enable tests for stats and fastqreader

CMakeLists.txt

@@ -73,6 +73,7 @@ set(
     test/globals.cpp
     test/polyx_test.cpp
     test/sequence_test.cpp
+    test/stats_test.cpp
 )
 include_directories(
     # intel mac install location
@@ -117,7 +118,12 @@ target_link_libraries(
 # tests target
 enable_testing()
 find_package(GTest CONFIG REQUIRED)
+configure_file(test/config.h.in ${CMAKE_BINARY_DIR}/include/config.h)
 add_executable(fastplong_tests ${FASTPLONG_TEST_SOURCES})
+target_include_directories(
+    fastplong_tests
+    PRIVATE ${CMAKE_BINARY_DIR}/include
+)
 target_link_libraries(
     fastplong_tests PRIVATE
     ${FASTPLONG_LIBS}

test/config.h.in

@@ -0,0 +1,7 @@
+// this file is necessary to help resolve the correct path when loading test data files.
+// When tests using the IDE and CLI the working directory can be different.
+// This substitute builds the absolute path to eliminate the need to depend on the working directory.
+#pragma once
+
+#define FP_TESTDATA_R1 "${CMAKE_SOURCE_DIR}/testdata/R1.fq"
+#define FP_TESTDATA_R2 "${CMAKE_SOURCE_DIR}/testdata/R2.fq"

test/fastqreader_test.cpp

@@ -1,22 +1,32 @@
 #include <gtest/gtest.h>
 #include "../src/fastqreader.h"
 
-TEST(fastqreader, test) {
-	/*FastqReader reader1("testdata/R1.fq");
-	FastqReader reader2("testdata/R1.fq");
-	Read* r1 = NULL;
-	Read* r2 = NULL;
-	int i=0;
-	while(true){
-		i++;
-		r1=reader1.read();
-		r2=reader2.read();
-		if(r1 == NULL || r2==NULL)
+#include "config.h"
+#include <vector>
+
+TEST(fastqreader, test)
+{
+	FastqReader reader1(FP_TESTDATA_R1);
+
+	Read *r1 = NULL;
+
+	std::vector<Read*> v;
+	while (true)
+	{
+		r1 = reader1.read();
+		if (r1 == nullptr) {
 			break;
-		r1->print();
-		r2->print();
-		delete r1;
-		delete r2;
-	}*/
-}
+		}
+		v.push_back(r1);
+	}
+	EXPECT_EQ(v.size(), 9);
+	EXPECT_EQ(*v[0]->mName, "@AS500713:64:HFKJJBGXY:1:11101:1675:1101 1:A:0:TATAGCCT+GACCCCCA");
+	EXPECT_EQ(*v[0]->mSeq, "");
+	EXPECT_EQ(*v[0]->mStrand, "+");
+	EXPECT_EQ(*v[0]->mQuality, "");
 
+	EXPECT_EQ(*v[1]->mName, "@AS500713:64:HFKJJBGXY:1:11101:17113:1101 1:A:0:TATAGCCT+GTTTCTTA");
+	EXPECT_EQ(*v[1]->mSeq, "TACAAAATGCACATCGCTGAAAGGGGTAAAGGAGAGAAATCGCTTTATAAAACCTTGAAAAGGAATATTCAAATATAAGCTGGGAAGGTATAAAAAACTCTGTACATCACAAGTAAACAAATGGAACCTGCAAAATATTAAACAAAGGATT");
+	EXPECT_EQ(*v[1]->mStrand, "+");
+	EXPECT_EQ(*v[1]->mQuality, "AAAAAEEEEE6EEAAAEEEEE6EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEEEEEEEEEECFE####EEEE6EE<AAEEEAEEEEEEEEEEEEAEEEEEEEA<E/AAEEEAEEEEE/EEEEAAEEE");
+}

test/stats_test.cpp

@@ -0,0 +1,23 @@
+#include <gtest/gtest.h>
+#include "../src/stats.h"
+#include "../src/evaluator.h"
+#include <algorithm>
+
+TEST(StatsTests, summarise) {
+	Read* left = new Read(
+        new string("@NS500713:64:HFKJJBGXY:1:11101:20469:1097 1:N:0:TATAGCCT+GGTCCCGA"),
+		new string("TTTTTTCTCTTGGACTCTAACACTGTTTTTTCTTATGAAAACACAGGAGTGATGACTAGTTGAGTGCATTCTTATGAGACTCATAGTCATTCTATGATGTAG"),
+		new string("+"),
+		new string("AAAAA6EEEEEEEEEEEEEEEEE#EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE"));
+
+    Options* options = new Options();
+    Stats stats(options);
+    stats.statRead(left);
+    stats.summarize();
+    EXPECT_EQ(stats.getCycles(), 102);
+    EXPECT_EQ(stats.getBases(), 102);
+    EXPECT_EQ(stats.getReads(), 1);
+    EXPECT_EQ(stats.getQ20(), 101);
+    EXPECT_EQ(stats.getQ30(), 100);
+    EXPECT_EQ(stats.getGCNumber(), 35);
+}

testdata/R1.fq

@@ -0,0 +1,36 @@
+@AS500713:64:HFKJJBGXY:1:11101:1675:1101 1:A:0:TATAGCCT+GACCCCCA
+
++
+
+@AS500713:64:HFKJJBGXY:1:11101:17113:1101 1:A:0:TATAGCCT+GTTTCTTA
+TACAAAATGCACATCGCTGAAAGGGGTAAAGGAGAGAAATCGCTTTATAAAACCTTGAAAAGGAATATTCAAATATAAGCTGGGAAGGTATAAAAAACTCTGTACATCACAAGTAAACAAATGGAACCTGCAAAATATTAAACAAAGGATT
++
+AAAAAEEEEE6EEAAAEEEEE6EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEEEEEEEEEECFE####EEEE6EE<AAEEEAEEEEEEEEEEEEAEEEEEEEA<E/AAEEEAEEEEE/EEEEAAEEE
+@AS500713:64:HFKJJBGXY:1:11101:1675:1101 1:A:0:TATAGCCT+GACCCCCA
+TAGGAGGCTTGGAGTACCAATAATAAAGTGAGCCCACCTTCCTGGTACCCAGACATTTCAGGAGGTCGGGAAATTTTTAAACCCAGGCAGCTTCCTGGCAGTGACATTTGGAGCATCAAAGTGGTAAATAAAATTTCATTTACATTAATAT
++
+6AAAAAEEEEE/E/EA/E/AEA6EE//AEE66/AAE//EEE/E//E/AA/EEE/A/AEE/EEA//EEEEEEEE6EEAAA/E###6E/6//6<EAAEEE/EEEA/EA/EEEEEE/<<EEEE//A/EE<AEEEEE/</AA</E<AAAE/E<E/
+@AS500713:64:HFKJJBGXY:1:11101:17113:1101 1:A:0:TATAGCCT+GTTTCTTA
+TACAAAATGCACATCGCTGAAAGGGGTAAAGGAGAGAAATCGCTTTATAAAACCTTGAAAAGGAATATTCAAATATAAGCTGGGAAGGTATAAAAAACTCTGTACATCACAAGTAAACAAATGGAACCTGCAAAATATTAAACAAAGGATT
++
+AAAAAEEEEE6EEAAAEEEEE6EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEEEEEEEEEEEEE/EEEEEEE6EE<AAEEEAEEEEEEEEEEEEAEEEEEEEA<E/AAEEEAEEEEE/EEEEAAEEE
+@AS500713:64:HFKJJBGXY:1:11101:1675:1101 1:A:0:TATAGCCT+GACCCCCA
+TAGGAGGCTTGGAGTACCAATAATAAAGTGAGCCCACCTTCCTGGTACCCAGACATTTCAGGAGGTCGGGAAATTTTTAAACCCAGGCAGCTTCCTGGCAGTGACATTTGGAGCATCAAAGTGGTAAATAAAATTTCATTTACATTAATAT
++
+6AAAAAEEEEE/E/EA/E/AEA6EE//AEE66/AAE//EEE/E//E/AA/EEE/A/AEE/EEA//EEEEEEEE6EEAAA/E/A/6E/6//6<EAAEEE/EEEA/EA/EEEEEE/<<EEEE//A/EE<AEEEEE/</AA</E<AAAE/E<E/
+@AS500713:64:HFKJJBGXY:1:11101:17113:1101 1:A:0:TATAGCCT+GTTTCTTA
+TACAAAATGCACATCGCTGAAAGGGGTAAAGGAGAGAAATCGCTTTATAAAACCTTGAAAAGGAATATTCAAATATAAGCTGGGAAGGTATAAAAAACTCTGTACATCACAAGTAAACAAATGGAACCTGCAAAATATTAAACAAAGGATT
++
+AAAAAEEEEE6EEAAAEEEEE6EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEEEEEEEEEEEEE/EEEEEEE6EE<AAEEEAEEEEEEEEEEEEAEEEEEEEA<E/AAEEEAEEEEE/EEEEAAEEE
+@AS500713:64:HFKJJBGXY:1:11101:1675:1101 1:A:0:TATAGCCT+GACCCCCA
+TAGGAGGCTTGGAGTACCAATAATAAAGTGAGCCCACCTTCCTGGTACCCAGACATTTCAGGAGGTCGGGAAATTTTTAAACCCAGGCAGCTTCCTGGCAGTGACATTTGGAGCATCAAAGTGGTAAATAAAATTTCATTTACATTAATAT
++
+6AAAAAEEEEE/E/EA/E/AEA6EE//AEE66/AAE//EEE/E//E/AA/EEE/A/AEE/EEA//EEEEEEEE6EEAAA/E/A/6E/6//6<EAAEEE/EEEA/EA/EEEEEE/<<EEEE//A/EE<AEEEEE/</AA</E<AAAE/E<E/
+@AS500713:64:HFKJJBGXY:1:11101:17113:1101 1:A:0:TATAGCCT+GTTTCTTA
+TACAAAATGCACATCGCTGAAAGGGGTAAAGGAGAGAAATCGCTTTATAAAACCTTGAAAAGGAATATTCAAATATAAGCTGGGAAGGTATAAAAAACTCTGTACATCACAAGTAAACAAATGGAACCTGCAAAATATTAAACAAAGGATT
++
+AAAAAEEEEE6EEAAAEEEEE6EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEEEEEEEEEEEEE/EEEEEEE6EE<AAEEEAEEEEEEEEEEEEAEEEEEEEA<E/AAEEEAEEEEE/EEEEAAEEE
+@AS500713:64:HFKJJBGXY:1:11101:17113:1101 1:A:0:TATAGCCT+GTTTCTTA
+CCCCCCCCCCACATCGCTGAAAGGGGTAAAGGAGAGAAATCGCTTTATAAAACCTTGAAAAGGAATATTCAAATATAAGCTGGGAAGGTATAAAAAACTCTGTACATCACAAGTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++
+AAAAAEEEEE6EEAAAEEEEE6EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEEEEEEEEEEEEE/EEEEEEE6EE<AAEEEAEEEEEEEEEEEEAEEEEEEEA<E/AAEEEAEEEEE/EEEEAAEEE

testdata/R2.fq

@@ -0,0 +1,36 @@
+@AS500713:64:HFKJJBGXY:1:11101:1675:1101 2:A:0:TATAGCCT+GACCCCCA
+TAGGGCAAAACAAATAAGACAAAAAAAAAAAATGAATGAAAATGCAATTTTATTTACCACTTTGATGCTCAAAATGGCACTGCCAGGAAGCTGCCTGGGTTTAAAAATTTCCCGACCTCCTGAAATGTCTGGGGACCAGGAAGGTGGGCTC
++
+AAAAA/EEEA/EEEE#AEA<####E######EE/A#E/##EEEE/E<<EEEE6EEAA/EAE<AEEEAAEE/EEEA/</EEEE6//</A///A6E<6E/AEEEEEEEEEEA<<6//<A</<<AAEEE/</A///<E<<A//EEAE</E/AA6
+@AS500713:64:HFKJJBGXY:1:11101:17113:1101 2:A:0:TATAGCCT+GTTTCTTA
+CTAAATTGAGTAATGAAGATAAAATAAAAAATAACAAAAACTTTGTTTAATATTTTGCAGGTTCCATTTGTTTACTTGTGATGTACAGAGTTTTTTATACCTTCCCAGCTTATATTTGAATATTCCTTTTCAAGGTTTTATAAAGCGATTT
++
+AAAAAEEEEEEEEEE#EEEE####E######E#EE#E###EEEEEEE/AEEEEEEEE/EEEE<EAEEEEEEEEE/EEEEEEEEEE<EEEEAEEEEEEEE<6EEA6<EE6EEEEEEEEEEAEAEEE/A<AE<AEEAEEEEEEEEE/</AAAA
+@AS500713:64:HFKJJBGXY:1:11101:1675:1101 2:A:0:TATAGCCT+GACCCCCA
+TAGGGCAAAACAAATAAGACAAAAAAAAAAAATGAATGAAAATGCAATTTTATTTACCACTTTGATGCTCAAAATGGCACTGCCAGGAAGCTGCCTGGGTTTAAAAATTTCCCGACCTCCTGAAATGTCTGGGGACCAGGAAGGTGGGCTC
++
+AAAAA/EEEA/EEEE#AEA<####E######EE/A#E/##EEEE/E<<EEEE6EEAA/EAE<AEEEAAEE/EEEA/</EEEE6//</A///A6E<6E/AEEEEEEEEEEA<<6//<A</<<AAEEE/</A///<E<<A//EEAE</E/AA6
+@AS500713:64:HFKJJBGXY:1:11101:17113:1101 2:A:0:TATAGCCT+GTTTCTTA
+CTAAATTGAGTAATGAAGATAAAATAAAAAATAACAAAAACTTTGTTTAATATTTTGCAGGTTCCATTTGTTTACTTGTGATGTACAGAGTTTTTTATACCTTCCCAGCTTATATTTGAATATTCCTTTTCAAGGTTTTATAAAGCGATTT
++
+AAAAAEEEEEEEEEE#EEEE####E######E#EE#E###EEEEEEE/AEEEEEEEE/EEEE<EAEEEEEEEEE/EEEEEEEEEE<EEEEAEEEEEEEE<6EEA6<EE6EEEEEEEEEEAEAEEE/A<AE<AEEAEEEEEEEEE/</AAAA
+@AS500713:64:HFKJJBGXY:1:11101:1675:1101 2:A:0:TATAGCCT+GACCCCCA
+TAGGGCAAAACAAATAAGACAAAAAAAAAAAATGAATGAAAATGCAATTTTATTTACCACTTTGATGCTCAAAATGGCACTGCCAGGAAGCTGCCTGGGTTTAAAAATTTCCCGACCTCCTGAAATGTCTGGGGACCAGGAAGGTGGGCTC
++
+AAAAA/EEEA/EEEE#AEA<####E######EE/A#E/##EEEE/E<<EEEE6EEAA/EAE<AEEEAAEE/EEEA/</EEEE6//</A///A6E<6E/AEEEEEEEEEEA<<6//<A</<<AAEEE/</A///<E<<A//EEAE</E/AA6
+@AS500713:64:HFKJJBGXY:1:11101:17113:1101 2:A:0:TATAGCCT+GTTTCTTA
+CTAAATTGAGTAATGAAGATAAAATAAAAAATAACAAAAACTTTGTTTAATATTTTGCAGGTTCCATTTGTTTACTTGTGATGTACAGAGTTTTTTATACCTTCCCAGCTTATATTTGAATATTCCTTTTCAAGGTTTTATAAAGCGATTT
++
+AAAAAEEEEEEEEEE#EEEE####E######E#EE#E###EEEEEEE/AEEEEEEEE/EEEE<EAEEEEEEEEE/EEEEEEEEEE<EEEEAEEEEEEEE<6EEA6<EE6EEEEEEEEEEAEAEEE/A<AE<AEEAEEEEEEEEE/</AAAA
+@AS500713:64:HFKJJBGXY:1:11101:1675:1101 2:A:0:TATAGCCT+GACCCCCA
+TAGGGCAAAACAAATAAGACAAAAAAAAAAAATGAATGAAAATGCAATTTTATTTACCACTTTGATGCTCAAAATGGCACTGCCAGGAAGCTGCCTGGGTTTAAAAATTTCCCGACCTCCTGAAATGTCTGGGGACCAGGAAGGTGGGCTC
++
+AAAAA/EEEA/EEEE#AEA<####E######EE/A#E/##EEEE/E<<EEEE6EEAA/EAE<AEEEAAEE/EEEA/</EEEE6//</A///A6E<6E/AEEEEEEEEEEA<<6//<A</<<AAEEE/</A///<E<<A//EEAE</E/AA6
+@AS500713:64:HFKJJBGXY:1:11101:17113:1101 2:A:0:TATAGCCT+GTTTCTTA
+CTAAATTGAGTAATGAAGATAAAATAAAAAATAACAAAAACTTTGTTTAATATTTTGCAGGTTCCATTTGTTTACTTGTGATGTACAGAGTTTTTTATACCTTCCCAGCTTATATTTGAATATTCCTTTTCAAGGTTTTATAAAGCGATTT
++
+AAAAAEEEEEEEEEE#EEEE####E######E#EE#E###EEEEEEE/AEEEEEEEE/EEEE<EAEEEEEEEEE/EEEEEEEEEE<EEEEAEEEEEEEE<6EEA6<EE6EEEEEEEEEEAEAEEE/A<AE<AEEAEEEEEEEEE/</AAAA
+@AS500713:64:HFKJJBGXY:1:11101:17113:1101 1:A:0:TATAGCCT+GTTTCTTA
+TACAAAATGCACATCGCTGAAAGGGGTAAAGGAGAGAAATCGCTTTATAAAACCTTGAAAAGGAATATTCAAATATAAGCTGGGAAGGTATAAAAAACTCTGTACATCACAAGTAAATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
++
+AAAAAEEEEE6EEAAAEEEEE6EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEEEEEEEEEEEEE/EEEEEEE6EE<AAEEEAEEEEEEEEEEEEAEEEEEEEA<E/AAEEEAEEEEE/EEEEAAEEE