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//
// testOligos.cpp
// Mothur
//
// Created by Sarah Westcott on 7/30/18.
// Copyright © 2018 Schloss Lab. All rights reserved.
//
#include "testOligos.hpp"
/**************************************************************************************************/
TestOligos::TestOligos() { //setup
//m = MothurOut::getInstance();
TestDataSet data;
oligosfiles = data.getOligosFiles(); //single, paired, indexes, comboNamesTest
}
/**************************************************************************************************/
TestOligos::~TestOligos() {
//teardown
}
/**************************************************************************************************/
TEST(Test_Container_Oligos, Constructors) {
TestOligos test;
Oligos oligos;
EXPECT_EQ(oligos.hasPairedPrimers(), false);
EXPECT_EQ(oligos.hasPairedBarcodes(), false);
Oligos singleOligos(test.oligosfiles[0]);
EXPECT_EQ(singleOligos.hasPairedPrimers(), false);
EXPECT_EQ(singleOligos.hasPairedBarcodes(), false);
//did it read properly
map<string, int> singleBarcodes = singleOligos.getBarcodes();
int F003D000Index = singleBarcodes["AATGGTAC"];
EXPECT_EQ("F003D000", singleOligos.getBarcodeName(F003D000Index));
int MOCKGQY1XT001Index = singleBarcodes["AACCGTGTC"];
EXPECT_EQ("MOCK.GQY1XT001", singleOligos.getBarcodeName(MOCKGQY1XT001Index));
//read with reverseCompliment of reverse primer or barcode
Oligos pairedOligos(test.oligosfiles[1]);
EXPECT_EQ(pairedOligos.hasPairedPrimers(), true);
EXPECT_EQ(pairedOligos.hasPairedBarcodes(), true);
map<int, oligosPair> pairedBarcodes = pairedOligos.getPairedBarcodes();
map<int, oligosPair> pairedPrimers = pairedOligos.getPairedPrimers();
oligosPair F01R2A = pairedBarcodes[0];
EXPECT_EQ("F01R2A", pairedOligos.getBarcodeName(0));
EXPECT_EQ("CCAAC", F01R2A.forward);
EXPECT_EQ("CAGTG", F01R2A.reverse);
oligosPair V3 = pairedPrimers[0];
EXPECT_EQ("V3", pairedOligos.getPrimerName(0));
EXPECT_EQ("CCTACGGGAGGCAGCAG", V3.forward);
EXPECT_EQ("CCAGCAGCCGCGGTAAT", V3.reverse);
//read WITHOUT reverseCompliment of reverse primer or barcode
Oligos pairedOligosNoReverse; pairedOligosNoReverse.read(test.oligosfiles[1], false);
EXPECT_EQ(pairedOligosNoReverse.hasPairedPrimers(), true);
EXPECT_EQ(pairedOligosNoReverse.hasPairedBarcodes(), true);
pairedBarcodes = pairedOligosNoReverse.getPairedBarcodes();
pairedPrimers = pairedOligosNoReverse.getPairedPrimers();
F01R2A = pairedBarcodes[0];
EXPECT_EQ("F01R2A", pairedOligosNoReverse.getBarcodeName(0));
EXPECT_EQ("CCAAC", F01R2A.forward);
EXPECT_EQ("CACTG", F01R2A.reverse);
V3 = pairedPrimers[0];
EXPECT_EQ("V3", pairedOligosNoReverse.getPrimerName(0));
EXPECT_EQ("CCTACGGGAGGCAGCAG", V3.forward);
EXPECT_EQ("ATTACCGCGGCTGCTGG", V3.reverse);
//oligos for indexed barcode files
Oligos indexedOligos(test.oligosfiles[2]);
EXPECT_EQ(indexedOligos.hasPairedPrimers(), true);
EXPECT_EQ(indexedOligos.hasPairedBarcodes(), true);
pairedBarcodes = indexedOligos.getPairedBarcodes();
pairedPrimers = indexedOligos.getPairedPrimers();
oligosPair Mock3 = pairedBarcodes[0];
EXPECT_EQ("Mock3", indexedOligos.getBarcodeName(0));
EXPECT_EQ("NONE", Mock3.forward);
EXPECT_EQ("CAGCTCATCAGC", Mock3.reverse);
oligosPair testPrimer = pairedPrimers[0];
EXPECT_EQ("testPrimer", indexedOligos.getPrimerName(0));
EXPECT_EQ("NONE", testPrimer.forward);
EXPECT_EQ("ACTYAAAKGAATTGACGG", testPrimer.reverse);
}
TEST(Test_Container_Oligos, testComboNames) {
TestOligos test;
Oligos pairedOligos(test.oligosfiles[1]);
EXPECT_EQ("F01R2A.V3", pairedOligos.getGroupName(0,0));
EXPECT_EQ("F01R2D.V5", pairedOligos.getGroupName(3,1));
Oligos singleOligos(test.oligosfiles[0]);
EXPECT_EQ("F003D000", singleOligos.getGroupName(0,0));
EXPECT_EQ("F003D006", singleOligos.getGroupName(3,1));
Oligos indexedOligos(test.oligosfiles[2]);
EXPECT_EQ("Mock3.testPrimer", indexedOligos.getGroupName(0,0));
EXPECT_EQ("CKD_f31.testPrimer2", indexedOligos.getGroupName(1,1));
EXPECT_EQ("CKD_f31.testPrimer", indexedOligos.getGroupName(1,0));
EXPECT_EQ("Mock3.testPrimer2", indexedOligos.getGroupName(0,1));
}
/**************************************************************************************************/
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