debian/patches/fix_tests.patch

@@ -6,8 +6,8 @@ Last-Update: 2019-07-20
 
 Index: mmseqs2/src/test/TestScoreMatrixSerialization.cpp
 ===================================================================
---- 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
+--- mmseqs2.orig/src/test/TestScoreMatrixSerialization.cpp	2019-07-21 00:09:22.726611181 +0100
++++ mmseqs2/src/test/TestScoreMatrixSerialization.cpp	2019-07-21 00:09:22.722611147 +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 20:46:12.299793354 +0100
-+++ mmseqs2/src/test/TestBestAlphabet.cpp	2019-07-20 20:46:12.295793321 +0100
+--- mmseqs2.orig/src/test/TestBestAlphabet.cpp	2019-07-21 00:09:22.726611181 +0100
++++ mmseqs2/src/test/TestBestAlphabet.cpp	2019-07-21 00:09:22.722611147 +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 20:46:12.299793354 +0100
-+++ mmseqs2/src/test/TestAlignmentPerformance.cpp	2019-07-20 20:46:12.295793321 +0100
+--- mmseqs2.orig/src/test/TestAlignmentPerformance.cpp	2019-07-21 00:09:22.726611181 +0100
++++ mmseqs2/src/test/TestAlignmentPerformance.cpp	2019-07-21 00:09:22.722611147 +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 20:46:12.299793354 +0100
-+++ mmseqs2/src/test/TestDBReader.cpp	2019-07-20 20:46:12.295793321 +0100
+--- mmseqs2.orig/src/test/TestDBReader.cpp	2019-07-21 00:09:22.726611181 +0100
++++ mmseqs2/src/test/TestDBReader.cpp	2019-07-21 00:09:22.722611147 +0100
 @@ -14,7 +14,7 @@
  
  int main (int, const char**) {
@@ -94,8 +94,8 @@ Index: mmseqs2/src/test/TestDBReader.cpp
          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
+--- mmseqs2.orig/src/test/TestDBReaderIndexSerialization.cpp	2019-07-21 00:09:22.726611181 +0100
++++ mmseqs2/src/test/TestDBReaderIndexSerialization.cpp	2019-07-21 00:09:22.722611147 +0100
 @@ -4,7 +4,7 @@
  const char* binary_name = "test_dbreaderindexserialization";
  
@@ -105,3 +105,38 @@ Index: mmseqs2/src/test/TestDBReaderIndexSerialization.cpp
      reader.open(DBReader<unsigned int>::NOSORT);
  
      Debug(Debug::INFO) << reader.getSize() << " " << reader.getAminoAcidDBSize() << "\n";
+Index: mmseqs2/src/test/TestDBReaderZstd.cpp
+===================================================================
+--- mmseqs2.orig/src/test/TestDBReaderZstd.cpp	2019-07-21 00:09:22.726611181 +0100
++++ mmseqs2/src/test/TestDBReaderZstd.cpp	2019-07-21 00:09:22.722611147 +0100
+@@ -129,9 +129,11 @@
+                         "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();
+Index: mmseqs2/src/test/TestIndexTable.cpp
+===================================================================
+--- mmseqs2.orig/src/test/TestIndexTable.cpp	2019-07-20 22:31:34.645118021 +0100
++++ mmseqs2/src/test/TestIndexTable.cpp	2019-07-21 00:11:43.055794731 +0100
+@@ -17,11 +17,7 @@
+     Parameters &par = Parameters::getInstance();
+     SubstitutionMatrix subMat(par.scoringMatrixFile.c_str(), 8.0, -0.2f);
+     DBReader<unsigned int> dbr(
+-                               "/Users/mad/Documents/databases/db_small/db_small",
+-//                               "/Users/mad/Documents/databases/mmseqs_benchmark/benchmarks/protein_search_uniscop/db/mmseqs/db_sw",
+-                               "/Users/mad/Documents/databases/db_small/db_small.index"
+-//                               "/Users/mad/Documents/databases/mmseqs_benchmark/benchmarks/protein_search_uniscop/db/mmseqs/db_sw.index"
+-                               , 1, 0);
++                               "../example-data/DB", "../example-data/DB.index", 1, 1);
+     dbr.open(DBReader<unsigned int>::LINEAR_ACCCESS);
+ 
+     Sequence *s = new Sequence(32000, Parameters::DBTYPE_AMINO_ACIDS, &subMat, 6, true, false);

debian/tests/run-unit-test

@@ -71,6 +71,8 @@ echo "Invoking test_dbreader"
 ./test_dbreader
 echo "Invoking test_dbreaderindexserialization"
 ./test_dbreaderindexserialization
+echo "Invoking test_dbreaderzstd"
+./test_dbreaderzstd
 
 # Takes a very long time to complete
 #echo "Invoke test_alignmentperformance"