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unittests_genomictools.cpp
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Sat, Nov 16, 13:07

unittests_genomictools.cpp
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#include <UnitTest++/UnitTest++.h>
#include <seqan/bam_io.h>
#include <GenomeRegion.hpp>
#include <CorrelationMatrixCreator.hpp>
#include <Matrix2D.hpp>
#include <iostream>
#include <string>
#include <vector>
#include <list>
#include <stdexcept> // std::invalid_argument
std::string file_bed = "/local/groux/scATAC-seq/data/toy_data/peaks.bed" ;
std::string file_bam = "/local/groux/scATAC-seq/data/toy_data/sc_reads.bam" ;
std::string file_bai = "/local/groux/scATAC-seq/data/toy_data/sc_reads.bam.bai" ;
// GenomeRegion test suite
SUITE(GenomeRegion)
{
// displays message
TEST(message)
{ std::cout << "Starting GenomicTools tests..." << std::endl ; }
// tests vonstructor with value
TEST(constructor_value)
{ std::string chr = "chr1" ;
int idx = 0 ;
GenomeRegion r1(chr, idx, 0, 10) ;
CHECK_EQUAL(chr, r1.chromosome) ;
CHECK_EQUAL(0, r1.start) ;
CHECK_EQUAL(10, r1.end) ;
CHECK_EQUAL(10, r1.length) ;
GenomeRegion r2(chr, idx, 1, 10) ;
CHECK_EQUAL(chr, r2.chromosome) ;
CHECK_EQUAL(1, r2.start) ;
CHECK_EQUAL(10, r2.end) ;
CHECK_EQUAL(9, r2.length) ;
CHECK_THROW(GenomeRegion(chr, idx, -1, 10), std::invalid_argument) ;
CHECK_THROW(GenomeRegion(chr, idx, 0, -10), std::invalid_argument) ;
}
// tests constructFragment factory function to create regions from bam
/*
TEST(test_contructFragment)
{
// expected content of bam file
std::vector<GenomeRegion> regions ;
regions.push_back(GenomeRegion("chr1", 400, 480)) ;
regions.push_back(GenomeRegion("chr1", 470, 550)) ;
regions.push_back(GenomeRegion("chr1", 560, 800)) ;
regions.push_back(GenomeRegion("chr1", 560, 640)) ;
regions.push_back(GenomeRegion("chr1", 610, 690)) ;
regions.push_back(GenomeRegion("chr1", 670, 750)) ;
regions.push_back(GenomeRegion("chr1", 730, 810)) ;
regions.push_back(GenomeRegion("chr1", 770, 850)) ;
regions.push_back(GenomeRegion("chr1", 950, 1150)) ;
regions.push_back(GenomeRegion("chr1", 960, 1040)) ;
regions.push_back(GenomeRegion("chr1", 1010, 1090)) ;
regions.push_back(GenomeRegion("chr1", 1060, 1140)) ;
regions.push_back(GenomeRegion("chr1", 1070, 1150)) ;
regions.push_back(GenomeRegion("chr1", 1350, 1430)) ;
regions.push_back(GenomeRegion("chr1", 1360, 1440)) ;
regions.push_back(GenomeRegion("chr1", 1410, 1490)) ;
regions.push_back(GenomeRegion("chr1", 1500, 1600)) ;
regions.push_back(GenomeRegion("chr1", 1600, 1700)) ;
regions.push_back(GenomeRegion("chr2", 400, 480)) ;
regions.push_back(GenomeRegion("chr2", 470, 550)) ;
regions.push_back(GenomeRegion("chr2", 560, 800)) ;
regions.push_back(GenomeRegion("chr2", 560, 640)) ;
regions.push_back(GenomeRegion("chr2", 610, 690)) ;
regions.push_back(GenomeRegion("chr2", 670, 750)) ;
regions.push_back(GenomeRegion("chr2", 730, 810)) ;
regions.push_back(GenomeRegion("chr2", 770, 850)) ;
regions.push_back(GenomeRegion("chr2", 950, 1150)) ;
regions.push_back(GenomeRegion("chr2", 960, 1040)) ;
regions.push_back(GenomeRegion("chr2", 1010, 1090)) ;
regions.push_back(GenomeRegion("chr2", 1060, 1140)) ;
regions.push_back(GenomeRegion("chr2", 1070, 1150)) ;
regions.push_back(GenomeRegion("chr2", 1350, 1430)) ;
regions.push_back(GenomeRegion("chr2", 1360, 1440)) ;
regions.push_back(GenomeRegion("chr2", 1410, 1490)) ;
regions.push_back(GenomeRegion("chr2", 1500, 1600)) ;
regions.push_back(GenomeRegion("chr2", 1600, 1700)) ;
seqan::BamAlignmentRecord record ;
std::string bam_path = "src/Unittests/data/sc_reads.bam" ;
// read file for fragments starting on + strand
seqan::BamFileIn bam_file(bam_path.c_str()) ;
// header
seqan::BamHeader bam_header ;
seqan::readHeader(bam_header, bam_file) ;
for(size_t i=0; not seqan::atEnd(bam_file); i++)
{ seqan::readRecord(record, bam_file) ;
if(seqan::hasFlagFirst(record) and not seqan::hasFlagRC(record))
{ std::cout << regions[i] << " "
<< GenomeRegion::constructFragment(record)
<< std::endl ;
CHECK_EQUAL(regions[i], GenomeRegion::constructFragment(record)) ; }
}
seqan::close(bam_file) ;
// read file for fragments starting on - strand
seqan::BamFileIn bam_file(bam_path.c_str()) ;
// header
seqan::BamHeader bam_header ;
seqan::readHeader(bam_header, bam_file) ;
for(size_t i=0; not seqan::atEnd(bam_file); i++)
{ seqan::readRecord(record, bam_file) ;
if(seqan::hasFlagFirst(record) and seqan::hasFlagRC(record))
{ CHECK_EQUAL(regions[i], GenomeRegion::constructFragment(record)) ; }
}
seqan::close(bam_file) ;
}
*/
TEST(test_contructRead)
{ // expected content of bam file
std::list<GenomeRegion> regions_exp ;
// chromosome 1 -> has index 0 in BAM file header
regions_exp.push_back(GenomeRegion("chr1", 0, 400, 435)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 400, 435)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 445, 480)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 445, 480)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 470, 505)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 470, 505)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 515, 550)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 515, 550)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 560, 595)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 560, 595)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 560, 595)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 560, 595)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 605, 640)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 605, 640)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 610, 645)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 610, 645)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 655, 690)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 655, 690)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 670, 705)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 670, 705)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 715, 750)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 715, 750)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 730, 765)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 730, 765)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 765, 800)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 765, 800)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 770, 805)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 770, 805)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 775, 810)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 775, 810)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 815, 850)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 815, 850)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 950, 985)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 950, 985)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 960, 995)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 960, 995)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 1005, 1040)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 1005, 1040)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 1010, 1045)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 1010, 1045)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 1055, 1090)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 1055, 1090)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 1060, 1095)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 1060, 1095)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 1070, 1105)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 1070, 1105)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 1105, 1140)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 1105, 1140)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 1115, 1150)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 1115, 1150)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 1115, 1150)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 1115, 1150)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 1350, 1385)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 1350, 1385)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 1360, 1395)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 1360, 1395)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 1395, 1430)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 1395, 1430)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 1405, 1440)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 1405, 1440)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 1410, 1445)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 1410, 1445)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 1455, 1490)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 1455, 1490)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 1500, 1535)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 1500, 1535)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 1565, 1600)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 1565, 1600)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 1600, 1635)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 1600, 1635)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 1665, 1700)) ;
regions_exp.push_back(GenomeRegion("chr1", 0, 1665, 1700)) ;
// chromosome 2 -> has index 1 in BAM file header
regions_exp.push_back(GenomeRegion("chr2", 1, 400, 435)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 400, 435)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 445, 480)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 445, 480)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 470, 505)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 470, 505)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 515, 550)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 515, 550)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 560, 595)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 560, 595)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 560, 595)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 560, 595)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 605, 640)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 605, 640)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 610, 645)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 610, 645)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 655, 690)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 655, 690)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 670, 705)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 670, 705)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 715, 750)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 715, 750)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 730, 765)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 730, 765)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 765, 800)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 765, 800)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 770, 805)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 770, 805)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 775, 810)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 775, 810)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 815, 850)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 815, 850)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 950, 985)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 950, 985)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 960, 995)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 960, 995)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 1005, 1040)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 1005, 1040)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 1010, 1045)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 1010, 1045)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 1055, 1090)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 1055, 1090)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 1060, 1095)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 1060, 1095)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 1070, 1105)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 1070, 1105)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 1105, 1140)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 1105, 1140)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 1115, 1150)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 1115, 1150)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 1115, 1150)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 1115, 1150)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 1350, 1385)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 1350, 1385)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 1360, 1395)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 1360, 1395)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 1395, 1430)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 1395, 1430)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 1405, 1440)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 1405, 1440)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 1410, 1445)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 1410, 1445)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 1455, 1490)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 1455, 1490)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 1500, 1535)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 1500, 1535)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 1565, 1600)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 1565, 1600)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 1600, 1635)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 1600, 1635)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 1665, 1700)) ;
regions_exp.push_back(GenomeRegion("chr2", 1, 1665, 1700)) ;
// open file
seqan::BamFileIn bam_file ;
if (!seqan::open(bam_file, file_bam.c_str()))
{ char msg[4096] ;
sprintf(msg, "ERROR: could not open input file %s", file_bam.c_str()) ;
}
// read file
seqan::BamAlignmentRecord record ;
seqan::BamHeader header ;
seqan::readHeader(header, bam_file) ;
std::list<GenomeRegion> regions_val ;
while(not seqan::atEnd(bam_file))
{ seqan::readRecord(record, bam_file) ;
regions_val.push_back(GenomeRegion::constructRead(record, bam_file)) ;
}
seqan::close(bam_file) ;
// compare
CHECK_EQUAL(regions_exp.size(), regions_val.size()) ;
auto iter_exp = regions_exp.begin() ;
auto iter_val = regions_val.begin() ;
while(iter_exp != regions_exp.end())
{ CHECK_EQUAL(*iter_exp, *iter_val) ;
iter_exp++ ;
iter_val++ ;
}
}
// tests the method to check overlaps
TEST(overlap)
{ GenomeRegion r1("chr1", 0, 20, 30) ; // reference
GenomeRegion r2("chr1", 0, 20, 30) ; // same as reference
GenomeRegion r3("chr1", 0, 0, 45) ; // totally contain reference
GenomeRegion r4("chr1", 0, 0, 10) ; // no overlap, upstream reference
GenomeRegion r5("chr1", 0, 15, 25) ; // partial overlap reference
GenomeRegion r6("chr1", 0, 22, 29) ; // inside reference
GenomeRegion r7("chr1", 0, 25, 35) ; // partial overlap reference
GenomeRegion r8("chr1", 0, 35, 45) ; // no overlap, downstream reference
GenomeRegion r9("chr2", 1, 20, 30) ; // diff chromosome
// always check reciprocity
CHECK_EQUAL(true, r1 | r1) ;
CHECK_EQUAL(true, r1 | r2) ; CHECK_EQUAL(true, r2 | r1) ;
CHECK_EQUAL(true, r1 | r3) ; CHECK_EQUAL(true, r3 | r1) ;
CHECK_EQUAL(false, r1 | r4) ; CHECK_EQUAL(false, r4 | r1) ;
CHECK_EQUAL(true, r1 | r5) ; CHECK_EQUAL(true, r5 | r1) ;
CHECK_EQUAL(true, r1 | r6) ; CHECK_EQUAL(true, r6 | r1) ;
CHECK_EQUAL(true, r1 | r7) ; CHECK_EQUAL(true, r7 | r1) ;
CHECK_EQUAL(false, r1 | r8) ; CHECK_EQUAL(false, r8 | r1) ;
CHECK_EQUAL(false, r1 | r9) ; CHECK_EQUAL(false, r9 | r1) ;
}
// tests the methods to get overlap length
TEST(overlap_len)
{ GenomeRegion r1("chr1", 0, 10, 20) ; // reference
GenomeRegion r2("chr1", 0, 10, 20) ; // same as reference
GenomeRegion r3("chr1", 0, 0, 45) ; // totally contain reference
GenomeRegion r4("chr2", 1, 10, 20) ; // diff chromosome
// always check reciprocity
CHECK_EQUAL(10, r1.overlap_len(r1)) ;
CHECK_EQUAL(10, r1.overlap_len(r2)) ; CHECK_EQUAL(10, r1.overlap_len(r2)) ;
CHECK_EQUAL(10, r1.overlap_len(r3)) ; CHECK_EQUAL(10, r1.overlap_len(r3)) ;
CHECK_EQUAL(0, r1.overlap_len(r4)) ; CHECK_EQUAL(0, r1.overlap_len(r4)) ;
// slide a smaller region along reference, from before to after
std::vector<int> overlaps = {0,0,1,2,3,4,4,4,4,4,4,4,3,2,1,0,0,0} ;
int len = 4 ;
for(int i=0, start=5; start<23; i++, start++)
{ int end = start + len ;
GenomeRegion s1("chr1", 0, start, end) ;
CHECK_EQUAL(overlaps[i], r1.overlap_len(s1)) ;
CHECK_EQUAL(overlaps[i], s1.overlap_len(r1)) ;
}
}
// tests the is upstream and is downstream operators
TEST(upstream_downstream)
{ GenomeRegion r1("chr1", 0, 10, 20) ; // reference
GenomeRegion r2("chr1", 0, 10, 20) ; // same as reference
GenomeRegion r3("chr1", 0, 0, 45) ; // totally contain reference
GenomeRegion r4("chr2", 1, 10, 20) ; // diff chromosome (downstream has 0 < 1)
// always check reciprocity
CHECK_EQUAL(false, r1 < r1) ; CHECK_EQUAL(false, r1 > r1) ;
CHECK_EQUAL(false, r1 < r2) ; CHECK_EQUAL(false, r1 > r2) ;
CHECK_EQUAL(false, r1 < r3) ; CHECK_EQUAL(false, r1 < r3) ;
CHECK_EQUAL(false, r3 < r1) ; CHECK_EQUAL(false, r3 < r1) ;
// not on the same chromosome -> depends on the index value
CHECK_EQUAL(r1 < r4, true) ; CHECK_EQUAL(r1 > r4, false) ;
CHECK_EQUAL(r4 < r1, false) ; CHECK_EQUAL(r4 > r1, true) ;
// slide a smaller region along reference, from before to after
std::vector<bool> s1_upstream = {1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0} ; // s1 < r1
std::vector<bool> r1_downstream = {1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0} ; // r1 > s1
std::vector<bool> s1_downstream = {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1} ; // s1 > r1
std::vector<bool> r1_upstream = {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1} ; // r1 < s1
int len = 4 ;
for(int i=0, start=5; start<23; i++, start++)
{ // the sliding one
int end = start + len ;
GenomeRegion s1("chr1", 0, start, end) ;
CHECK_EQUAL(s1_upstream[i], s1 < r1) ;
CHECK_EQUAL(r1_downstream[i], r1 > s1) ;
CHECK_EQUAL(r1_upstream[i], r1 < s1) ;
CHECK_EQUAL(s1_downstream[i], s1 > r1) ;
}
}
}
// CorrelationMatrixCreator test suite
SUITE(CorrelationMatrixCreator)
{
// displays message
TEST(message)
{ std::cout << "Starting CorrelationMatrixCreator tests..." << std::endl ; }
// tests matrix creation with full fragments
TEST(create_matrix_fragment)
{ CorrelationMatrixCreator creator(file_bed,
file_bam,
file_bai,
-500,
500,
100,
CorrelationMatrixCreator::FRAGMENT) ;
Matrix2D<int> m_val = creator.create_matrix() ;
Matrix2D<int> m_exp(2, 9, 0) ;
m_exp(0,0) = 420 ; m_exp(0,1) = 480 ; m_exp(0,2) = 380 ;
m_exp(0,3) = 0 ; m_exp(0,4) = 440 ; m_exp(0,5) = 600 ;
m_exp(0,6) = 0 ; m_exp(0,7) = 0 ; m_exp(0,8) = 400 ;
m_exp(1,0) = 420 ; m_exp(1,1) = 480 ; m_exp(1,2) = 380 ;
m_exp(1,3) = 0 ; m_exp(1,4) = 440 ; m_exp(1,5) = 600 ;
m_exp(1,6) = 0 ; m_exp(1,7) = 0 ; m_exp(1,8) = 400 ;
CHECK_EQUAL(m_exp.get_nrow(), m_val.get_nrow()) ;
CHECK_EQUAL(m_exp.get_ncol(), m_val.get_ncol()) ;
for(size_t i=0; i<m_exp.get_nrow(); i++)
{ for(size_t j=0; j<m_exp.get_ncol(); j++)
{ CHECK_EQUAL(m_exp(i,j), m_val(i,j)) ; }
}
}
// tests matrix creation with fragment centers
TEST(create_matrix_fragment_center)
{ CorrelationMatrixCreator creator(file_bed,
file_bam,
file_bai,
-500,
500,
100,
CorrelationMatrixCreator::FRAGMENT_CENTER) ;
Matrix2D<int> m_val = creator.create_matrix() ;
Matrix2D<int> m_exp(2, 9, 0) ;
m_exp(0,0) = 2 ; m_exp(0,1) = 6 ; m_exp(0,2) = 4 ;
m_exp(0,3) = 0 ; m_exp(0,4) = 2 ; m_exp(0,5) = 8 ;
m_exp(0,6) = 0 ; m_exp(0,7) = 0 ; m_exp(0,8) = 4 ;
m_exp(1,0) = 2 ; m_exp(1,1) = 6 ; m_exp(1,2) = 4 ;
m_exp(1,3) = 0 ; m_exp(1,4) = 2 ; m_exp(1,5) = 8 ;
m_exp(1,6) = 0 ; m_exp(1,7) = 0 ; m_exp(1,8) = 4 ;
CHECK_EQUAL(m_exp.get_nrow(), m_val.get_nrow()) ;
CHECK_EQUAL(m_exp.get_ncol(), m_val.get_ncol()) ;
for(size_t i=0; i<m_exp.get_nrow(); i++)
{ for(size_t j=0; j<m_exp.get_ncol(); j++)
{ CHECK_EQUAL(m_exp(i,j), m_val(i,j)) ; }
}
}
// tests matrix creation with reads
TEST(create_matrix_read)
{ CorrelationMatrixCreator creator(file_bed,
file_bam,
file_bai,
-500,
500,
100,
CorrelationMatrixCreator::READ) ;
Matrix2D<int> m_val = creator.create_matrix() ;
Matrix2D<int> m_exp(2, 9, 0) ;
m_exp(0,0) = 280 ; m_exp(0,1) = 250 ; m_exp(0,2) = 310 ;
m_exp(0,3) = 0 ; m_exp(0,4) = 280 ; m_exp(0,5) = 420 ;
m_exp(0,6) = 0 ; m_exp(0,7) = 0 ; m_exp(0,8) = 350 ;
m_exp(1,0) = 280 ; m_exp(1,1) = 250 ; m_exp(1,2) = 310 ;
m_exp(1,3) = 0 ; m_exp(1,4) = 280 ; m_exp(1,5) = 420 ;
m_exp(1,6) = 0 ; m_exp(1,7) = 0 ; m_exp(1,8) = 350 ;
CHECK_EQUAL(m_exp.get_nrow(), m_val.get_nrow()) ;
CHECK_EQUAL(m_exp.get_ncol(), m_val.get_ncol()) ;
for(size_t i=0; i<m_exp.get_nrow(); i++)
{ for(size_t j=0; j<m_exp.get_ncol(); j++)
{ CHECK_EQUAL(m_exp(i,j), m_val(i,j)) ; }
}
}
// tests matrix creation with ATAC-seq reads
TEST(create_matrix_read_atac)
{ CorrelationMatrixCreator creator(file_bed,
file_bam,
file_bai,
-500,
500,
100,
CorrelationMatrixCreator::READ_ATAC) ;
Matrix2D<int> m_val = creator.create_matrix() ;
Matrix2D<int> m_exp(2, 9, 0) ;
m_exp(0,0) = 8 ; m_exp(0,1) = 8 ; m_exp(0,2) = 8 ;
m_exp(0,3) = 0 ; m_exp(0,4) = 8 ; m_exp(0,5) = 12 ;
m_exp(0,6) = 0 ; m_exp(0,7) = 0 ; m_exp(0,8) = 10 ;
m_exp(1,0) = 8 ; m_exp(1,1) = 8 ; m_exp(1,2) = 8 ;
m_exp(1,3) = 0 ; m_exp(1,4) = 8 ; m_exp(1,5) = 12 ;
m_exp(1,6) = 0 ; m_exp(1,7) = 0 ; m_exp(1,8) = 10 ;
CHECK_EQUAL(m_exp.get_nrow(), m_val.get_nrow()) ;
CHECK_EQUAL(m_exp.get_ncol(), m_val.get_ncol()) ;
for(size_t i=0; i<m_exp.get_nrow(); i++)
{ for(size_t j=0; j<m_exp.get_ncol(); j++)
{ CHECK_EQUAL(m_exp(i,j), m_val(i,j)) ; }
}
}
}

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