Commit 63dd4936 authored by Shayan Doust's avatar Shayan Doust
Browse files

Patch dbreaderserialization test and include in unit test

parent 72d91fc0

debian/patches/fix_tests.patch

+21 −8
Original line number Diff line number Diff line
@@ -6,8 +6,8 @@ Last-Update: 2019-07-20 


Index: mmseqs2/src/test/TestScoreMatrixSerialization.cpp

===================================================================

--- mmseqs2.orig/src/test/TestScoreMatrixSerialization.cpp	2019-07-20 19:59:12.396009495 +0100

+++ mmseqs2/src/test/TestScoreMatrixSerialization.cpp	2019-07-20 19:59:12.388009427 +0100

--- mmseqs2.orig/src/test/TestScoreMatrixSerialization.cpp	2019-07-20 20:46:12.299793354 +0100

+++ mmseqs2/src/test/TestScoreMatrixSerialization.cpp	2019-07-20 20:46:12.295793321 +0100

@@ -18,10 +18,12 @@

     ScoreMatrix* unserialized = ScoreMatrix::unserialize(serialized, subMat.alphabetSize, 3);
@@ -26,8 +26,8 @@ Index: mmseqs2/src/test/TestScoreMatrixSerialization.cpp 
 }

Index: mmseqs2/src/test/TestBestAlphabet.cpp

===================================================================

--- mmseqs2.orig/src/test/TestBestAlphabet.cpp	2019-07-20 19:59:12.396009495 +0100

+++ mmseqs2/src/test/TestBestAlphabet.cpp	2019-07-20 19:59:12.392009461 +0100

--- mmseqs2.orig/src/test/TestBestAlphabet.cpp	2019-07-20 20:46:12.299793354 +0100

+++ mmseqs2/src/test/TestBestAlphabet.cpp	2019-07-20 20:46:12.295793321 +0100

@@ -58,7 +58,7 @@

     /////////                                 |   ////////////////

     ///////// Choose substitution matrix here V ! ////////////////
@@ -50,8 +50,8 @@ Index: mmseqs2/src/test/TestBestAlphabet.cpp 
 

Index: mmseqs2/src/test/TestAlignmentPerformance.cpp

===================================================================

--- mmseqs2.orig/src/test/TestAlignmentPerformance.cpp	2019-07-20 19:59:12.396009495 +0100

+++ mmseqs2/src/test/TestAlignmentPerformance.cpp	2019-07-20 19:59:12.392009461 +0100

--- mmseqs2.orig/src/test/TestAlignmentPerformance.cpp	2019-07-20 20:46:12.299793354 +0100

+++ mmseqs2/src/test/TestAlignmentPerformance.cpp	2019-07-20 20:46:12.295793321 +0100

@@ -83,7 +83,7 @@

     int gap_extend = 1;

     int mode = 0;
@@ -63,8 +63,8 @@ Index: mmseqs2/src/test/TestAlignmentPerformance.cpp 
         aligner.ssw_init(query, tinySubMat, &subMat, subMat.alphabetSize, 2);

Index: mmseqs2/src/test/TestDBReader.cpp

===================================================================

--- mmseqs2.orig/src/test/TestDBReader.cpp	2019-07-20 08:12:45.250499276 +0100

+++ mmseqs2/src/test/TestDBReader.cpp	2019-07-20 20:00:32.384684139 +0100

--- mmseqs2.orig/src/test/TestDBReader.cpp	2019-07-20 20:46:12.299793354 +0100

+++ mmseqs2/src/test/TestDBReader.cpp	2019-07-20 20:46:12.295793321 +0100

@@ -14,7 +14,7 @@

 

 int main (int, const char**) {
@@ -92,3 +92,16 @@ Index: mmseqs2/src/test/TestDBReader.cpp 
     reader3.open(DBReader<unsigned int>::SORT_BY_LENGTH);

     for(size_t i = 0; i < reader3.getSize(); i++){

         size_t id =  reader3.getDbKey(i);

Index: mmseqs2/src/test/TestDBReaderIndexSerialization.cpp

===================================================================

--- mmseqs2.orig/src/test/TestDBReaderIndexSerialization.cpp	2019-07-20 08:12:45.250499276 +0100

+++ mmseqs2/src/test/TestDBReaderIndexSerialization.cpp	2019-07-20 20:47:05.360240870 +0100

@@ -4,7 +4,7 @@

 const char* binary_name = "test_dbreaderindexserialization";

 

 int main (int, const char**) {

-    DBReader<unsigned int> reader("", "/Users/mirdita/tmp/db.index", 1, DBReader<unsigned int>::USE_INDEX);

+    DBReader<unsigned int> reader("", "../example-data/DB.index", 1, DBReader<unsigned int>::USE_INDEX);

     reader.open(DBReader<unsigned int>::NOSORT);

 

     Debug(Debug::INFO) << reader.getSize() << " " << reader.getAminoAcidDBSize() << "\n";

debian/tests/run-unit-test

+2 −0
Original line number Diff line number Diff line
@@ -69,6 +69,8 @@ echo "Invoking test_bestalphabet" 
./test_bestalphabet

echo "Invoking test_dbreader"

./test_dbreader

echo "Invoking test_dbreaderindexserialization"

./test_dbreaderindexserialization



# Takes a very long time to complete

#echo "Invoke test_alignmentperformance"