[med-svn] [Git][med-team/mmseqs2][master] 2 commits: Patch to fix test_alignmentperformance

[Shayan Doust]

Shayan Doust pushed to branch master at Debian Med / mmseqs2


Commits:
a5b18b08 by Shayan Doust at 2019-07-20T18:45:20Z
Patch to fix test_alignmentperformance
I have excluded this as it takes a *very* long time to perform and probably isn't worth it. Probably should be used alongside a profiler

- - - - -
72d91fc0 by Shayan Doust at 2019-07-20T19:16:25Z
Patch test_dbreader and include this in the unit test

- - - - -


2 changed files:

- debian/patches/fix_tests.patch
- debian/tests/run-unit-test


Changes:

=====================================
debian/patches/fix_tests.patch
=====================================
@@ -6,17 +6,16 @@ Last-Update: 2019-07-20
 
 Index: mmseqs2/src/test/TestScoreMatrixSerialization.cpp
 ===================================================================
---- mmseqs2.orig/src/test/TestScoreMatrixSerialization.cpp	2019-07-20 17:51:23.891331720 +0100
-+++ mmseqs2/src/test/TestScoreMatrixSerialization.cpp	2019-07-20 17:51:23.879331619 +0100
+--- 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
 @@ -18,10 +18,12 @@
      ScoreMatrix* unserialized = ScoreMatrix::unserialize(serialized, subMat.alphabetSize, 3);
  
      Debug(Debug::INFO) << unserialized->elementSize << " " << unserialized->rowSize << " "
 -                       << unserialized->score[0] << " " << unserialized->index[0] << "\n";
--
--    ScoreMatrix::cleanup(unserialized);
 +                       << unserialized->score[0] << "\n";
-+    
+ 
+-    ScoreMatrix::cleanup(unserialized);
      free(serialized);
 -    ScoreMatrix::cleanup(extMattwo);
 +    free(extMattwo);
@@ -27,8 +26,8 @@ Index: mmseqs2/src/test/TestScoreMatrixSerialization.cpp
  }
 Index: mmseqs2/src/test/TestBestAlphabet.cpp
 ===================================================================
---- mmseqs2.orig/src/test/TestBestAlphabet.cpp	2019-07-20 08:12:45.250499276 +0100
-+++ mmseqs2/src/test/TestBestAlphabet.cpp	2019-07-20 17:52:58.384128682 +0100
+--- 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
 @@ -58,7 +58,7 @@
      /////////                                 |   ////////////////
      ///////// Choose substitution matrix here V ! ////////////////
@@ -49,3 +48,47 @@ Index: mmseqs2/src/test/TestBestAlphabet.cpp
      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);
  
+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
+@@ -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());
+         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
+@@ -14,7 +14,7 @@
+ 
+ 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();
+@@ -24,7 +24,7 @@
+         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++){
+@@ -45,7 +45,7 @@
+     std::cout << "Check length: " << (reader2.getSeqLens(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);


=====================================
debian/tests/run-unit-test
=====================================
@@ -67,3 +67,9 @@ echo "Invoking test_scorematrixserialization"
 ./test_scorematrixserialization
 echo "Invoking test_bestalphabet"
 ./test_bestalphabet
+echo "Invoking test_dbreader"
+./test_dbreader
+
+# Takes a very long time to complete
+#echo "Invoke test_alignmentperformance"
+#./test_alignmentperformance



View it on GitLab: https://salsa.debian.org/med-team/mmseqs2/compare/968f4d6ec81844e7d448281bfed3a52b3b01fba1...72d91fc09d93cb8fde052ba1bb0e5bc69e9c54a5

-- 
View it on GitLab: https://salsa.debian.org/med-team/mmseqs2/compare/968f4d6ec81844e7d448281bfed3a52b3b01fba1...72d91fc09d93cb8fde052ba1bb0e5bc69e9c54a5
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