[med-svn] [Git][med-team/mmseqs2][master] 2 commits: Patch to fix test_dbreaderzstd and include it in the unit test
Shayan Doust
gitlab at salsa.debian.org
Mon Jul 22 01:39:51 BST 2019
Shayan Doust pushed to branch master at Debian Med / mmseqs2
Commits:
e4e360cb by Shayan Doust at 2019-07-20T22:59:55Z
Patch to fix test_dbreaderzstd and include it in the unit test
- - - - -
46be5d63 by Shayan Doust at 2019-07-20T23:25:43Z
Patch to fix test_indextable
- - - - -
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 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"
View it on GitLab: https://salsa.debian.org/med-team/mmseqs2/compare/63dd49363845a0825a126935bfb0516e866dde9d...46be5d63539b8a9f1ec1744ef9f38ec416f4837d
--
View it on GitLab: https://salsa.debian.org/med-team/mmseqs2/compare/63dd49363845a0825a126935bfb0516e866dde9d...46be5d63539b8a9f1ec1744ef9f38ec416f4837d
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