[med-svn] [Git][med-team/mmseqs2][master] Patch dbreaderserialization test and include in unit test

[Shayan Doust]

Shayan Doust pushed to branch master at Debian Med / mmseqs2


Commits:
63dd4936 by Shayan Doust at 2019-07-20T20:00:45Z
Patch dbreaderserialization test and include in unit test

- - - - -


2 changed files:

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


Changes:

=====================================
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 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
=====================================
@@ -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"



View it on GitLab: https://salsa.debian.org/med-team/mmseqs2/commit/63dd49363845a0825a126935bfb0516e866dde9d

-- 
View it on GitLab: https://salsa.debian.org/med-team/mmseqs2/commit/63dd49363845a0825a126935bfb0516e866dde9d
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