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/*
* =====================================================================================
*
* Filename: CCSSequence_gtest.cpp
*
* Description: Test pbdata/CCSSequence.hpp
*
* Version: 1.0
* Created: 10/29/2012 05:17:04 PM
* Revision: none
* Compiler: gcc
*
* Author: Yuan Li (yli), yli@pacificbiosciences.com
* Company: Pacific Biosciences
*
* =====================================================================================
*/
#include "gtest/gtest.h"
#include "CCSSequence.hpp"
using namespace std;
Nucleotide sr0[] = "ATATGGGGATTAGGGGATA";
Nucleotide sr1[] = "TAATCCCGTAATCCCGGTAT"; //rc = TAATCCCGTAATCCCGGTAT
Nucleotide sr2[] = "ATAGGGGGATTAGGGGATTCA";
Nucleotide adapter[] = "CCC";
Nucleotide unrolled_seq[] = "ATATGGGGATTAGGGGATACCCTAATCCCGTAATCCCGGTATCCCATAGGGGGATTAGGGGATTCA";
int sz0 = 19;
int sz1 = 20;
int sz2 = 21;
int adaptersz = 3;
int unrolledsz = sz0 + sz1 + sz2 + adaptersz * 2;
const int numSubreads = 3;
class CCSSequenceTest: public:: testing:: Test{
public:
void CreateSMRTSequence(SMRTSequence & smrt, Nucleotide* seq,
int holeNumber, int start, int end) {
int size = end - start;
smrt.seq = new Nucleotide[size];
memcpy(smrt.seq, seq, size*sizeof(Nucleotide));
smrt.length = size;
smrt.deleteOnExit = false;
smrt.HoleNumber (holeNumber);
smrt.SubreadStart(start);
smrt.SubreadEnd (end);
stringstream ss;
}
void SetUp() {
//Create a vector of subreads.
subreads.resize(numSubreads);
int s = 0;
CreateSMRTSequence(subreads[0], &sr0[0], 1, s, s + sz0);
s += sz0 + adaptersz;
CreateSMRTSequence(subreads[1], &sr1[0], 1, s, s + sz1);
s += sz1 + adaptersz;
CreateSMRTSequence(subreads[2], &sr2[0], 1, s, s + sz2);
//Create ccs
stringstream ss;
subreads[0].Print(ss);
CreateSMRTSequence(ccs.unrolledRead, &unrolled_seq[0], 1, 0, unrolledsz);
ccs.numPasses = numSubreads;
CreateSMRTSequence((SMRTSequence&)ccs, &sr0[0], 1, 0, sz0);
ccs.numConsensusBases = sz0;
ccs.passStartBase.resize(numSubreads);
ccs.passNumBases.resize(numSubreads);
ccs.passDirection.resize(numSubreads);
s = 0;
for(int i=0; i < ccs.numPasses; i++) {
ccs.passStartBase[i] = subreads[i].SubreadStart();
ccs.passDirection[i] = (i%2==0)?(0):(1);
ccs.passNumBases[i] = subreads[i].length;
}
}
void TearDown() {
ccs.Free();
for(int i=0; i<numSubreads; i++) {
subreads[i].Free();
}
}
CCSSequence ccs;
vector<SMRTSequence> subreads;
};
TEST_F(CCSSequenceTest, Print) {
stringstream ss, ss1;
ccs.Print(ss);
ccs.unrolledRead.Print(ss1);
ASSERT_EQ(ss.str(), (string(
"SMRTSequence for zmw 1, [0, 19)\nATATGGGGATTAGGGGATA\n")));
ASSERT_EQ(ss1.str(), (string(
"SMRTSequence for zmw 1, [0, 66)\nATATGGGGATTAGGGGATACCCTAATCCCGTAATCCCGGTATCCCATAGG\nGGGATTAGGGGATTCA\n")));
}
TEST_F(CCSSequenceTest, Explode) {
vector<SMRTSequence> exploded_subreads;
ccs.Explode(exploded_subreads);
for(int i = 0; i < numSubreads; i++){
stringstream ss, ss1;
subreads[i].PrintSeq(ss);
exploded_subreads[i].PrintSeq(ss1);
ASSERT_EQ(ss.str(), ss1.str());
}
}
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