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Description: Fix some of the test src files to work in autopkgtest
as some of the tests do not work as the paths have either been hardcoded or SIGSEGV is thrown
Author: Shayan Doust <hello@shayandoust.me>
Last-Update: 2019-07-20
Forwarded: not-needed
---
--- mmseqs2.orig/src/test/TestScoreMatrixSerialization.cpp
+++ mmseqs2/src/test/TestScoreMatrixSerialization.cpp
@@ -20,8 +20,12 @@
ScoreMatrix unserialized = ScoreMatrix::unserialize(serialized, subMat.alphabetSize, 2);
Debug(Debug::INFO) << unserialized.elementSize << " " << unserialized.rowSize << " "
- << unserialized.score[0] << " " << unserialized.index[0] << "\n";
+ << unserialized.score[0] << "\n";
free(serialized);
+ free(extMattwo);
+ // Why not use an operator. Will free & destruct & will not SIGSEGV
+ delete(unserialized);
+
return EXIT_SUCCESS;
}
--- mmseqs2.orig/src/test/TestBestAlphabet.cpp
+++ mmseqs2/src/test/TestBestAlphabet.cpp
@@ -58,7 +58,7 @@
///////// | ////////////////
///////// Choose substitution matrix here V ! ////////////////
//SubstitutionMatrix subMat("/Users/soeding/Projects/MMseqs2/MMseqs2/data/blosum100.out", 2.0, -0.0f);
- SubstitutionMatrix subMat("/Users/soeding/Projects/MMseqs2/MMseqs2/data/PAM70.out", 2.0, -0.0f);
+ SubstitutionMatrix subMat("../example-data/PAM70.out", 2.0, -0.0f);
const size_t numAAs = subMat.alphabetSize-1; // size of original alphabet
const size_t numKmers = pow(numAAs,kmerSize);
@@ -72,8 +72,8 @@
//////////////////////////////////////////////////////////////////////////////////////////////
// Compute probabilities for all 20^k k-mers in a sequence database "seqDB"
- std::string dbPath = "seqDB";
- std::string dbIndexPath = "seqDB.index";
+ std::string dbPath = "../example-data/DB";
+ std::string dbIndexPath = "../example-data/DB.index";
DBReader<unsigned int> seqDb(dbPath.c_str(), dbIndexPath.c_str(), 1, DBReader<unsigned int>::USE_DATA|DBReader<unsigned int>::USE_INDEX);
seqDb.open(DBReader<unsigned int>::NOSORT);
--- mmseqs2.orig/src/test/TestAlignmentPerformance.cpp
+++ mmseqs2/src/test/TestAlignmentPerformance.cpp
@@ -83,7 +83,7 @@
int gap_extend = 1;
int mode = 0;
size_t cells = 0;
- std::vector<std::string> sequences = readData("/Users/mad/Documents/databases/rfam/Rfam.fasta");
+ std::vector<std::string> sequences = readData("../example-data/DB.fasta");
for(size_t seq_i = 0; seq_i < sequences.size(); seq_i++){
query->mapSequence(1,1,sequences[seq_i].c_str(), sequences[seq_i].size());
aligner.ssw_init(query, tinySubMat, &subMat);
--- mmseqs2.orig/src/test/TestDBReader.cpp
+++ mmseqs2/src/test/TestDBReader.cpp
@@ -11,7 +11,7 @@
int main (int, const char**) {
// DBReader test
- DBReader<unsigned int> reader("dataLinear", "dataLinear.index", 1, 0);
+ DBReader<unsigned int> reader("dataLinear", "dataLinear.index", 1, 1);
reader.open(0);
reader.readMmapedDataInMemory();
reader.printMagicNumber();
@@ -21,7 +21,7 @@
std::cout << reader.getData(i, 0) << std::endl;
}
reader.close();
- DBReader<unsigned int> reader2("dataGap", "dataGap.index", 1, 0);
+ DBReader<unsigned int> reader2("dataGap", "dataGap.index", 1, 1);
reader2.open(0);
std::cout << reader2.getSize() << std::endl;
for(size_t i = 0; i < reader2.getSize(); i++){
@@ -42,7 +42,7 @@
std::cout << "Check length: " << (reader2.getSeqLen(reader2.getId(12)) == 10) << std::endl;
reader2.close();
// test sort mode
- DBReader<unsigned int> reader3("dataGap", "dataGap.index", 1, 0);
+ DBReader<unsigned int> reader3("dataGap", "dataGap.index", 1, 1);
reader3.open(DBReader<unsigned int>::SORT_BY_LENGTH);
for(size_t i = 0; i < reader3.getSize(); i++){
size_t id = reader3.getDbKey(i);
--- mmseqs2.orig/src/test/TestDBReaderIndexSerialization.cpp
+++ mmseqs2/src/test/TestDBReaderIndexSerialization.cpp
@@ -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";
--- mmseqs2.orig/src/test/TestDBReaderZstd.cpp
+++ mmseqs2/src/test/TestDBReaderZstd.cpp
@@ -125,9 +125,11 @@
"GCTATTATATCGCTCTCTTTAACCCATTCTGTTTTATCGATTCTAATCCTGAAGACGCCT"
"CGCATTTTTATGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCA";
- writer.writeData((char*)data,strlen(data), 1,0);
+ writer.writeData((char*)data,strlen(data), 1, 0);
writer.close();
- DBReader<unsigned int> reader("dataLinear", "dataLinear.index", 1, 0);
+ std::cout << "Before reader" << "\n";
+ DBReader<unsigned int> reader("dataLinear", "dataLinear.index", 1, 1);
+ std::cout << "After reader" << "\n";
reader.open(0);
reader.readMmapedDataInMemory();
reader.printMagicNumber();
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