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//
// testtrimoligos.cpp
// Mothur
//
// Created by Sarah Westcott on 7/14/16.
// Copyright © 2016 Schloss Lab. All rights reserved.
//
#include "testtrimoligos.hpp"
/**************************************************************************************************/
TestTrimOligos::TestTrimOligos() { //setup
}
/**************************************************************************************************/
TestTrimOligos::~TestTrimOligos() {
}
/**************************************************************************************************/
TEST(Test_TrimOligos, SingleDirectionStripBarcodes) {
TestTrimOligos testTrim;
testTrim.oligos.loadSingle();
//no diffs allowed
TrimOligos noDiffSingleTrim(0,0,0,testTrim.oligos.primers, testTrim.oligos.barcodes, nullVector); //pdiffs, bdiffs, primers, barcodes, revPrimers
Sequence F003D150("GQY1XT001ASWK1", "TGGTGAACCCGTCAATTCCTTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGAATGCTTAACGCTTTCGCTGTGCCACCCAGGGGTCAATCCCCCCGGACAGCTAGCATTCATCGTTTACTGTGCGGACTACCAGGGTATCTAATCCTGTTTGATCCCCGCACTTTCGTGCCTCAGCGTCAGTAGGGCGCCGGTATGCTGCCTTCGCAATCGGGGTTCTGCGTGATATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTT");
int groupIndex;
vector<int> results = noDiffSingleTrim.stripBarcode(F003D150, groupIndex);
EXPECT_EQ(9, groupIndex);
EXPECT_EQ(0, results[0]);
EXPECT_EQ("match", noDiffSingleTrim.getCodeValue(results[1], 0));
EXPECT_EQ("CCGTCAATTCCTTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGAATGCTTAACGCTTTCGCTGTGCCACCCAGGGGTCAATCCCCCCGGACAGCTAGCATTCATCGTTTACTGTGCGGACTACCAGGGTATCTAATCCTGTTTGATCCCCGCACTTTCGTGCCTCAGCGTCAGTAGGGCGCCGGTATGCTGCCTTCGCAATCGGGGTTCTGCGTGATATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTT", F003D150.getUnaligned()); //TGGTGAAC barcode removed
//1 barcode diff, 2 primer diffs
TrimOligos someDiffsSingleTrim(2,0,1,testTrim.oligos.primers, testTrim.oligos.barcodes, nullVector); //pdiffs, bdiffs, primers, barcodes, revPrimers
F003D150.setAligned("TGGTGTACCCGTCAATTCCTTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGAATGCTTAACGCTTTCGCTGTGCCACCCAGGGGTCAATCCCCCCGGACAGCTAGCATTCATCGTTTACTGTGCGGACTACCAGGGTATCTAATCCTGTTTGATCCCCGCACTTTCGTGCCTCAGCGTCAGTAGGGCGCCGGTATGCTGCCTTCGCAATCGGGGTTCTGCGTGATATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTT");
results = someDiffsSingleTrim.stripBarcode(F003D150, groupIndex);
EXPECT_EQ(9, groupIndex);
EXPECT_EQ(1, results[0]);
EXPECT_EQ("match", someDiffsSingleTrim.getCodeValue(results[1], 1));
EXPECT_EQ("CCGTCAATTCCTTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGAATGCTTAACGCTTTCGCTGTGCCACCCAGGGGTCAATCCCCCCGGACAGCTAGCATTCATCGTTTACTGTGCGGACTACCAGGGTATCTAATCCTGTTTGATCCCCGCACTTTCGTGCCTCAGCGTCAGTAGGGCGCCGGTATGCTGCCTTCGCAATCGGGGTTCTGCGTGATATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTT", F003D150.getUnaligned()); //TGGTGAAC barcode removed
//nomatch option
F003D150.setAligned("GTACCCGTCAATTCCTTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGAATGCTTAACGCTTTCGCTGTGCCACCCAGGGGTCAATCCCCCCGGACAGCTAGCATTCATCGTTTACTGTGCGGACTACCAGGGTATCTAATCCTGTTTGATCCCCGCACTTTCGTGCCTCAGCGTCAGTAGGGCGCCGGTATGCTGCCTTCGCAATCGGGGTTCTGCGTGATATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTT");
results = someDiffsSingleTrim.stripBarcode(F003D150, groupIndex);
EXPECT_EQ(3, results[0]);
EXPECT_EQ("noMatch", someDiffsSingleTrim.getCodeValue(results[1], 1));
//4 barcode diff, 2 primer diffs - force multiMatch
//barcode TTC GT G G C F003D004
//barcode TTC TT G A C F003D006
TrimOligos lotsOfDiffsSingleTrim(2,0,4,testTrim.oligos.primers, testTrim.oligos.barcodes, nullVector); //pdiffs, bdiffs, primers, barcodes, revPrimers
Sequence F003D006("GQY1XT001CAJGU", "TTCAATACCCGTCAATTCCTTTAAGTTTCAACCTTGCGATCGTACTCCCCAGGTGGGATACTTATTGCGTTAGCTGCGGCACGCAGGGGGTCAGTCCCCGCACACCTAGTATCCATCGTTTACAGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCGCCTCACCGTCAGTTGTCGTCCAGCAGGCCGCCTTCGCCACTGGTGTTCCTCCTAATATCTACGCATTTCACCGCTACACTAGGAATTCCGCCTGCCTCTCCGATACTCAAGACCTACAGTTTCAAATGCA");
results = lotsOfDiffsSingleTrim.stripBarcode(F003D006, groupIndex);
EXPECT_EQ(3, results[0]); //three diffs to find match, but matches F003D004 and F003D006
EXPECT_EQ("multipleMatches", lotsOfDiffsSingleTrim.getCodeValue(results[1], 4));
}
TEST(Test_TrimOligos, SingleDirectionStripQualBarcodes) {
TestTrimOligos testTrim;
testTrim.oligos.loadSingle();
//no diffs allowed
TrimOligos noDiffSingleTrim(0,0,0,testTrim.oligos.primers, testTrim.oligos.barcodes, nullVector); //pdiffs, bdiffs, primers, barcodes, revPrimers
Sequence F003D150("GQY1XT001ASWK1", "TGGTGAACCCGTCAATTCCTTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGG"); //fragment
vector<int> qualScores(53, 38);
QualityScores F003D150Q("GQY1XT001ASWK1", qualScores); //fragment
int groupIndex;
vector<int> results = noDiffSingleTrim.stripBarcode(F003D150, F003D150Q, groupIndex);
EXPECT_EQ(9, groupIndex);
EXPECT_EQ(0, results[0]);
EXPECT_EQ("match", noDiffSingleTrim.getCodeValue(results[1], 0));
EXPECT_EQ("CCGTCAATTCCTTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGG", F003D150.getUnaligned());//TGGTGAAC barcode removed
EXPECT_EQ(45, F003D150Q.getLength()); //barcode removed
//1 barcode diff, 2 primer diffs
TrimOligos someDiffsSingleTrim(2,0,1,testTrim.oligos.primers, testTrim.oligos.barcodes, nullVector); //pdiffs, bdiffs, primers, barcodes, revPrimers
F003D150.setAligned("TGGTGCACCCGTCAATTCCTTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGG");
F003D150Q.setScores(qualScores);
results = someDiffsSingleTrim.stripBarcode(F003D150, F003D150Q, groupIndex);
EXPECT_EQ(9, groupIndex);
EXPECT_EQ(1, results[0]);
EXPECT_EQ("match", someDiffsSingleTrim.getCodeValue(results[1], 1));
EXPECT_EQ("CCGTCAATTCCTTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGG", F003D150.getUnaligned()); //TGGTGAAC barcode removed
EXPECT_EQ(45, F003D150Q.getLength()); //barcode removed
//nomatch option
F003D150.setAligned("TCAATTCCTTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGG");
results = someDiffsSingleTrim.stripBarcode(F003D150, groupIndex);
EXPECT_EQ(5, results[0]);
EXPECT_EQ("noMatch", someDiffsSingleTrim.getCodeValue(results[1], 1));
//4 barcode diff, 2 primer diffs - force multiMatch TTCTTGAC
//barcode TTC G TG G C F003D004
//barcode TTC T TG A C F003D006
TrimOligos lotsOfDiffsSingleTrim(2,0,2,testTrim.oligos.primers, testTrim.oligos.barcodes, nullVector); //pdiffs, bdiffs, primers, barcodes, revPrimers
Sequence F003D006("GQY1XT001CAJGU", "TTCATTGCCCGTCAATTCCTTTAAGTTTCAACCTTGCGATCGTACTCCCCAGG");
F003D150Q.setScores(qualScores);
results = lotsOfDiffsSingleTrim.stripBarcode(F003D006, F003D150Q, groupIndex);
EXPECT_EQ(2, results[0]); //three diffs to find match, but matches F003D004 and F003D006
EXPECT_EQ("multipleMatches", lotsOfDiffsSingleTrim.getCodeValue(results[1], 2));
}
TEST(Test_TrimOligos, SingleDirectionStripPrimers) {
TestTrimOligos testTrim;
testTrim.oligos.loadSingle();
//no diffs allowed
TrimOligos noDiffSingleTrim(0,0,0,testTrim.oligos.primers, testTrim.oligos.barcodes, nullVector); //pdiffs, bdiffs, primers, barcodes, revPrimers
Sequence F003D150("GQY1XT001ASWK1", "CCGTCAATTCCTTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGAATGCTTAACGCTTTCGCTGTGCCACCCAGGGGTCAATCCCCCCGGACAGCTAGCATTCATCGTTTACTGTGCGGACTACCAGGGTATCTAATCCTGTTTGATCCCCGCACTTTCGTGCCTCAGCGTCAGTAGGGCGCCGGTATGCTGCCTTCGCAATCGGGGTTCTGCGTGATATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTT");
int groupIndex;
vector<int> results = noDiffSingleTrim.stripForward(F003D150, groupIndex);
EXPECT_EQ(0, groupIndex);
EXPECT_EQ(0, results[0]);
EXPECT_EQ("match", noDiffSingleTrim.getCodeValue(results[1], 0));
//CCGTCAATTCMTTTRAGT primer removed
EXPECT_EQ("TTCACCGTTGCCGGCGTACTCCCCAGGTGGAATGCTTAACGCTTTCGCTGTGCCACCCAGGGGTCAATCCCCCCGGACAGCTAGCATTCATCGTTTACTGTGCGGACTACCAGGGTATCTAATCCTGTTTGATCCCCGCACTTTCGTGCCTCAGCGTCAGTAGGGCGCCGGTATGCTGCCTTCGCAATCGGGGTTCTGCGTGATATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTT", F003D150.getUnaligned()); //primer removed
//1 barcode diff, 2 primer diffs
TrimOligos someDiffsSingleTrim(2,0,1,testTrim.oligos.primers, testTrim.oligos.barcodes, nullVector); //pdiffs, bdiffs, primers, barcodes, revPrimers
F003D150.setAligned("CCTTCAATTCCTTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGAATGCTTAACGCTTTCGCTGTGCCACCCAGGGGTCAATCCCCCCGGACAGCTAGCATTCATCGTTTACTGTGCGGACTACCAGGGTATCTAATCCTGTTTGATCCCCGCACTTTCGTGCCTCAGCGTCAGTAGGGCGCCGGTATGCTGCCTTCGCAATCGGGGTTCTGCGTGATATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTT");
results = someDiffsSingleTrim.stripForward(F003D150, groupIndex);
EXPECT_EQ(0, groupIndex);
EXPECT_EQ(1, results[0]);
EXPECT_EQ("match", someDiffsSingleTrim.getCodeValue(results[1], 1));
//TGGTGAAC barcode removed
EXPECT_EQ("TTCACCGTTGCCGGCGTACTCCCCAGGTGGAATGCTTAACGCTTTCGCTGTGCCACCCAGGGGTCAATCCCCCCGGACAGCTAGCATTCATCGTTTACTGTGCGGACTACCAGGGTATCTAATCCTGTTTGATCCCCGCACTTTCGTGCCTCAGCGTCAGTAGGGCGCCGGTATGCTGCCTTCGCAATCGGGGTTCTGCGTGATATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTT", F003D150.getUnaligned()); //barcode removed
//nomatch option
F003D150.setAligned("CCTTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGAATGCTTAACGCTTTCGCTGTGCCACCCAGGGGTCAATCCCCCCGGACAGCTAGCATTCATCGTTTACTGTGCGGACTACCAGGGTATCTAATCCTGTTTGATCCCCGCACTTTCGTGCCTCAGCGTCAGTAGGGCGCCGGTATGCTGCCTTCGCAATCGGGGTTCTGCGTGATATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTT");
results = someDiffsSingleTrim.stripForward(F003D150, groupIndex);
EXPECT_EQ(9, results[0]);
EXPECT_EQ("noMatch", someDiffsSingleTrim.getCodeValue(results[1], 1));
}
TEST(Test_TrimOligos, SingleDirectionStripQualPrimers) {
TestTrimOligos testTrim;
testTrim.oligos.loadSingle();
//no diffs allowed
TrimOligos noDiffSingleTrim(0,0,0,testTrim.oligos.primers, testTrim.oligos.barcodes, nullVector); //pdiffs, bdiffs, primers, barcodes, revPrimers
Sequence F003D150("GQY1XT001ASWK1", "CCGTCAATTCCTTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGG"); //fragment
vector<int> qualScores(45, 38);
QualityScores F003D150Q("GQY1XT001ASWK1", qualScores); //fragment
int groupIndex;
vector<int> results = noDiffSingleTrim.stripForward(F003D150, F003D150Q, groupIndex, false);
EXPECT_EQ(0, results[0]);
EXPECT_EQ("match", noDiffSingleTrim.getCodeValue(results[1], 0));
EXPECT_EQ("TTCACCGTTGCCGGCGTACTCCCCAGG", F003D150.getUnaligned());//TGGTGAAC barcode removed
EXPECT_EQ(27, F003D150Q.getLength()); //barcode removed
//1 barcode diff, 2 primer diffs
TrimOligos someDiffsSingleTrim(2,0,1,testTrim.oligos.primers, testTrim.oligos.barcodes, nullVector); //pdiffs, bdiffs, primers, barcodes, revPrimers
F003D150.setAligned("CGGTCAATTCCTTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGG");
F003D150Q.setScores(qualScores);
results = someDiffsSingleTrim.stripForward(F003D150, F003D150Q, groupIndex, false);
EXPECT_EQ(1, results[0]);
EXPECT_EQ("match", someDiffsSingleTrim.getCodeValue(results[1], 1));
EXPECT_EQ("TTCACCGTTGCCGGCGTACTCCCCAGG", F003D150.getUnaligned()); //TGGTGAAC barcode removed
EXPECT_EQ(27, F003D150Q.getLength()); //barcode removed
//nomatch option
F003D150.setAligned("TTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGG");
F003D150Q.setScores(qualScores);
results = someDiffsSingleTrim.stripForward(F003D150, F003D150Q, groupIndex, false);
EXPECT_EQ(11, results[0]);
EXPECT_EQ("noMatch", someDiffsSingleTrim.getCodeValue(results[1], 1));
}
TEST(Test_TrimOligos, SingleDirectionStripReversePrimers) {
TestTrimOligos testTrim;
testTrim.oligos.loadSingle();
//no diffs allowed
TrimOligos noDiffSingleTrim(0,0,0,testTrim.oligos.primers, testTrim.oligos.barcodes, testTrim.oligos.revPrimer); //pdiffs, bdiffs, primers, barcodes, revPrimers
Sequence F003D150("GQY1XT001ASWK1", "TATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTTATTACCGCGGCTGCTGG");
vector<int> results = noDiffSingleTrim.stripReverse(F003D150);
EXPECT_EQ(0, results[0]);
EXPECT_EQ("match", noDiffSingleTrim.getCodeValue(results[1], 0));
EXPECT_EQ("TATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTT", F003D150.getUnaligned()); //primer removed
//1 barcode diff, 2 primer diffs
TrimOligos someDiffsSingleTrim(2,0,1,testTrim.oligos.primers, testTrim.oligos.barcodes, testTrim.oligos.revPrimer); //pdiffs, bdiffs, primers, barcodes, revPrimers
F003D150.setAligned("TATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTTATTACCGCGGCTGCTCC");
results = someDiffsSingleTrim.stripReverse(F003D150);
EXPECT_EQ(2, results[0]);
EXPECT_EQ("match", someDiffsSingleTrim.getCodeValue(results[1], 2));
EXPECT_EQ("TATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTT", F003D150.getUnaligned()); //barcode removed
//nomatch option
F003D150.setAligned("TATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTTATTACCGCGGCTGCCCC");
results = someDiffsSingleTrim.stripReverse(F003D150);
EXPECT_EQ(3, results[0]);
EXPECT_EQ("noMatch", someDiffsSingleTrim.getCodeValue(results[1], 2));
}
TEST(Test_TrimOligos, SingleDirectionStripQualReversePrimers) {
TestTrimOligos testTrim;
testTrim.oligos.loadSingle();
//no diffs allowed
TrimOligos noDiffSingleTrim(0,0,0,testTrim.oligos.primers, testTrim.oligos.barcodes, testTrim.oligos.revPrimer); //pdiffs, bdiffs, primers, barcodes, revPrimers
Sequence F003D150("GQY1XT001ASWK1", "TATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTTATTACCGCGGCTGCTGG");
vector<int> qualScores(84, 38);
QualityScores F003D150Q("GQY1XT001ASWK1", qualScores); //fragment
vector<int> results = noDiffSingleTrim.stripReverse(F003D150, F003D150Q);
EXPECT_EQ(0, results[0]);
EXPECT_EQ("match", noDiffSingleTrim.getCodeValue(results[1], 0));
EXPECT_EQ("TATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTT", F003D150.getUnaligned());
EXPECT_EQ(67, F003D150Q.getLength()); //reverse removed
//1 barcode diff, 2 primer diffs
TrimOligos someDiffsSingleTrim(2,0,1,testTrim.oligos.primers, testTrim.oligos.barcodes, testTrim.oligos.revPrimer); //pdiffs, bdiffs, primers, barcodes, revPrimers
F003D150.setAligned("TATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTTATTACCGCGGCTGCTCC");
F003D150Q.setScores(qualScores);
results = someDiffsSingleTrim.stripReverse(F003D150, F003D150Q);
EXPECT_EQ(2, results[0]);
EXPECT_EQ("match", someDiffsSingleTrim.getCodeValue(results[1], 2));
EXPECT_EQ("TATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTT", F003D150.getUnaligned());
EXPECT_EQ(67, F003D150Q.getLength()); //reverse removed
//nomatch option
F003D150.setAligned("TATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTTATTACCGCGGCTGCCCC");
F003D150Q.setScores(qualScores);
results = someDiffsSingleTrim.stripReverse(F003D150);
EXPECT_EQ(3, results[0]);
EXPECT_EQ("noMatch", someDiffsSingleTrim.getCodeValue(results[1], 2));
EXPECT_EQ(84, F003D150Q.getLength()); //reverse not removed
}
TEST(Test_TrimOligos, TwoDirectionStripBarcodes) {
TestTrimOligos testTrim;
testTrim.oligos.loadPaired();
//no diffs allowed
TrimOligos noDiffTwoDirectionTrim(0,0,0,0,testTrim.oligos.ipprimers, testTrim.oligos.ipbarcodes, false); //pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, hasIndex
Sequence F05R2F_forward("F05R2F_forward" ,"CTTACATTAGATACCCGGGTAGTCCACGCAGTAAACGATGCATGCTAACTGTCAGGTGCGTTGAGCGCGGTGCGATGCAGCG");
Sequence F05R2F_reverse("F05R2F_reverse" ,"GGGTTCCCGTCAATTCATTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGAATGCTTAACGCTTTCGCTGTACCGCCC");
int groupIndex;
vector<int> results = noDiffTwoDirectionTrim.stripBarcode(F05R2F_forward, F05R2F_reverse, groupIndex); //cttac gggtt
EXPECT_EQ(8, groupIndex);
EXPECT_EQ(0, (results[0]+results[2]));
EXPECT_EQ("match", noDiffTwoDirectionTrim.getCodeValue(results[3], 0));
EXPECT_EQ("ATTAGATACCCGGGTAGTCCACGCAGTAAACGATGCATGCTAACTGTCAGGTGCGTTGAGCGCGGTGCGATGCAGCG", F05R2F_forward.getUnaligned()); //cttac barcode removed
EXPECT_EQ("CCCGTCAATTCATTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGAATGCTTAACGCTTTCGCTGTACCGCCC", F05R2F_reverse.getUnaligned()); //gggtt barcode removed
//diffs allowed
TrimOligos someDiffTwoDirectionTrim(0,1,0,0,testTrim.oligos.ipprimers, testTrim.oligos.ipbarcodes, false); //pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, hasIndex
F05R2F_forward.setAligned("CTTACATTAGATACCCGGGTAGTCCACGCAGTAAACGATGCATGCTAACTGTCAGGTGCGTTGAGCGCGGTGCGATGCAGCG");
F05R2F_reverse.setAligned("CGGTTCCCGTCAATTCATTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGAATGCTTAACGCTTTCGCTGTACCGCCC");
results = someDiffTwoDirectionTrim.stripBarcode(F05R2F_forward, F05R2F_reverse, groupIndex); //cttac gggtt
EXPECT_EQ(8, groupIndex);
EXPECT_EQ(1, (results[0]+results[2]));
EXPECT_EQ("match", someDiffTwoDirectionTrim.getCodeValue(results[3], 1));
EXPECT_EQ("ATTAGATACCCGGGTAGTCCACGCAGTAAACGATGCATGCTAACTGTCAGGTGCGTTGAGCGCGGTGCGATGCAGCG", F05R2F_forward.getUnaligned()); //cttac barcode removed
EXPECT_EQ("CCCGTCAATTCATTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGAATGCTTAACGCTTTCGCTGTACCGCCC", F05R2F_reverse.getUnaligned()); //gggtt barcode removed
F05R2F_forward.setAligned("CATACATTAGATACCCGGGTAGTCCACGCAGTAAACGATGCATGCTAACTGTCAGGTGCGTTGAGCGCGGTGCGATGCAGCG");
F05R2F_reverse.setAligned("GGGTTCCCGTCAATTCATTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGAATGCTTAACGCTTTCGCTGTACCGCCC");
results = someDiffTwoDirectionTrim.stripBarcode(F05R2F_forward, F05R2F_reverse, groupIndex); //cttac gggtt
EXPECT_EQ(8, groupIndex);
EXPECT_EQ(1, (results[0]+results[2]));
EXPECT_EQ("match", someDiffTwoDirectionTrim.getCodeValue(results[3], 1));
EXPECT_EQ("ATTAGATACCCGGGTAGTCCACGCAGTAAACGATGCATGCTAACTGTCAGGTGCGTTGAGCGCGGTGCGATGCAGCG", F05R2F_forward.getUnaligned()); //cttac barcode removed
EXPECT_EQ("CCCGTCAATTCATTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGAATGCTTAACGCTTTCGCTGTACCGCCC", F05R2F_reverse.getUnaligned()); //gggtt barcode removed
F05R2F_forward.setAligned("GTTACATTAGATACCCGGGTAGTCCACGCAGTAAACGATGCATGCTAACTGTCAGGTGCGTTGAGCGCGGTGCGATGCAGCG");
F05R2F_reverse.setAligned("CCGTTCCCGTCAATTCATTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGAATGCTTAACGCTTTCGCTGTACCGCCC");
results = someDiffTwoDirectionTrim.stripBarcode(F05R2F_forward, F05R2F_reverse, groupIndex); //cttac gggtt
EXPECT_EQ(3, (results[0]+results[2]));
EXPECT_EQ("noMatch", someDiffTwoDirectionTrim.getCodeValue(results[3], 1));
EXPECT_EQ("GTTACATTAGATACCCGGGTAGTCCACGCAGTAAACGATGCATGCTAACTGTCAGGTGCGTTGAGCGCGGTGCGATGCAGCG", F05R2F_forward.getUnaligned()); //cttac barcode removed
EXPECT_EQ("CCGTTCCCGTCAATTCATTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGAATGCTTAACGCTTTCGCTGTACCGCCC", F05R2F_reverse.getUnaligned()); //gggtt barcode removed
}
TEST(Test_TrimOligos, TwoDirectionStripQualBarcodes) {
TestTrimOligos testTrim;
testTrim.oligos.loadPaired();
//no diffs allowed
TrimOligos noDiffTwoDirectionTrim(0,0,0,0,testTrim.oligos.ipprimers, testTrim.oligos.ipbarcodes, false); //pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, hasIndex
Sequence F05R2F_forward("F05R2F_forward" ,"CTTACATTAGATACCCGGGTAGTCCACGCAGTAAACGATGCATGCTAACTGTCAGGTGCGTTGAGCGCGGTGCGATGCAGCG");
Sequence F05R2F_reverse("F05R2F_reverse" ,"GGGTTCCCGTCAATTCATTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGAATGCTTAACGCTTTCGCTGTACCGCCC");
vector<int> qualScores(82, 38);
QualityScores F05R2F_forwardQual("F05R2F_forward", qualScores); //fragment
QualityScores F05R2F_reverseQual("F05R2F_reverse", qualScores); //fragment
int groupIndex;
vector<int> results = noDiffTwoDirectionTrim.stripBarcode(F05R2F_forward, F05R2F_reverse, F05R2F_forwardQual, F05R2F_reverseQual, groupIndex); //cttac gggtt
EXPECT_EQ(8, groupIndex);
EXPECT_EQ(0, (results[0]+results[2]));
EXPECT_EQ("match", noDiffTwoDirectionTrim.getCodeValue(results[3], 0));
EXPECT_EQ("ATTAGATACCCGGGTAGTCCACGCAGTAAACGATGCATGCTAACTGTCAGGTGCGTTGAGCGCGGTGCGATGCAGCG", F05R2F_forward.getUnaligned()); //cttac barcode removed
EXPECT_EQ("CCCGTCAATTCATTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGAATGCTTAACGCTTTCGCTGTACCGCCC", F05R2F_reverse.getUnaligned()); //gggtt barcode removed
EXPECT_EQ(77, F05R2F_forwardQual.getLength()); //barcode removed
EXPECT_EQ(77, F05R2F_reverseQual.getLength()); //barcode removed
//diffs allowed
TrimOligos someDiffTwoDirectionTrim(0,1,0,0,testTrim.oligos.ipprimers, testTrim.oligos.ipbarcodes, false); //pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, hasIndex
F05R2F_forward.setAligned("CTTACATTAGATACCCGGGTAGTCCACGCAGTAAACGATGCATGCTAACTGTCAGGTGCGTTGAGCGCGGTGCGATGCAGCG");
F05R2F_reverse.setAligned("CGGTTCCCGTCAATTCATTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGAATGCTTAACGCTTTCGCTGTACCGCCC");
F05R2F_forwardQual.setScores(qualScores);
F05R2F_reverseQual.setScores(qualScores);
results = someDiffTwoDirectionTrim.stripBarcode(F05R2F_forward, F05R2F_reverse, F05R2F_forwardQual, F05R2F_reverseQual, groupIndex); //cttac gggtt
EXPECT_EQ(8, groupIndex);
EXPECT_EQ(1, (results[0]+results[2]));
EXPECT_EQ("match", someDiffTwoDirectionTrim.getCodeValue(results[3], 1));
EXPECT_EQ("ATTAGATACCCGGGTAGTCCACGCAGTAAACGATGCATGCTAACTGTCAGGTGCGTTGAGCGCGGTGCGATGCAGCG", F05R2F_forward.getUnaligned()); //cttac barcode removed
EXPECT_EQ("CCCGTCAATTCATTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGAATGCTTAACGCTTTCGCTGTACCGCCC", F05R2F_reverse.getUnaligned()); //gggtt barcode removed
EXPECT_EQ(77, F05R2F_forwardQual.getLength()); //barcode removed
EXPECT_EQ(77, F05R2F_reverseQual.getLength()); //barcode removed
F05R2F_forward.setAligned("CATACATTAGATACCCGGGTAGTCCACGCAGTAAACGATGCATGCTAACTGTCAGGTGCGTTGAGCGCGGTGCGATGCAGCG");
F05R2F_reverse.setAligned("GGGTTCCCGTCAATTCATTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGAATGCTTAACGCTTTCGCTGTACCGCCC");
F05R2F_forwardQual.setScores(qualScores);
F05R2F_reverseQual.setScores(qualScores);
results = someDiffTwoDirectionTrim.stripBarcode(F05R2F_forward, F05R2F_reverse, F05R2F_forwardQual, F05R2F_reverseQual, groupIndex); //cttac gggtt
EXPECT_EQ(8, groupIndex);
EXPECT_EQ(1, (results[0]+results[2]));
EXPECT_EQ("match", someDiffTwoDirectionTrim.getCodeValue(results[3], 1));
EXPECT_EQ("ATTAGATACCCGGGTAGTCCACGCAGTAAACGATGCATGCTAACTGTCAGGTGCGTTGAGCGCGGTGCGATGCAGCG", F05R2F_forward.getUnaligned()); //cttac barcode removed
EXPECT_EQ("CCCGTCAATTCATTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGAATGCTTAACGCTTTCGCTGTACCGCCC", F05R2F_reverse.getUnaligned()); //gggtt barcode removed
EXPECT_EQ(77, F05R2F_forwardQual.getLength()); //barcode removed
EXPECT_EQ(77, F05R2F_reverseQual.getLength()); //barcode removed
F05R2F_forward.setAligned("GTTACATTAGATACCCGGGTAGTCCACGCAGTAAACGATGCATGCTAACTGTCAGGTGCGTTGAGCGCGGTGCGATGCAGCG");
F05R2F_reverse.setAligned("CCGTTCCCGTCAATTCATTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGAATGCTTAACGCTTTCGCTGTACCGCCC");
F05R2F_forwardQual.setScores(qualScores);
F05R2F_reverseQual.setScores(qualScores);
results = someDiffTwoDirectionTrim.stripBarcode(F05R2F_forward, F05R2F_reverse, F05R2F_forwardQual, F05R2F_reverseQual, groupIndex); //cttac gggtt
EXPECT_EQ(3, (results[0]+results[2]));
EXPECT_EQ("noMatch", someDiffTwoDirectionTrim.getCodeValue(results[3], 1));
EXPECT_EQ("GTTACATTAGATACCCGGGTAGTCCACGCAGTAAACGATGCATGCTAACTGTCAGGTGCGTTGAGCGCGGTGCGATGCAGCG", F05R2F_forward.getUnaligned()); //cttac barcode removed
EXPECT_EQ("CCGTTCCCGTCAATTCATTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGAATGCTTAACGCTTTCGCTGTACCGCCC", F05R2F_reverse.getUnaligned()); //gggtt barcode removed
EXPECT_EQ(82, F05R2F_forwardQual.getLength()); //barcode removed
EXPECT_EQ(82, F05R2F_reverseQual.getLength()); //barcode removed
}
TEST(Test_TrimOligos, TwoDirectionStripPrimers) {
TestTrimOligos testTrim;
testTrim.oligos.loadPaired();
//no diffs allowed
TrimOligos noDiffTwoDirectionTrim(0,0,0,0,testTrim.oligos.ipprimers, testTrim.oligos.ipbarcodes, false); //pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, hasIndex
Sequence F05R2F_forward("F05R2F_forward" ,"ATTAGATACCCGGGTAGTCCACGCAGTAAACGATGCATGCTAACTGTCAGGTGCGTTGAGCGCGGTGCGATGCAGCG");
Sequence F05R2F_reverse("F05R2F_reverse" ,"CCCGTCAATTCATTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGAATGCTTAACGCTTTCGCTGTACCGCCC");
int groupIndex; vector<int> results = noDiffTwoDirectionTrim.stripForward(F05R2F_forward, F05R2F_reverse, groupIndex);
EXPECT_EQ(1, groupIndex);
EXPECT_EQ(0, (results[0]+results[2]));
EXPECT_EQ("match", noDiffTwoDirectionTrim.getCodeValue(results[3], 0));
EXPECT_EQ("ACGCAGTAAACGATGCATGCTAACTGTCAGGTGCGTTGAGCGCGGTGCGATGCAGCG", F05R2F_forward.getUnaligned());
EXPECT_EQ("TTCACCGTTGCCGGCGTACTCCCCAGGTGGAATGCTTAACGCTTTCGCTGTACCGCCC", F05R2F_reverse.getUnaligned());
//allows for 2 diffs on each end - the command code decides pass/fail
TrimOligos someDiffTwoDirectionTrim(2,0,0,0,testTrim.oligos.ipprimers, testTrim.oligos.ipbarcodes, false); //pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, hasIndex
F05R2F_forward.setAligned("TTTAGATACCCGGGTAGTCCACGCAGTAAACGATGCATGCTAACTGTCAGGTGCGTTGAGCGCGGTGCGATGCAGCG");
F05R2F_reverse.setAligned("GCCGTCAATTCATTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGAATGCTTAACGCTTTCGCTGTACCGCCC");
results = someDiffTwoDirectionTrim.stripForward(F05R2F_forward, F05R2F_reverse, groupIndex);
EXPECT_EQ(1, groupIndex);
EXPECT_EQ(2, (results[0]+results[2]));
EXPECT_EQ("match", someDiffTwoDirectionTrim.getCodeValue(results[3], 2));
EXPECT_EQ("match", someDiffTwoDirectionTrim.getCodeValue(results[1], 2));
EXPECT_EQ("ACGCAGTAAACGATGCATGCTAACTGTCAGGTGCGTTGAGCGCGGTGCGATGCAGCG", F05R2F_forward.getUnaligned());
EXPECT_EQ("TTCACCGTTGCCGGCGTACTCCCCAGGTGGAATGCTTAACGCTTTCGCTGTACCGCCC", F05R2F_reverse.getUnaligned());
//allows for 2 diffs on each end - the command code decides pass/fail
F05R2F_forward.setAligned("TTTTGATACCCGGGTAGTCCACGCAGTAAACGATGCATGCTAACTGTCAGGTGCGTTGAGCGCGGTGCGATGCAGCG");
F05R2F_reverse.setAligned("GGCGTGAATTCATTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGAATGCTTAACGCTTTCGCTGTACCGCCC");
results = someDiffTwoDirectionTrim.stripForward(F05R2F_forward, F05R2F_reverse, groupIndex);
EXPECT_EQ(1, groupIndex);
EXPECT_EQ(5, (results[0]+results[2]));
EXPECT_EQ("noMatch", someDiffTwoDirectionTrim.getCodeValue(results[3], 2));
EXPECT_EQ("noMatch", someDiffTwoDirectionTrim.getCodeValue(results[1], 2));
EXPECT_EQ("TTTTGATACCCGGGTAGTCCACGCAGTAAACGATGCATGCTAACTGTCAGGTGCGTTGAGCGCGGTGCGATGCAGCG", F05R2F_forward.getUnaligned());
EXPECT_EQ("GGCGTGAATTCATTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGAATGCTTAACGCTTTCGCTGTACCGCCC", F05R2F_reverse.getUnaligned());
}
TEST(Test_TrimOligos, TwoDirectionStripQualPrimers) {
TestTrimOligos testTrim;
testTrim.oligos.loadPaired();
//no diffs allowed
TrimOligos noDiffTwoDirectionTrim(0,0,0,0,testTrim.oligos.ipprimers, testTrim.oligos.ipbarcodes, false); //pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, hasIndex
Sequence F05R2F_forward("F05R2F_forward" ,"ATTAGATACCCGGGTAGTCCACGCAGTAAACGATGCATGCTAACTGTCAGGTGCGTTGAGCGCGGTGCGATGCAGCG");
vector<int> qualScores(77, 38);
QualityScores F05R2F_forwardQual("F05R2F_forward", qualScores); //fragment
Sequence F05R2F_reverse("F05R2F_reverse" ,"CCCGTCAATTCATTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGAATGCTTAACGCTTTCGCTGTACCGCCC");
QualityScores F05R2F_reverseQual("F05R2F_reverse", qualScores); //fragment
int groupIndex; vector<int> results = noDiffTwoDirectionTrim.stripForward(F05R2F_forward, F05R2F_reverse, F05R2F_forwardQual, F05R2F_reverseQual, groupIndex);
EXPECT_EQ(1, groupIndex);
EXPECT_EQ(0, (results[0]+results[2]));
EXPECT_EQ("match", noDiffTwoDirectionTrim.getCodeValue(results[3], 0));
EXPECT_EQ("ACGCAGTAAACGATGCATGCTAACTGTCAGGTGCGTTGAGCGCGGTGCGATGCAGCG", F05R2F_forward.getUnaligned());
EXPECT_EQ("TTCACCGTTGCCGGCGTACTCCCCAGGTGGAATGCTTAACGCTTTCGCTGTACCGCCC", F05R2F_reverse.getUnaligned());
EXPECT_EQ(57, F05R2F_forwardQual.getLength()); //primer removed
EXPECT_EQ(58, F05R2F_reverseQual.getLength()); //primer removed
//allows for 2 diffs on each end - the command code decides pass/fail
TrimOligos someDiffTwoDirectionTrim(2,0,0,0,testTrim.oligos.ipprimers, testTrim.oligos.ipbarcodes, false); //pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, hasIndex
F05R2F_forward.setAligned("TTTAGATACCCGGGTAGTCCACGCAGTAAACGATGCATGCTAACTGTCAGGTGCGTTGAGCGCGGTGCGATGCAGCG");
F05R2F_reverse.setAligned("GCCGTCAATTCATTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGAATGCTTAACGCTTTCGCTGTACCGCCC");
F05R2F_forwardQual.setScores(qualScores);
F05R2F_reverseQual.setScores(qualScores);
results = someDiffTwoDirectionTrim.stripForward(F05R2F_forward, F05R2F_reverse, F05R2F_forwardQual, F05R2F_reverseQual, groupIndex);
EXPECT_EQ(1, groupIndex);
EXPECT_EQ(2, (results[0]+results[2]));
EXPECT_EQ("match", someDiffTwoDirectionTrim.getCodeValue(results[3], 2));
EXPECT_EQ("match", someDiffTwoDirectionTrim.getCodeValue(results[1], 2));
EXPECT_EQ("ACGCAGTAAACGATGCATGCTAACTGTCAGGTGCGTTGAGCGCGGTGCGATGCAGCG", F05R2F_forward.getUnaligned());
EXPECT_EQ("TTCACCGTTGCCGGCGTACTCCCCAGGTGGAATGCTTAACGCTTTCGCTGTACCGCCC", F05R2F_reverse.getUnaligned());
EXPECT_EQ(57, F05R2F_forwardQual.getLength()); //primer removed
EXPECT_EQ(58, F05R2F_reverseQual.getLength()); //primer removed
//allows for 2 diffs on each end - the command code decides pass/fail
F05R2F_forward.setAligned("TTTTGATACCCGGGTAGTCCACGCAGTAAACGATGCATGCTAACTGTCAGGTGCGTTGAGCGCGGTGCGATGCAGCG");
F05R2F_reverse.setAligned("GGCGTGAATTCATTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGAATGCTTAACGCTTTCGCTGTACCGCCC");
F05R2F_forwardQual.setScores(qualScores);
F05R2F_reverseQual.setScores(qualScores);
results = someDiffTwoDirectionTrim.stripForward(F05R2F_forward, F05R2F_reverse, F05R2F_forwardQual, F05R2F_reverseQual, groupIndex);
EXPECT_EQ(1, groupIndex);
EXPECT_EQ(5, (results[0]+results[2]));
EXPECT_EQ("noMatch", someDiffTwoDirectionTrim.getCodeValue(results[3], 2));
EXPECT_EQ("noMatch", someDiffTwoDirectionTrim.getCodeValue(results[1], 2));
EXPECT_EQ("TTTTGATACCCGGGTAGTCCACGCAGTAAACGATGCATGCTAACTGTCAGGTGCGTTGAGCGCGGTGCGATGCAGCG", F05R2F_forward.getUnaligned());
EXPECT_EQ("GGCGTGAATTCATTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGAATGCTTAACGCTTTCGCTGTACCGCCC", F05R2F_reverse.getUnaligned());
EXPECT_EQ(77, F05R2F_forwardQual.getLength()); //primer removed
EXPECT_EQ(77, F05R2F_reverseQual.getLength()); //primer removed
}
TEST(Test_TrimOligos, SingleDirectionStripLinkers) {
TestTrimOligos testTrim;
testTrim.oligos.loadSingle();
//no diffs allowed
TrimOligos noDiffSingleTrim(0,0,0,0,testTrim.oligos.primers, testTrim.oligos.barcodes, testTrim.oligos.revPrimer, testTrim.oligos.linker, testTrim.oligos.spacer); //pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, revPrimers, linker, spacer
Sequence F003D150("GQY1XT001ASWK1", "TGACTATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTTATTACCGCGGCTGCTGG");
int result = noDiffSingleTrim.stripLinker(F003D150);
EXPECT_EQ(0, result);
EXPECT_EQ("TATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTTATTACCGCGGCTGCTGG", F003D150.getUnaligned());
//1 linker diff
TrimOligos someDiffsSingleTrim(0,0,1,0,testTrim.oligos.primers, testTrim.oligos.barcodes, testTrim.oligos.revPrimer, testTrim.oligos.linker, testTrim.oligos.spacer);
F003D150.setAligned("AGACTATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTTATTACCGCGGCTGCTGG");
result = someDiffsSingleTrim.stripLinker(F003D150);
EXPECT_EQ(1, result);
EXPECT_EQ("TATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTTATTACCGCGGCTGCTGG", F003D150.getUnaligned());
//nomatch option
F003D150.setAligned("TTCATATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTTATTACCGCGGCTGCTGG");
result = someDiffsSingleTrim.stripLinker(F003D150);
EXPECT_EQ(7, result);
EXPECT_EQ("TTCATATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTTATTACCGCGGCTGCTGG", F003D150.getUnaligned());
}
TEST(Test_TrimOligos, SingleDirectionStripQualLinkers) {
TestTrimOligos testTrim;
testTrim.oligos.loadSingle();
//no diffs allowed
TrimOligos noDiffSingleTrim(0,0,0,0,testTrim.oligos.primers, testTrim.oligos.barcodes, testTrim.oligos.revPrimer, testTrim.oligos.linker, testTrim.oligos.spacer); //pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, revPrimers, linker, spacer
Sequence F003D150("GQY1XT001ASWK1", "TGACTATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTTATTACCGCGGCTGCTGG");
vector<int> qualScores(88, 38);
QualityScores F003D150Q("F003D150Q", qualScores); //fragment
int result = noDiffSingleTrim.stripLinker(F003D150, F003D150Q);
EXPECT_EQ(0, result);
EXPECT_EQ("TATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTTATTACCGCGGCTGCTGG", F003D150.getUnaligned());
EXPECT_EQ(84, F003D150Q.getLength());
//1 linker diff
TrimOligos someDiffsSingleTrim(0,0,1,0,testTrim.oligos.primers, testTrim.oligos.barcodes, testTrim.oligos.revPrimer, testTrim.oligos.linker, testTrim.oligos.spacer);
F003D150.setAligned("AGACTATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTTATTACCGCGGCTGCTGG");
F003D150Q.setScores(qualScores);
result = someDiffsSingleTrim.stripLinker(F003D150, F003D150Q);
EXPECT_EQ(1, result);
EXPECT_EQ("TATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTTATTACCGCGGCTGCTGG", F003D150.getUnaligned());
EXPECT_EQ(84, F003D150Q.getLength());
//nomatch option
F003D150.setAligned("TTCATATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTTATTACCGCGGCTGCTGG");
F003D150Q.setScores(qualScores);
result = someDiffsSingleTrim.stripLinker(F003D150, F003D150Q);
EXPECT_EQ(7, result);
EXPECT_EQ("TTCATATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTTATTACCGCGGCTGCTGG", F003D150.getUnaligned());
EXPECT_EQ(88, F003D150Q.getLength());
}
TEST(Test_TrimOligos, SingleDirectionStripSpacers) { //CACTG, CCAAC
TestTrimOligos testTrim;
testTrim.oligos.loadSingle();
//no diffs allowed
TrimOligos noDiffSingleTrim(0,0,0,0,testTrim.oligos.primers, testTrim.oligos.barcodes, testTrim.oligos.revPrimer, testTrim.oligos.linker, testTrim.oligos.spacer); //pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, revPrimers, linker, spacer
Sequence F003D150("GQY1XT001ASWK1", "CCAACTATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTTATTACCGCGGCTGCTGG");
int result = noDiffSingleTrim.stripSpacer(F003D150);
EXPECT_EQ(0, result);
EXPECT_EQ("TATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTTATTACCGCGGCTGCTGG", F003D150.getUnaligned());
//1 linker diff
TrimOligos someDiffsSingleTrim(0,0,0,1,testTrim.oligos.primers, testTrim.oligos.barcodes, testTrim.oligos.revPrimer, testTrim.oligos.linker, testTrim.oligos.spacer);
F003D150.setAligned("CAGTGTATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTTATTACCGCGGCTGCTGG");
result = someDiffsSingleTrim.stripSpacer(F003D150);
EXPECT_EQ(1, result);
EXPECT_EQ("TATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTTATTACCGCGGCTGCTGG", F003D150.getUnaligned());
//nomatch option
F003D150.setAligned("CGTACTATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTTATTACCGCGGCTGCTGG");
result = someDiffsSingleTrim.stripSpacer(F003D150);
EXPECT_EQ(2, result);
EXPECT_EQ("CGTACTATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTTATTACCGCGGCTGCTGG", F003D150.getUnaligned());
}
TEST(Test_TrimOligos, SingleDirectionFindForward) { //CCGTCAATTCMTTTRAGT
TestTrimOligos testTrim;
testTrim.oligos.loadSingle();
//no diffs allowed - unaligned
TrimOligos noDiffSingleTrim(0,0,0,testTrim.oligos.primers, testTrim.oligos.barcodes, nullVector); //pdiffs, rpdiffs, bdiffs, primers, barcodes, revPrimers
Sequence F003D150("GQY1XT001ASWK1", "CCAACCCGTCAATTCMTTTRAGTTATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTTATTACCGCGGCTGCTGG");
int primerStart, primerEnd;
vector<int> results = noDiffSingleTrim.findForward(F003D150, primerStart, primerEnd);
EXPECT_EQ(5, primerStart);
EXPECT_EQ(23, primerEnd);
EXPECT_EQ("match", noDiffSingleTrim.getCodeValue(results[1], 0));
string primerRemoved = (F003D150.getUnaligned().substr(primerEnd));
string primerKept = (F003D150.getUnaligned().substr(primerStart));
EXPECT_EQ("CCGTCAATTCMTTTRAGTTATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTTATTACCGCGGCTGCTGG", primerKept);
EXPECT_EQ("TATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTTATTACCGCGGCTGCTGG", primerRemoved);
//no diffs allowed - aligned gap between primer and sequence
F003D150.setAligned("......CC--AACCCGTCAATTCMTTTRAGT-TATCTATGC--ATTTCACCG-C-T-ACACCACGCATTCC--GCATACTTCTCGCCCACTC--GAGCCCGGCAGTTTATTACC-GCGGC-GCTGG.....");
Sequence F003D150_1("GQY1XT001ASWK1", "......CC--AACCCGTCAATTCMTTTRAGT-TATCTATGC--ATTTCACCG-C-T-ACACCACGCATTCC--GCATACTTCTCGCCCACTC--GAGCCCGGCAGTTTATTACC-GCGGC-GCTGG.....");
Sequence F003D150_2("GQY1XT001ASWK1", "......CC--AACCCGTCAATTCMTTTRAGT-TATCTATGC--ATTTCACCG-C-T-ACACCACGCATTCC--GCATACTTCTCGCCCACTC--GAGCCCGGCAGTTTATTACC-GCGGC-GCTGG.....");
int countBases = 0;
string temp = F003D150.getAligned();
map<int, int> mapAligned;
for (int i = 0; i < temp.length(); i++) {
if (isalpha(temp[i])) { mapAligned[countBases] = i; countBases++; } //maps location in unaligned -> location in aligned.
} //ie. the 3rd base may be at spot 10 in the alignment
results = noDiffSingleTrim.findForward(F003D150, primerStart, primerEnd);
EXPECT_EQ(5, primerStart);
EXPECT_EQ(23, primerEnd);
F003D150_1.filterToPos(mapAligned[primerEnd-1]+1);
string primerRemovedKeepDots = F003D150_1.getAligned();
primerRemoved = F003D150.getAligned().substr(mapAligned[primerEnd-1]+1);
primerKept = F003D150.getAligned().substr(mapAligned[primerStart]);
F003D150_2.filterToPos(mapAligned[primerStart]);
string primerKeptKeepDots = F003D150_2.getAligned();
EXPECT_EQ("CCGTCAATTCMTTTRAGT-TATCTATGC--ATTTCACCG-C-T-ACACCACGCATTCC--GCATACTTCTCGCCCACTC--GAGCCCGGCAGTTTATTACC-GCGGC-GCTGG.....", primerKept);
EXPECT_EQ("-TATCTATGC--ATTTCACCG-C-T-ACACCACGCATTCC--GCATACTTCTCGCCCACTC--GAGCCCGGCAGTTTATTACC-GCGGC-GCTGG.....", primerRemoved);
EXPECT_EQ(".............CCGTCAATTCMTTTRAGT-TATCTATGC--ATTTCACCG-C-T-ACACCACGCATTCC--GCATACTTCTCGCCCACTC--GAGCCCGGCAGTTTATTACC-GCGGC-GCTGG.....", primerKeptKeepDots);
EXPECT_EQ("................................TATCTATGC--ATTTCACCG-C-T-ACACCACGCATTCC--GCATACTTCTCGCCCACTC--GAGCCCGGCAGTTTATTACC-GCGGC-GCTGG.....", primerRemovedKeepDots);
//no diffs allowed - aligned no gap between primer and sequence
F003D150.setAligned("......CC--AACCCGTCAATTCMTTTRAGTTATCTATGC--ATTTCACCG-C-T-ACACCACGCATTCC--GCATACTTCTCGCCCACTC--GAGCCCGGCAGTTTATTACC-GCGGC-GCTGG.....");
F003D150_1.setAligned("......CC--AACCCGTCAATTCMTTTRAGTTATCTATGC--ATTTCACCG-C-T-ACACCACGCATTCC--GCATACTTCTCGCCCACTC--GAGCCCGGCAGTTTATTACC-GCGGC-GCTGG.....");
F003D150_2.setAligned("......CC--AACCCGTCAATTCMTTTRAGTTATCTATGC--ATTTCACCG-C-T-ACACCACGCATTCC--GCATACTTCTCGCCCACTC--GAGCCCGGCAGTTTATTACC-GCGGC-GCTGG.....");
countBases = 0; temp = F003D150.getAligned(); mapAligned.clear();
for (int i = 0; i < temp.length(); i++) { if (isalpha(temp[i])) { mapAligned[countBases] = i; countBases++; } }
results = noDiffSingleTrim.findForward(F003D150, primerStart, primerEnd);
EXPECT_EQ(5, primerStart);
EXPECT_EQ(23, primerEnd);
F003D150_1.filterToPos(mapAligned[primerEnd-1]+1);
primerRemovedKeepDots = F003D150_1.getAligned();
primerRemoved = F003D150.getAligned().substr(mapAligned[primerEnd-1]+1);
primerKept = F003D150.getAligned().substr(mapAligned[primerStart]);
F003D150_2.filterToPos(mapAligned[primerStart]);
primerKeptKeepDots = F003D150_2.getAligned();
EXPECT_EQ("CCGTCAATTCMTTTRAGTTATCTATGC--ATTTCACCG-C-T-ACACCACGCATTCC--GCATACTTCTCGCCCACTC--GAGCCCGGCAGTTTATTACC-GCGGC-GCTGG.....", primerKept);
EXPECT_EQ("TATCTATGC--ATTTCACCG-C-T-ACACCACGCATTCC--GCATACTTCTCGCCCACTC--GAGCCCGGCAGTTTATTACC-GCGGC-GCTGG.....", primerRemoved);
EXPECT_EQ(".............CCGTCAATTCMTTTRAGTTATCTATGC--ATTTCACCG-C-T-ACACCACGCATTCC--GCATACTTCTCGCCCACTC--GAGCCCGGCAGTTTATTACC-GCGGC-GCTGG.....", primerKeptKeepDots);
EXPECT_EQ("...............................TATCTATGC--ATTTCACCG-C-T-ACACCACGCATTCC--GCATACTTCTCGCCCACTC--GAGCCCGGCAGTTTATTACC-GCGGC-GCTGG.....", primerRemovedKeepDots);
//2 diffs allowed //CCGTCAATTCMTTTRAGT
TrimOligos someDiffSingleTrim(2,0,0,testTrim.oligos.primers, testTrim.oligos.barcodes, nullVector); //pdiffs, rpdiffs, bdiffs, primers, barcodes, revPrimers
//CCGTCAATTCMTTTRAGT
F003D150.setAligned("......CC--AACCCGTGTATTCMTTTRAGTTATCTATGC--ATTTCACCG-C-T-ACACCACGCATTCC--GCATACTTCTCGCCCACTC--GAGCCCGGCAGTTTATTACC-GCGGC-GCTGG.....");
F003D150_1.setAligned("......CC--AACCCGTGTATTCMTTTRAGTTATCTATGC--ATTTCACCG-C-T-ACACCACGCATTCC--GCATACTTCTCGCCCACTC--GAGCCCGGCAGTTTATTACC-GCGGC-GCTGG.....");
F003D150_2.setAligned("......CC--AACCCGTGTATTCMTTTRAGTTATCTATGC--ATTTCACCG-C-T-ACACCACGCATTCC--GCATACTTCTCGCCCACTC--GAGCCCGGCAGTTTATTACC-GCGGC-GCTGG.....");
results = someDiffSingleTrim.findForward(F003D150, primerStart, primerEnd);
EXPECT_EQ(5, primerStart);
EXPECT_EQ(23, primerEnd);
F003D150_1.filterToPos(mapAligned[primerEnd-1]+1);
primerRemovedKeepDots = F003D150_1.getAligned();
primerRemoved = F003D150.getAligned().substr(mapAligned[primerEnd-1]+1);
primerKept = F003D150.getAligned().substr(mapAligned[primerStart]);
F003D150_2.filterToPos(mapAligned[primerStart]);
primerKeptKeepDots = F003D150_2.getAligned();
EXPECT_EQ("CCGTGTATTCMTTTRAGTTATCTATGC--ATTTCACCG-C-T-ACACCACGCATTCC--GCATACTTCTCGCCCACTC--GAGCCCGGCAGTTTATTACC-GCGGC-GCTGG.....", primerKept);
EXPECT_EQ("TATCTATGC--ATTTCACCG-C-T-ACACCACGCATTCC--GCATACTTCTCGCCCACTC--GAGCCCGGCAGTTTATTACC-GCGGC-GCTGG.....", primerRemoved);
EXPECT_EQ(".............CCGTGTATTCMTTTRAGTTATCTATGC--ATTTCACCG-C-T-ACACCACGCATTCC--GCATACTTCTCGCCCACTC--GAGCCCGGCAGTTTATTACC-GCGGC-GCTGG.....", primerKeptKeepDots);
EXPECT_EQ("...............................TATCTATGC--ATTTCACCG-C-T-ACACCACGCATTCC--GCATACTTCTCGCCCACTC--GAGCCCGGCAGTTTATTACC-GCGGC-GCTGG.....", primerRemovedKeepDots);
//CCGTCAATTCMTTTRAGT
F003D150.setAligned("......CC--AACCCGTGTTTTCMTTTRAGTTATCTATGC--ATTTCACCG-C-T-ACACCACGCATTCC--GCATACTTCTCGCCCACTC--GAGCCCGGCAGTTTATTACC-GCGGC-GCTGG.....");
results = someDiffSingleTrim.findForward(F003D150, primerStart, primerEnd);
EXPECT_EQ(0, primerStart); //indicates failure
EXPECT_EQ(0, primerEnd); //indicates failure
EXPECT_EQ("......CC--AACCCGTGTTTTCMTTTRAGTTATCTATGC--ATTTCACCG-C-T-ACACCACGCATTCC--GCATACTTCTCGCCCACTC--GAGCCCGGCAGTTTATTACC-GCGGC-GCTGG.....", F003D150.getAligned());
}
TEST(Test_TrimOligos, SingleDirectionFindReverse) { //ATTACCGCGGCTGCTGG
TestTrimOligos testTrim;
testTrim.oligos.loadSingle();
//no diffs allowed - unaligned
TrimOligos noDiffSingleTrim(0,0,0,testTrim.oligos.primers, testTrim.oligos.barcodes, testTrim.oligos.revPrimer); //pdiffs, rpdiffs, bdiffs, primers, barcodes, revPrimers
//ATTACCGCGGCTGCTGG
Sequence F003D150("GQY1XT001ASWK1", "TATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTTATTACCGCGGCTGCTGGATTACCGCGGCTGCTGGTGGTCCAGT");
int primerStart, primerEnd;
vector<int> results = noDiffSingleTrim.findReverse(F003D150, primerStart, primerEnd);
EXPECT_EQ(84, primerStart);
EXPECT_EQ(101, primerEnd);
EXPECT_EQ("match", noDiffSingleTrim.getCodeValue(results[1], 0));
string primerRemoved = (F003D150.getUnaligned().substr(0, primerStart));
string primerKept = (F003D150.getUnaligned().substr(0, primerEnd));
EXPECT_EQ("TATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTTATTACCGCGGCTGCTGGATTACCGCGGCTGCTGG", primerKept);
EXPECT_EQ("TATCTATGCATTTCACCGCTACACCACGCATTCCGCATACTTCTCGCCCACTCGAGCCCGGCAGTTTATTACCGCGGCTGCTGG", primerRemoved);
//no diffs allowed - aligned gap between primer and sequence ATTACCGCGGCTGCTGG
F003D150.setAligned("......CC--AACCCGTCAATTCMTTTRAGT-TATCTATGC--ATTTCACCG-C-T-ACACCACGCATTCC--GCATACTTCTCGCCCACTC-ATTACCGCGGCTGCTGG-GAGCCCGGCAGTTTATTACC-GCGGC-GCTGG.....");
Sequence F003D150_1("GQY1XT001ASWK1", "......CC--AACCCGTCAATTCMTTTRAGT-TATCTATGC--ATTTCACCG-C-T-ACACCACGCATTCC--GCATACTTCTCGCCCACTC-ATTACCGCGGCTGCTGG-GAGCCCGGCAGTTTATTACC-GCGGC-GCTGG.....");
Sequence F003D150_2("GQY1XT001ASWK1", "......CC--AACCCGTCAATTCMTTTRAGT-TATCTATGC--ATTTCACCG-C-T-ACACCACGCATTCC--GCATACTTCTCGCCCACTC-ATTACCGCGGCTGCTGG-GAGCCCGGCAGTTTATTACC-GCGGC-GCTGG.....");
int countBases = 0;
string temp = F003D150.getAligned();
map<int, int> mapAligned;
for (int i = 0; i < temp.length(); i++) {
if (isalpha(temp[i])) { mapAligned[countBases] = i; countBases++; } //maps location in unaligned -> location in aligned.
} //ie. the 3rd base may be at spot 10 in the alignment
results = noDiffSingleTrim.findReverse(F003D150, primerStart, primerEnd);
EXPECT_EQ(76, primerStart);
EXPECT_EQ(93, primerEnd);
F003D150_1.filterFromPos(mapAligned[primerStart]);
string primerRemovedKeepDots = F003D150_1.getAligned();
primerRemoved = F003D150.getAligned().substr(0, mapAligned[primerStart]);
primerKept = F003D150.getAligned().substr(0, mapAligned[primerEnd-1]+1);
F003D150_2.filterFromPos(mapAligned[primerEnd-1]+1);
string primerKeptKeepDots = F003D150_2.getAligned();
EXPECT_EQ("......CC--AACCCGTCAATTCMTTTRAGT-TATCTATGC--ATTTCACCG-C-T-ACACCACGCATTCC--GCATACTTCTCGCCCACTC-ATTACCGCGGCTGCTGG", primerKept);
EXPECT_EQ("......CC--AACCCGTCAATTCMTTTRAGT-TATCTATGC--ATTTCACCG-C-T-ACACCACGCATTCC--GCATACTTCTCGCCCACTC-ATTACCGCGGCTGCTGG......................................", primerKeptKeepDots);
EXPECT_EQ("......CC--AACCCGTCAATTCMTTTRAGT-TATCTATGC--ATTTCACCG-C-T-ACACCACGCATTCC--GCATACTTCTCGCCCACTC-", primerRemoved);
EXPECT_EQ("......CC--AACCCGTCAATTCMTTTRAGT-TATCTATGC--ATTTCACCG-C-T-ACACCACGCATTCC--GCATACTTCTCGCCCACTC-.......................................................", primerRemovedKeepDots);
//2 diffs allowed
TrimOligos someDiffSingleTrim(0,2,0,testTrim.oligos.primers, testTrim.oligos.barcodes, testTrim.oligos.revPrimer); //pdiffs, bdiffs, primers, barcodes, revPrimers
//ATTACCGCGGCTGCTGG
F003D150.setAligned("......CC--AA-C-T-ACACCACGCATTCC--GCATACTTCTCGCCCACTC-ATTACC-TTGCS-GCGGCTGCTGG-GAGCCCGGCAGTTT-ATTAGGGCGGCTGCTGG-TTACG.....");
F003D150_1.setAligned("......CC--AA-C-T-ACACCACGCATTCC--GCATACTTCTCGCCCACTC-ATTACC-TTGCS-GCGGCTGCTGG-GAGCCCGGCAGTTT-ATTAGGGCGGCTGCTGG-TTACG.....");
F003D150_2.setAligned("......CC--AA-C-T-ACACCACGCATTCC--GCATACTTCTCGCCCACTC-ATTACC-TTGCS-GCGGCTGCTGG-GAGCCCGGCAGTTT-ATTAGGGCGGCTGCTGG-TTACG.....");
mapAligned.clear(); countBases=0;
temp = F003D150.getAligned();
for (int i = 0; i < temp.length(); i++) {
if (isalpha(temp[i])) { mapAligned[countBases] = i; countBases++; } //maps location in unaligned -> location in aligned.
}
results = someDiffSingleTrim.findReverse(F003D150, primerStart, primerEnd);
EXPECT_EQ(75, primerStart);
EXPECT_EQ(92, primerEnd);
F003D150_1.filterFromPos(mapAligned[primerStart]);
primerRemovedKeepDots = F003D150_1.getAligned();
primerRemoved = F003D150.getAligned().substr(0, mapAligned[primerStart]);
primerKept = F003D150.getAligned().substr(0, mapAligned[primerEnd-1]+1);
F003D150_2.filterFromPos(mapAligned[primerEnd-1]+1);
primerKeptKeepDots = F003D150_2.getAligned();
EXPECT_EQ("......CC--AA-C-T-ACACCACGCATTCC--GCATACTTCTCGCCCACTC-ATTACC-TTGCS-GCGGCTGCTGG-GAGCCCGGCAGTTT-ATTAGGGCGGCTGCTGG", primerKept);
EXPECT_EQ("......CC--AA-C-T-ACACCACGCATTCC--GCATACTTCTCGCCCACTC-ATTACC-TTGCS-GCGGCTGCTGG-GAGCCCGGCAGTTT-ATTAGGGCGGCTGCTGG...........", primerKeptKeepDots);
EXPECT_EQ("......CC--AA-C-T-ACACCACGCATTCC--GCATACTTCTCGCCCACTC-ATTACC-TTGCS-GCGGCTGCTGG-GAGCCCGGCAGTTT-", primerRemoved);
EXPECT_EQ("......CC--AA-C-T-ACACCACGCATTCC--GCATACTTCTCGCCCACTC-ATTACC-TTGCS-GCGGCTGCTGG-GAGCCCGGCAGTTT-............................", primerRemovedKeepDots);
//no match option
F003D150.setAligned("......CC--AA-C-T-ACACCACGCATTCC--GCATACTTCTCGCCCACTC-ATTACC-TTGCS-GCGGCTGCTGG-GAGCCCGGCAGTTT-ATTAGGGCGGCTGCTAA-TTACG.....");
F003D150_1.setAligned("......CC--AA-C-T-ACACCACGCATTCC--GCATACTTCTCGCCCACTC-ATTACC-TTGCS-GCGGCTGCTGG-GAGCCCGGCAGTTT-ATTAGGGCGGCTGCTAA-TTACG.....");
F003D150_2.setAligned("......CC--AA-C-T-ACACCACGCATTCC--GCATACTTCTCGCCCACTC-ATTACC-TTGCS-GCGGCTGCTGG-GAGCCCGGCAGTTT-ATTAGGGCGGCTGCTAA-TTACG.....");
mapAligned.clear(); countBases=0;
temp = F003D150.getAligned();
for (int i = 0; i < temp.length(); i++) {
if (isalpha(temp[i])) { mapAligned[countBases] = i; countBases++; } //maps location in unaligned -> location in aligned.
}
results = someDiffSingleTrim.findReverse(F003D150, primerStart, primerEnd);
EXPECT_EQ(0, primerStart);
EXPECT_EQ(0, primerEnd);
}
TEST(Test_TrimOligos, SingleDirectionReverseOligos) { //ATTACCGCGGCTGCTGG
TestTrimOligos testTrim;
testTrim.oligos.loadSingle();
//no diffs allowed - unaligned
TrimOligos noDiffSingleTrim(0,0,0,testTrim.oligos.primers, testTrim.oligos.barcodes, testTrim.oligos.revPrimer); //pdiffs, rpdiffs, bdiffs, primers, barcodes, revPrimers
string testOligos = "ATTACCGCGGCTGCTGG";
EXPECT_EQ("CCAGCAGCCGCGGTAAT" , noDiffSingleTrim.reverseOligo(testOligos));
testOligos = "CCGTCAATTCMTTTRAGT";
EXPECT_EQ("ACTYAAAKGAATTGACGG" , noDiffSingleTrim.reverseOligo(testOligos));
}
/**************************************************************************************************/
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