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/*
* =====================================================================================
*
* Filename: SMRTSequenceSequence_gtest.cpp
*
* Description: Test pbdata/SMRTSequenceSequence.h
*
* Version: 1.0
* Created: 10/29/2012 05:17:04 PM
* Revision: 08/19/2014
* Compiler: gcc
*
* Author: Yuan Li (yli), yli@pacificbiosciences.com
* Company: Pacific Biosciences
*
* =====================================================================================
*/
#include <sstream>
#include <string>
#include <gtest/gtest.h>
#include <pbdata/SMRTSequence.hpp>
Nucleotide seqnt[] = "ATATGGGGATTAGGGGATA";
const std::string seqst("ATATGGGGATTAGGGGATA");
SMRTSequence _make_a_smrt_read_(const std::string& movieName, const UInt& holeNumber,
const DNALength subreadStart, const DNALength subreadEnd,
const std::string& seqst, const bool hasInsertion,
const bool hasDeletion, const bool hasSubstitution,
const int insertionQVValue, const int deletionQVValue,
const char deletionTagValue, const int substitutionQVValue,
const char substitutionTagValue)
{
DNALength length = seqst.size();
SMRTSequence smrt;
static_cast<DNASequence*>(&smrt)->Copy(seqst);
std::stringstream ss;
ss << movieName << "/" << holeNumber << "/" << subreadStart << "_" << subreadEnd;
smrt.CopyTitle(ss.str());
if (hasInsertion) {
smrt.AllocateInsertionQVSpace(length);
smrt.insertionQV.Fill(insertionQVValue);
}
if (hasDeletion) {
smrt.AllocateDeletionQVSpace(length);
smrt.AllocateDeletionTagSpace(length);
smrt.deletionQV.Fill(deletionQVValue);
memset(smrt.deletionTag, deletionTagValue, sizeof(char) * length);
}
if (hasSubstitution) {
smrt.AllocateSubstitutionQVSpace(length);
smrt.AllocateSubstitutionTagSpace(length);
smrt.substitutionQV.Fill(substitutionQVValue);
memset(smrt.substitutionTag, substitutionTagValue, sizeof(char) * length);
}
smrt.SubreadStart(subreadStart);
smrt.SubreadEnd(subreadEnd);
smrt.HoleNumber(holeNumber);
assert(length == subreadEnd - subreadStart);
return smrt;
}
class SMRTSequenceTest : public ::testing::Test
{
public:
void SetUp()
{
smrt.seq = seqnt;
int len = sizeof(seqnt) / sizeof(Nucleotide) - 1;
smrt.length = len;
smrt.HoleNumber(1);
smrt.SubreadStart(0);
smrt.SubreadEnd(19);
smrt.AllocateDeletionQVSpace(len);
for (int i = 0; i < 19; i++) {
smrt.deletionQV[i] = i;
}
}
void TearDown() { smrt.Free(); }
SMRTSequence smrt;
};
TEST_F(SMRTSequenceTest, Print)
{
std::stringstream ss;
smrt.Print(ss);
ASSERT_EQ(ss.str(), (std::string("SMRTSequence for zmw 1, [0, 19)\n") + seqst + "\n"));
}
TEST_F(SMRTSequenceTest, GetDeletionQV)
{
for (size_t i = 0; i < smrt.length; i++) {
ASSERT_EQ(smrt.GetDeletionQV(i), i);
}
}
TEST_F(SMRTSequenceTest, MadeFromSubreadsAsPolymerase)
{
std::string movieName = "mymovie";
UInt holeNumber = 12354;
std::string seq1 = "ATGGC";
std::string seq2 = "GGCT";
std::string expected_seq3 = "NATGGCNNNNGGCT";
DNALength expected_hqstart = 0, expected_hqend = 14;
DNALength expected_lqprefix = 1, expected_lqsuffix = 0;
int expected_insertionQV[14] = {0, 1, 1, 1, 1, 1, 0, 0, 0, 0, 11, 11, 11, 11};
int expected_deletionQV[14] = {0, 2, 2, 2, 2, 2, 0, 0, 0, 0, 12, 12, 12, 12};
int expected_substitutionQV[14] = {0, 3, 3, 3, 3, 3, 0, 0, 0, 0, 13, 13, 13, 13};
std::string expected_deletionTag = "NAAAAANNNNCCCC";
std::string expected_substitutionTag = "NGGGGGNNNNTTTT";
bool expected_hasInsertionQV = true;
bool expected_hasDeletionQV = true;
bool expected_hasDeletionTag = true;
bool expected_hasSubstitutionQV = true;
bool expected_hasSubstitutionTag = true;
SMRTSequence read1 =
_make_a_smrt_read_(movieName, holeNumber, 1, 6, seq1, true, true, true, 1, 2, 'A', 3, 'G');
SMRTSequence read2 = _make_a_smrt_read_(movieName, holeNumber, 10, 14, seq2, true, true, true,
11, 12, 'C', 13, 'T');
SMRTSequence read3;
read3.MadeFromSubreadsAsPolymerase({read1, read2});
EXPECT_EQ(read3.HoleNumber(), holeNumber);
EXPECT_EQ(read3.SubreadStart(), expected_hqstart);
EXPECT_EQ(read3.SubreadEnd(), expected_hqend);
EXPECT_EQ(read3.lowQualityPrefix, expected_lqprefix);
EXPECT_EQ(read3.lowQualitySuffix, expected_lqsuffix);
EXPECT_EQ(read3.length, expected_seq3.size());
EXPECT_EQ(not read3.insertionQV.Empty(), expected_hasInsertionQV);
EXPECT_EQ(not read3.deletionQV.Empty(), expected_hasDeletionQV);
EXPECT_EQ(not read3.substitutionQV.Empty(), expected_hasSubstitutionQV);
EXPECT_EQ(read3.deletionTag != nullptr, expected_hasDeletionTag);
EXPECT_EQ(read3.substitutionTag != nullptr, expected_hasSubstitutionTag);
EXPECT_TRUE(read3.qual.Empty());
EXPECT_TRUE(read3.preBaseFrames == nullptr);
EXPECT_TRUE(read3.widthInFrames == nullptr);
EXPECT_TRUE(read3.pulseIndex == nullptr);
EXPECT_TRUE(read3.preBaseDeletionQV.Empty());
EXPECT_TRUE(read3.mergeQV.Empty());
for (size_t i = 0; i < read3.length; i++) {
EXPECT_EQ(read3.seq[i], expected_seq3[i]);
EXPECT_EQ(read3.insertionQV.data[i], expected_insertionQV[i]);
EXPECT_EQ(read3.deletionQV.data[i], expected_deletionQV[i]);
EXPECT_EQ(read3.deletionTag[i], expected_deletionTag[i]);
EXPECT_EQ(read3.substitutionQV.data[i], expected_substitutionQV[i]);
EXPECT_EQ(read3.substitutionTag[i], expected_substitutionTag[i]);
}
}
TEST_F(SMRTSequenceTest, MadeFromSubreadsAsPolymeraseNoInsertionNoDeletion)
{
std::string movieName = "mymovie";
UInt holeNumber = 12354;
std::string seq1 = "ATGGC";
std::string seq2 = "GGCT";
std::string expected_seq3 = "NATGGCNNNNGGCT";
DNALength expected_hqstart = 0, expected_hqend = 14;
DNALength expected_lqprefix = 1, expected_lqsuffix = 0;
int expected_substitutionQV[14] = {0, 3, 3, 3, 3, 3, 0, 0, 0, 0, 13, 13, 13, 13};
std::string expected_substitutionTag = "NGGGGGNNNNTTTT";
bool expected_hasInsertionQV = false;
bool expected_hasDeletionQV = false;
bool expected_hasDeletionTag = false;
bool expected_hasSubstitutionQV = true;
bool expected_hasSubstitutionTag = true;
SMRTSequence read1 =
_make_a_smrt_read_(movieName, holeNumber, 1, 6, seq1, false, true, true, 1, 2, 'A', 3, 'G');
SMRTSequence read2 = _make_a_smrt_read_(movieName, holeNumber, 10, 14, seq2, true, true, true,
11, 12, 'C', 13, 'T');
// read3 should contain neither insertionQV nor deletionQV nor deletionTag
SMRTSequence read3;
read3.MadeFromSubreadsAsPolymerase({read1, read2});
EXPECT_EQ(read3.HoleNumber(), holeNumber);
EXPECT_EQ(read3.SubreadStart(), expected_hqstart);
EXPECT_EQ(read3.SubreadEnd(), expected_hqend);
EXPECT_EQ(read3.lowQualityPrefix, expected_lqprefix);
EXPECT_EQ(read3.lowQualitySuffix, expected_lqsuffix);
EXPECT_EQ(read3.length, expected_seq3.size());
EXPECT_EQ(not read3.insertionQV.Empty(), expected_hasInsertionQV);
EXPECT_EQ(not read3.deletionQV.Empty(), expected_hasDeletionQV);
EXPECT_EQ(not read3.substitutionQV.Empty(), expected_hasSubstitutionQV);
EXPECT_EQ(read3.deletionTag != nullptr, expected_hasDeletionTag);
EXPECT_EQ(read3.substitutionTag != nullptr, expected_hasSubstitutionTag);
EXPECT_TRUE(read3.qual.Empty());
EXPECT_TRUE(read3.preBaseFrames == nullptr);
EXPECT_TRUE(read3.widthInFrames == nullptr);
EXPECT_TRUE(read3.pulseIndex == nullptr);
EXPECT_TRUE(read3.preBaseDeletionQV.Empty());
EXPECT_TRUE(read3.mergeQV.Empty());
for (size_t i = 0; i < read3.length; i++) {
EXPECT_EQ(read3.seq[i], expected_seq3[i]);
EXPECT_EQ(read3.substitutionQV.data[i], expected_substitutionQV[i]);
EXPECT_EQ(read3.substitutionTag[i], expected_substitutionTag[i]);
}
}
TEST_F(SMRTSequenceTest, MadeFromSubreadsAsPolymeraseNoInsertionNoDeletionNoSubstitution)
{
std::string movieName = "mymovie";
UInt holeNumber = 12354;
std::string seq1 = "ATGGC";
std::string seq2 = "GGCT";
std::string expected_seq3 = "NATGGCNNNNGGCT";
DNALength expected_hqstart = 0, expected_hqend = 14;
DNALength expected_lqprefix = 1, expected_lqsuffix = 0;
bool expected_hasInsertionQV = false;
bool expected_hasDeletionQV = false;
bool expected_hasDeletionTag = false;
bool expected_hasSubstitutionQV = false;
bool expected_hasSubstitutionTag = false;
SMRTSequence read1 =
_make_a_smrt_read_(movieName, holeNumber, 1, 6, seq1, false, true, true, 1, 2, 'A', 3, 'G');
SMRTSequence read2 = _make_a_smrt_read_(movieName, holeNumber, 10, 14, seq2, true, true, false,
11, 12, 'C', 13, 'T');
// read3 should contain neither insertionQV nor deletionQV nor deletionTag
SMRTSequence read3;
read3.MadeFromSubreadsAsPolymerase({read1, read2});
EXPECT_EQ(read3.HoleNumber(), holeNumber);
EXPECT_EQ(read3.SubreadStart(), expected_hqstart);
EXPECT_EQ(read3.SubreadEnd(), expected_hqend);
EXPECT_EQ(read3.lowQualityPrefix, expected_lqprefix);
EXPECT_EQ(read3.lowQualitySuffix, expected_lqsuffix);
EXPECT_EQ(read3.length, expected_seq3.size());
EXPECT_EQ(not read3.insertionQV.Empty(), expected_hasInsertionQV);
EXPECT_EQ(not read3.deletionQV.Empty(), expected_hasDeletionQV);
EXPECT_EQ(not read3.substitutionQV.Empty(), expected_hasSubstitutionQV);
EXPECT_EQ(read3.deletionTag != nullptr, expected_hasDeletionTag);
EXPECT_EQ(read3.substitutionTag != nullptr, expected_hasSubstitutionTag);
EXPECT_TRUE(read3.qual.Empty());
EXPECT_TRUE(read3.preBaseFrames == nullptr);
EXPECT_TRUE(read3.widthInFrames == nullptr);
EXPECT_TRUE(read3.pulseIndex == nullptr);
EXPECT_TRUE(read3.preBaseDeletionQV.Empty());
EXPECT_TRUE(read3.mergeQV.Empty());
for (size_t i = 0; i < read3.length; i++) {
EXPECT_EQ(read3.seq[i], expected_seq3[i]);
}
}
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