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#include <sstream>
#include <string>
#include "Common/SAM.h"
#include "gtest/gtest.h"
/** Verify SAM records are stored and used correctly */
using namespace std;
/** @Return whether two Alignments are equivalent. */
bool operator==(const Alignment& a, const Alignment& b)
{
return a.read_start_pos == b.read_start_pos &&
a.align_length == b.align_length &&
a.read_length == b.read_length;
}
// Test SAM::parseCigar()
TEST(parseCigar, check_alignment)
{
Alignment a;
a.align_length = 40;
a.read_start_pos = 0;
a.read_length = 40;
EXPECT_EQ(a, SAMAlignment::parseCigar("40M", false));
a.align_length = 40;
a.read_start_pos = 20;
a.read_length = 60;
EXPECT_EQ(a, SAMAlignment::parseCigar("20S40M", false));
a.align_length = 40;
a.read_start_pos = 0;
a.read_length = 60;
EXPECT_EQ(a, SAMAlignment::parseCigar("40M20S", false));
EXPECT_EQ(a, SAMAlignment::parseCigar("20S40M", true));
a.align_length = 40;
a.read_start_pos = 20;
a.read_length = 70;
EXPECT_EQ(a, SAMAlignment::parseCigar("20S40M10S", false));
EXPECT_EQ(a, SAMAlignment::parseCigar("10S40M20S", true));
a.align_length = 40;
a.read_start_pos = 20;
a.read_length = 70;
EXPECT_EQ(a, SAMAlignment::parseCigar("20I40M10S", false));
a.align_length = 40;
a.read_start_pos = 30;
a.read_length = 80;
EXPECT_EQ(a, SAMAlignment::parseCigar("20M10I40M10S", false));
a.align_length = 40;
a.read_start_pos = 0;
a.read_length = 80;
EXPECT_EQ(a, SAMAlignment::parseCigar("40M10I20M10S", false));
}
// Check that we error when an invalid CIGAR is given.
TEST(parseCigarDeath, invalid_cigar)
{
EXPECT_DEATH(SAMAlignment::parseCigar("20SS", false), "error: invalid CIGAR: `20SS'");
EXPECT_DEATH(SAMAlignment::parseCigar("20m", false), "error: invalid CIGAR: `20m'");
}
// Test friend std::istream& operator >>(std::istream& in, SAMRecord& o)
TEST(parseSAMInput, check_values)
{
std::string testSAMString( "1:497:R:-272+13M17D24M 113 1 497 37 37M 15 100338662 0 "
"CGGGTCTGACCTGAGGAGAACTGTGCTCCGCCTTCAG 0;==-==9;>>>>>=>>>>>>>>>>>=>>>>>>>>>> "
"XT:A:U NM:i:0 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:37"
"\n"
"19:20389:F:275+18M2D19M 99 1 17644 0 37M = 17919 314 "
"TATGACTGCTAATAATACCTACACATGTTAGAACCAT >>>>>>>>>>>>>>>>>>>><<>>><<>>4::>>:<9 "
"RG:Z:UM0098:1 XT:A:R NM:i:0 SM:i:0 AM:i:0 X0:i:4 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:37"
);
std::istringstream testSAMIStringStream(testSAMString);
SAMRecord testSAMRecord;
testSAMIStringStream >> testSAMRecord;
EXPECT_EQ("1:497:R:-272+13M17D24M", testSAMRecord.qname);
EXPECT_EQ(113, testSAMRecord.flag);
EXPECT_EQ("1", testSAMRecord.rname);
EXPECT_EQ(496, testSAMRecord.pos);
EXPECT_EQ(37, testSAMRecord.mapq);
EXPECT_EQ("37M", testSAMRecord.cigar);
EXPECT_EQ("15", testSAMRecord.mrnm);
EXPECT_EQ(100338661, testSAMRecord.mpos);
EXPECT_EQ(0, testSAMRecord.isize);
#if SAM_SEQ_QUAL
EXPECT_EQ("CGGGTCTGACCTGAGGAGAACTGTGCTCCGCCTTCAG", testSAMRecord.seq);
EXPECT_EQ("0;==-==9;>>>>>=>>>>>>>>>>>=>>>>>>>>>>", testSAMRecord.qual);
EXPECT_EQ("XT:A:U NM:i:0 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:37", testSAMRecord.tags);
#endif
testSAMIStringStream >> testSAMRecord;
EXPECT_EQ("19:20389:F:275+18M2D19M", testSAMRecord.qname);
EXPECT_EQ(99, testSAMRecord.flag);
EXPECT_EQ("1", testSAMRecord.rname);
EXPECT_EQ(17643, testSAMRecord.pos);
EXPECT_EQ(0, testSAMRecord.mapq);
EXPECT_EQ("37M", testSAMRecord.cigar);
EXPECT_EQ("1", testSAMRecord.mrnm);
EXPECT_EQ(17918, testSAMRecord.mpos);
EXPECT_EQ(314, testSAMRecord.isize);
#if SAM_SEQ_QUAL
EXPECT_EQ("TATGACTGCTAATAATACCTACACATGTTAGAACCAT", testSAMRecord.seq);
EXPECT_EQ(">>>>>>>>>>>>>>>>>>>><<>>><<>>4::>>:<9", testSAMRecord.qual);
EXPECT_EQ("RG:Z:UM0098:1 XT:A:R NM:i:0 SM:i:0 AM:i:0 X0:i:4 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:37", testSAMRecord.tags);
#endif
}
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