From 758adaf8e4caf3dda1e31ef818178e794d0853dd Mon Sep 17 00:00:00 2001
From: Hadi Quesneville <hadi.quesneville@inrae.fr>
Date: Tue, 31 Jan 2023 09:21:53 +0100
Subject: [PATCH 1/2] -Correct GFF3 output -Improve unit tests
---
src/BLRlib/BLRMatchPath.cpp | 4 +-
src/BLRlib/testfiles/Test_BLRMatchMap.cpp | 51 ++++------------------
src/BLRlib/testfiles/Test_BLRMatchMap.h | 7 ++-
src/BLRlib/testfiles/Test_BLRMatchPath.cpp | 24 ++++++++++
src/BLRlib/testfiles/Test_BLRMatchPath.h | 16 ++++---
5 files changed, 46 insertions(+), 56 deletions(-)
diff --git a/src/BLRlib/BLRMatchPath.cpp b/src/BLRlib/BLRMatchPath.cpp
index 9c7b9b5..af275c2 100644
--- a/src/BLRlib/BLRMatchPath.cpp
+++ b/src/BLRlib/BLRMatchPath.cpp
@@ -239,7 +239,7 @@ void BLRMatchPath::writeBED(std::ostream &out) {
//---------------------------------------------------------------------------
void BLRMatchPath::writeGFF3(const SDGString &filename) {
std::ostringstream gffStream;
- writeBED(gffStream);
+ writeGFF3(gffStream);
std::ofstream bedFile(filename);
bedFile << gffStream.str();
}
@@ -433,4 +433,4 @@ void BLRMatchPath::writeMatch(const BLRJoinParameter& para, const SDGString &fil
}
if (verbose > 0)
std::cout << " done" << std::endl;
-}
\ No newline at end of file
+}
diff --git a/src/BLRlib/testfiles/Test_BLRMatchMap.cpp b/src/BLRlib/testfiles/Test_BLRMatchMap.cpp
index b97b533..cbbbe2c 100644
--- a/src/BLRlib/testfiles/Test_BLRMatchMap.cpp
+++ b/src/BLRlib/testfiles/Test_BLRMatchMap.cpp
@@ -17,44 +17,15 @@ void Test_BLRMatchMap::tearDown()
{
}
-// clean_conflicts is never called in other submethod in MapPath.
-void Test_BLRMatchMap::test_clean_conflicts(void){
- SDGString match_file = "match.align";
- Test_BLRUtils::writeInputFile();
-
- BLRMatcherThreadsParameter para = createParameter();
- BLRMatchMap matchMap(para);
-
- matchMap.loadAlign(match_file);
-
- BLRMatchMap::MapAlign mapAlignBefore = matchMap.getMapAlign();
-
-
- /*std::cout<<" clean_conflicts before: "<<std::endl;
- Test_BLRUtils::viewMapAlign(mapAlignBefore);
- std::cout<<" "<<std::endl;*/
-
-
- matchMap.clean_conflicts();
- BLRMatchMap::MapAlign obsMapAlign = matchMap.getMapAlign();
-
- /*std::cout<<"clean_conflicts after: "<<std::endl;
- Test_BLRUtils::viewMapAlign(obsMapAlign);*/
-
- BLRMatchMap::MapAlign expMapAlign = Test_BLRUtils::createExpMapAlign_for_clean_conflicts();
-
- /* std::cout<<"expectation: "<<std::endl;
- Test_BLRUtils::viewMapAlign(expMapAlign);*/
-
- bool expComparaison = true;
- bool obsComparaison = (expMapAlign == obsMapAlign);
-
- CPPUNIT_ASSERT_EQUAL(expComparaison, obsComparaison);
-
- FileUtils::removeFile(match_file);
+void Test_BLRMatchMap::test_mapAlign_equality(void){
+ BLRMatchMap::MapAlign mapAlign1 = Test_BLRUtils::createMapAlign_instance_for_test_mapAlign_Equality();
+ BLRMatchMap::MapAlign mapAlign2 = Test_BLRUtils::createMapAlign_instance_for_test_mapAlign_Equality();
+ bool expComparaison = true;
+ bool obsComparaison = (mapAlign1 == mapAlign2);
+ CPPUNIT_ASSERT_EQUAL(expComparaison, obsComparaison);
}
-void Test_BLRMatchMap::test_mapPath(void){
+void Test_BLRMatchMap::test_mapPath_join_merge_clean_after(void){
bool joiningParameter = true;
bool cleanBefore = false;
bool cleanAfter = true;
@@ -149,13 +120,7 @@ void Test_BLRMatchMap::test_isOverlapFound_in_add_split_path(void){
CPPUNIT_ASSERT_EQUAL(expOverlap, obsOverlap);
}
-void Test_BLRMatchMap::test_mapAlign_equality(void){
- BLRMatchMap::MapAlign mapAlign1 = Test_BLRUtils::createMapAlign_instance_for_test_mapAlign_Equality();
- BLRMatchMap::MapAlign mapAlign2 = Test_BLRUtils::createMapAlign_instance_for_test_mapAlign_Equality();
- bool expComparaison = true;
- bool obsComparaison = (mapAlign1 == mapAlign2);
- CPPUNIT_ASSERT_EQUAL(expComparaison, obsComparaison);
-}
+
void Test_BLRMatchMap::test_merge_on_two_queries(void)
diff --git a/src/BLRlib/testfiles/Test_BLRMatchMap.h b/src/BLRlib/testfiles/Test_BLRMatchMap.h
index 6b6e442..a7b3818 100644
--- a/src/BLRlib/testfiles/Test_BLRMatchMap.h
+++ b/src/BLRlib/testfiles/Test_BLRMatchMap.h
@@ -15,8 +15,7 @@ class Test_BLRMatchMap: public CPPUNIT_NS::TestFixture
{
CPPUNIT_TEST_SUITE(Test_BLRMatchMap);
CPPUNIT_TEST(test_mapAlign_equality);
- CPPUNIT_TEST(test_clean_conflicts);
- CPPUNIT_TEST(test_mapPath);
+ CPPUNIT_TEST(test_mapPath_join_merge_clean_after);
CPPUNIT_TEST(view_add_clean_path_all_S);
CPPUNIT_TEST(test_isOverlapFound_in_add_split_path);
CPPUNIT_TEST(test_merge_on_two_queries);
@@ -46,8 +45,8 @@ class Test_BLRMatchMap: public CPPUNIT_NS::TestFixture
protected:
void test_mapAlign_equality(void);
- void test_clean_conflicts(void);
- void test_mapPath(void);
+ void test_mapPath_join_clean_before(void);
+ void test_mapPath_join_merge_clean_after(void);
void view_add_clean_path_all_S(void);
void test_isOverlapFound_in_add_split_path(void);
void test_merge_on_two_queries(void);
diff --git a/src/BLRlib/testfiles/Test_BLRMatchPath.cpp b/src/BLRlib/testfiles/Test_BLRMatchPath.cpp
index c8fb3e7..c35f59e 100644
--- a/src/BLRlib/testfiles/Test_BLRMatchPath.cpp
+++ b/src/BLRlib/testfiles/Test_BLRMatchPath.cpp
@@ -218,7 +218,31 @@ void Test_BLRMatchPath::test_writeBED(void){
CPPUNIT_ASSERT_EQUAL(exp.str(), obs.str());
}
+//---------------------------------------------------------------------------
+void Test_BLRMatchPath::test_writeGFF3(void){
+
+ BLRJoinParameter para = Test_BLRUtils::createParameter();
+ BLRMatchPath matchPath;
+
+ std::ostringstream inputData;
+ inputData << "10\tCHR1v01212004\t100\t250\tTNAT1A\t36\t523\t2e-128\t460\t81.56\n";
+ inputData << "10\tCHR1v01212004\t800\t1000\tTNAT1A\t36\t523\t2e-128\t460\t81.56\n";
+ inputData << "20\tCHR2v01212004\t1050\t2000\tTNAT1A\t580\t480\t7e-78\t87\t79.14\n";
+ std::istringstream inputDataStream(inputData.str());
+ matchPath.read(para,inputDataStream, 0);
+
+ std::ostringstream obs;
+ matchPath.writeGFF3(obs);
+
+ std::ostringstream exp;
+ exp << "CHR1v01212004\tmatcher\tmatch\t100\t1000\t868\t+\t.\tID=1;Name=TNAT1A;Target=TNAT1A 36 523;Note=e-value:2e-128,identity:81.56\n";
+ exp << "CHR1v01212004\tmatcher\tmatch_part\t100\t250\t460\t+\t.\tID=1.1;Parent=1;Name=TNAT1A.1;Target=TNAT1A 36 523;Note=e-value:2e-128,identity:81.56\n";
+ exp << "CHR1v01212004\tmatcher\tmatch_part\t800\t1000\t460\t+\t.\tID=1.2;Parent=1;Name=TNAT1A.2;Target=TNAT1A 36 523;Note=e-value:2e-128,identity:81.56\n";
+ exp << "CHR2v01212004\tmatcher\tmatch\t1050\t2000\t87\t-\t.\tID=2;Name=TNAT1A;Target=TNAT1A 480 580;Note=e-value:7e-78,identity:79.14\n";
+ exp << "CHR2v01212004\tmatcher\tmatch_part\t1050\t2000\t87\t-\t.\tID=2.1;Parent=2;Name=TNAT1A.1;Target=TNAT1A 480 580;Note=e-value:7e-78,identity:79.14\n";
+ CPPUNIT_ASSERT_EQUAL(exp.str(), obs.str());
+}
diff --git a/src/BLRlib/testfiles/Test_BLRMatchPath.h b/src/BLRlib/testfiles/Test_BLRMatchPath.h
index 0d7997b..0999c09 100644
--- a/src/BLRlib/testfiles/Test_BLRMatchPath.h
+++ b/src/BLRlib/testfiles/Test_BLRMatchPath.h
@@ -12,13 +12,14 @@
class Test_BLRMatchPath: public CPPUNIT_NS::TestFixture
{
- CPPUNIT_TEST_SUITE(Test_BLRMatchPath);
- CPPUNIT_TEST(test_read);
- CPPUNIT_TEST(test_load);
- CPPUNIT_TEST(test_setFromRpsList);
- CPPUNIT_TEST(test_setFromRpsList2);
- CPPUNIT_TEST(test_writeBED);
- CPPUNIT_TEST_SUITE_END();
+ CPPUNIT_TEST_SUITE(Test_BLRMatchPath);
+ CPPUNIT_TEST(test_read);
+ CPPUNIT_TEST(test_load);
+ CPPUNIT_TEST(test_setFromRpsList);
+ CPPUNIT_TEST(test_setFromRpsList2);
+ CPPUNIT_TEST(test_writeBED);
+ CPPUNIT_TEST(test_writeGFF3);
+ CPPUNIT_TEST_SUITE_END();
public:
void setUp();
@@ -30,6 +31,7 @@ class Test_BLRMatchPath: public CPPUNIT_NS::TestFixture
void test_setFromRpsList(void);
void test_setFromRpsList2(void);
void test_writeBED(void);
+ void test_writeGFF3(void);
};
#endif
--
GitLab
From f4a5fddfeed0c4c9ede8239c5bb63b1949a3d844 Mon Sep 17 00:00:00 2001
From: Hadi Quesneville <hadi.quesneville@inrae.fr>
Date: Tue, 31 Jan 2023 09:43:01 +0100
Subject: [PATCH 2/2] -Set clean before at false when clean after is set.
---
src/BLRlib/BLRMatcherThreadsParameter.cpp | 1 +
src/matcher.threads/matcherThreads.cpp | 2 --
2 files changed, 1 insertion(+), 2 deletions(-)
diff --git a/src/BLRlib/BLRMatcherThreadsParameter.cpp b/src/BLRlib/BLRMatcherThreadsParameter.cpp
index 5f2226f..4e588e7 100644
--- a/src/BLRlib/BLRMatcherThreadsParameter.cpp
+++ b/src/BLRlib/BLRMatcherThreadsParameter.cpp
@@ -80,6 +80,7 @@ void BLRMatcherThreadsParameter::parseOptArg(int numarg, char* tabarg[])
}
case 'x':
{
+ clean_before=false;
clean_after=true;
break;
}
diff --git a/src/matcher.threads/matcherThreads.cpp b/src/matcher.threads/matcherThreads.cpp
index 7608a8b..9d87cbd 100644
--- a/src/matcher.threads/matcherThreads.cpp
+++ b/src/matcher.threads/matcherThreads.cpp
@@ -109,8 +109,6 @@ int main(int argc, char *argv[]) {
std::cerr << "No file :" << para.getLoad_path() << std::endl << std::flush;
-
-
std::list<RangePair> rp_list = match_align.getRpListFromMatchAlign();
if(para.getVerbose()>0) std::cout<<"list size="<<rp_list.size()<<std::endl;
--
GitLab