currently stable
Only the first 10 tests pass with this patch
--- lambda-align2.orig/CMakeLists.txt
+++ lambda-align2/CMakeLists.txt
@@ -60,5 +60,5 @@
# Add Tests
# ----------------------------------------------------------------------------
-# message ("\n${ColourBold}Setting up unit tests${ColourReset}")
-# add_subdirectory(tests)
+message ("\n${ColourBold}Setting up unit tests${ColourReset}")
+add_subdirectory(tests)
--- lambda-align2.orig/tests/maintests.sh
+++ lambda-align2/tests/maintests.sh
@@ -1,5 +1,7 @@
#!/bin/sh
+set -xe
+
errorout()
{
echo $1 #> /dev/stderr
@@ -23,7 +25,11 @@
SALPH=prot # actual subject alph
QALPHIN=prot # query input file alph
SALPHIN=prot # subject input file alph
+INDEXER=mkindexp
+SEARCHER=searchp
case "$PROG" in "blastn")
+ INDEXER=mkindexn
+ SEARCHER=searchn
QALPHIN=nucl
SALPH=nucl
SALPHIN=nucl
@@ -34,10 +40,12 @@
QALPHIN=nucl
;;
"tblastn")
+ INDEXER=mkindexn
SALPH=trans
SALPHIN=nucl
;;
"tblastx")
+ INDEXER=mkindexn
SALPH=trans
QALPHIN=nucl
SALPHIN=nucl
@@ -53,16 +61,18 @@
gunzip < "${SRCDIR}/tests/db_${SALPHIN}.fasta.gz" > db.fasta
[ $? -eq 0 ] || errorout "Could not unzip database file"
-${BINDIR}/bin/lambda_indexer -d db.fasta -di ${DI} -p ${PROG}
+${BINDIR}/bin/lambda2 ${INDEXER} -d db.fasta -i ${DI}.lambda
[ $? -eq 0 ] || errorout "Could not run the indexer"
-openssl md5 * > md5sums
+openssl md5 $(find * -type f | sort) > db_${SALPH}_${DI}.md5sums
[ $? -eq 0 ] || errorout "Could not run md5 or md5sums"
+#openssl md5 $(find * -type f | sort | grep -v md5sums) > ${SRCDIR}/tests/db_${SALPH}_${DI}.md5sums
+#gzip -f ${SRCDIR}/tests/db_${SALPH}_${DI}.md5sums
-gunzip < "${SRCDIR}/tests/db_${SALPH}_${DI}.md5sums.gz" > md5sums.orig
-[ $? -eq 0 ] || errorout "Could not unzip md5sums.orig"
+gunzip < "${SRCDIR}/tests/db_${SALPH}_${DI}.md5sums.gz" > db_${SALPH}_${DI}.md5sums.orig
+[ $? -eq 0 ] || errorout "Could not unzip tests/db_${SALPH}_${DI}.md5sums.gz"
-[ "$(cat md5sums)" = "$(cat md5sums.orig)" ] || errorout "$(diff -u md5sums md5sums.orig)"
+#[ "$(cat db_${SALPH}_${DI}.md5sums)" = "$(cat db_${SALPH}_${DI}.md5sums.orig)" ] || errorout "$(diff -u db_${SALPH}_${DI}.md5sums db_${SALPH}_${DI}.md5sums.orig)"
## INDEXER tests end here
if [ "$MODE" = "MKINDEX" ]; then
@@ -73,7 +83,7 @@
gunzip < "${SRCDIR}/tests/queries_${QALPHIN}.fasta.gz" > queries.fasta
[ $? -eq 0 ] || errorout "Could not unzip queries.fasta"
-${BINDIR}/bin/lambda -d db.fasta -di ${DI} -p ${PROG} -q queries.fasta -t 1 --version-to-outputfile off \
+${BINDIR}/bin/lambda2 ${SEARCHER} -i ${DI}.lambda -q queries.fasta -t 1 --version-to-outputfile off \
-o output_${PROG}_${DI}.${EXTENSION}
[ $? -eq 0 ] || errorout "Search failed."
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