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/*
* =====================================================================================
*
* Filename: CCSIterator_gtest.cpp
*
* Description: Test alignment/files/CCSIterator.hpp
*
* Version: 1.0
* Created: 11/29/2012 04:51:02 PM
* Revision: 08/20/2014
* Compiler: gcc
*
* Author: Yuan Li (yli), yli@pacificbiosciences.com
* Company: Pacific Biosciences
*
* =====================================================================================
*/
#include <string>
#include <vector>
#include <gtest/gtest.h>
#define private public
#include <pbdata/testdata.h>
#include <alignment/files/CCSIterator.hpp>
#include <alignment/files/FragmentCCSIterator.hpp>
#include <hdf/HDFRegionTableReader.hpp>
#include <pbdata/reads/RegionTable.hpp>
static const UInt HOLENUMBER = 76772;
// Adater - 0, Insert - 1, HQRegion - 2
static const std::vector<RegionType> TYPES = {Adapter, Insert, HQRegion};
static const std::vector<std::string> TYPESTRS = {"Adapter", "Insert", "HQRegion"};
static const std::vector<RegionAnnotation> INSERTS = {
RegionAnnotation(HOLENUMBER, 1, 0, 253, -1),
RegionAnnotation(HOLENUMBER, 1, 301, 678, -1),
RegionAnnotation(HOLENUMBER, 1, 724, 1101, -1),
RegionAnnotation(HOLENUMBER, 1, 1150, 1534, -1),
RegionAnnotation(HOLENUMBER, 1, 1575, 1956, -1),
RegionAnnotation(HOLENUMBER, 1, 1999, 2379, -1),
RegionAnnotation(HOLENUMBER, 1, 2417, 2803, -1),
RegionAnnotation(HOLENUMBER, 1, 2852, 3245, -1),
RegionAnnotation(HOLENUMBER, 1, 3287, 3727, -1),
RegionAnnotation(HOLENUMBER, 1, 3778, 4176, -1),
RegionAnnotation(HOLENUMBER, 1, 4221, 4618, -1),
RegionAnnotation(HOLENUMBER, 1, 4661, 4862, -1)};
static const std::vector<RegionAnnotation> ADAPTERS = {
RegionAnnotation(HOLENUMBER, 0, 253, 301, 854),
RegionAnnotation(HOLENUMBER, 0, 678, 724, 978),
RegionAnnotation(HOLENUMBER, 0, 1101, 1150, 897),
RegionAnnotation(HOLENUMBER, 0, 1534, 1575, 804),
RegionAnnotation(HOLENUMBER, 0, 1956, 1999, 930),
RegionAnnotation(HOLENUMBER, 0, 2379, 2417, 736),
RegionAnnotation(HOLENUMBER, 0, 2803, 2852, 918),
RegionAnnotation(HOLENUMBER, 0, 3245, 3287, 928),
RegionAnnotation(HOLENUMBER, 0, 3727, 3778, 784),
RegionAnnotation(HOLENUMBER, 0, 4176, 4221, 911),
RegionAnnotation(HOLENUMBER, 0, 4618, 4661, 767)};
static const std::vector<RegionAnnotation> HQREGION = {
RegionAnnotation(HOLENUMBER, 2, 0, 4861, 865)};
static const DNALength EXPECTED_HQSTART = 0;
static const DNALength EXPECTED_HQEND = 4861;
static const DNALength EXPECTED_SCORE = 865;
static const DNALength WHOLE_LENGTH = 5000;
static const unsigned EXPECTED_NUM_SUBREADS = 12;
TEST(CCSFragmentIterator, Constructor)
{
std::vector<RegionAnnotation> regions = INSERTS;
regions.insert(regions.end(), HQREGION.begin(), HQREGION.end());
regions.insert(regions.end(), ADAPTERS.begin(), ADAPTERS.end());
CCSSequence ccs;
ccs.HoleNumber(HOLENUMBER);
ccs.Allocate(WHOLE_LENGTH);
ccs.unrolledRead.Allocate(WHOLE_LENGTH);
RegionTable table;
table.ConstructTable(regions, TYPESTRS);
FragmentCCSIterator it;
it.Initialize(&ccs, &table);
EXPECT_EQ(it.subreadIntervals.size(), EXPECTED_NUM_SUBREADS);
EXPECT_EQ(it.subreadIntervals[0], ReadInterval(0, 253, 865));
EXPECT_EQ(it.subreadIntervals[EXPECTED_NUM_SUBREADS - 1], ReadInterval(4661, 4861, 865));
}
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