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// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2020, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2020, Knut Reinert & MPI für molekulare Genetik
// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
// shipped with this file and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md
// -----------------------------------------------------------------------------------------------------
#include <gtest/gtest.h>
#include <seqan3/test/expect_range_eq.hpp>
#include "alignment_file_format_test_template.hpp"
template <>
struct alignment_file_read<seqan3::format_sam> : public alignment_file_data
{
// -----------------------------------------------------------------------------------------------------------------
// formatted input
// -----------------------------------------------------------------------------------------------------------------
using stream_type = std::istringstream;
std::string big_header_input{
R"(@HD VN:1.6 SO:coordinate SS:coordinate:queryname GO:none
@PG ID:qc PN:quality_control CL:qc -f file1 DS:trim reads with low qual VN:1.0.0
@PG ID:novoalign PN:novoalign VN:V3.02.07 CL:novoalign -d /path/hs37d5.ndx -f /path/file.fastq.gz PP:qc
@SQ SN:ref LN:249250621
@SQ SN:ref2 LN:243199373 AS:hs37d5
@RG ID:U0a_A2_L1 PL:illumina PU:1 LB:1 SM:NA12878
@RG ID:U0a_A2_L2 PL:illumina SM:NA12878 PU:1 LB:1
@CO Tralalalalalala this is a comment
)"};
std::string simple_three_reads_input{
R"(@HD VN:1.6
@SQ SN:ref LN:34
read1 41 ref 1 61 1S1M1D1M1I ref 10 300 ACGT !##$ AS:i:2 NM:i:7
read2 42 ref 2 62 1H7M1D1M1S2H ref 10 300 AGGCTGNAG !##$&'()* xy:B:S,3,4,5
read3 43 ref 3 63 1S1M1P1M1I1M1I1D1M1S ref 10 300 GGAGTATA !!*+,-./
)"};
std::string verbose_reads_input{
"read1\t41\tref\t1\t61\t1S1M1D1M1I\t=\t10\t300\tACGT\t!##$\taa:A:c"
"\tNM:i:-7"
"\tAS:i:2"
"\tff:f:3.1"
"\tzz:Z:str"
"\tCC:i:300"
"\tcc:i:-300\n"
"read2\t42\tref\t2\t62\t1H7M1D1M1S\tref\t10\t300\tAGGCTGNAG\t!##$&'()*\tbc:B:c,-3"
"\tbC:B:C,3,200"
"\tbs:B:s,-3,200,-300"
"\tbS:B:S,300,40,500"
"\tbi:B:i,-3,200,-66000"
"\tbI:B:I,294967296"
"\tbf:B:f,3.5,0.1,43.8\n"
"read3\t43\tref\t3\t63\t1S1M1P1M1I1M1I1D1M1S\tref\t10\t300\tGGAGTATA\t!!*+,-./\n"};
std::string empty_input{"@HD\tVN:1.6\n@SQ\tSN:ref\tLN:34\n*\t0\t*\t0\t0\t*\t*\t0\t0\t*\t*\n"};
std::string empty_cigar{"read1\t41\tref\t1\t61\t*\tref\t10\t300\tACGT\t!##$\n"};
std::string unknown_ref{"read1\t41\traf\t1\t61\t1S1M1D1M1I\t=\t10\t300\tACGT\t!##$\taa:A:c\tAS:i:2\tff:f:3.1\tzz:Z:str\n"};
std::string unknown_ref_header{"@HD\tVN:1.6\n@SQ\tSN:ref\tLN:34\n*\t0\tunknown_ref\t1\t0\t4M\t*\t0\t0\tAAAA\t*\n"};
// -----------------------------------------------------------------------------------------------------------------
// formatted output
// -----------------------------------------------------------------------------------------------------------------
std::string simple_three_reads_output{ // compared to simple_three_reads_input this has no hard clipping
R"(@HD VN:1.6
@SQ SN:ref LN:34
read1 41 ref 1 61 1S1M1D1M1I ref 10 300 ACGT !##$ AS:i:2 NM:i:7
read2 42 ref 2 62 7M1D1M1S ref 10 300 AGGCTGNAG !##$&'()* xy:B:S,3,4,5
read3 43 ref 3 63 1S1M1P1M1I1M1I1D1M1S ref 10 300 GGAGTATA !!*+,-./
)"};
std::string verbose_output{
R"(@HD VN:1.6 SO:unknown GO:none
@SQ SN:ref LN:34 AN:other_name
@RG ID:group1 more info
@PG ID:prog1 PN:cool_program CL:./prog1 PP:a DS:b VN:c
@CO This is a comment.
read1 41 ref 1 61 1S1M1D1M1I ref 10 300 ACGT !##$ AS:i:2 CC:i:300 NM:i:-7 aa:A:c cc:i:-300 ff:f:3.1 zz:Z:str
read2 42 ref 2 62 7M1D1M1S ref 10 300 AGGCTGNAG !##$&'()* bC:B:C,3,200 bI:B:I,294967296 bS:B:S,300,40,500 bc:B:c,-3 bf:B:f,3.5,0.1,43.8 bi:B:i,-3,200,-66000 bs:B:s,-3,200,-300
read3 43 ref 3 63 1S1M1P1M1I1M1I1D1M1S ref 10 300 GGAGTATA !!*+,-./
)"};
std::string special_output{
R"(@HD VN:1.6
@SQ SN:ref LN:34
read1 41 * 1 61 1S1M1D1M1I * 0 0 ACGT !##$
)"};
};
// ---------------------------------------------------------------------------------------------------------------------
// parametrized tests
// ---------------------------------------------------------------------------------------------------------------------
INSTANTIATE_TYPED_TEST_SUITE_P(sam, alignment_file_read, seqan3::format_sam, );
INSTANTIATE_TYPED_TEST_SUITE_P(sam, alignment_file_write, seqan3::format_sam, );
// ---------------------------------------------------------------------------------------------------------------------
// SAM specifics
// ---------------------------------------------------------------------------------------------------------------------
struct sam_format : public alignment_file_data
{};
// since BAM uses the same read header function from SAM, it only needs to be tested once
TEST_F(sam_format, header_errors)
{
{
std::string header_str
{
"@HD\tVN:1.0\tTT:this is not a valid tag\n"
};
std::istringstream istream(header_str);
seqan3::alignment_file_input fin{istream, seqan3::format_sam{}};
EXPECT_THROW(fin.begin(), seqan3::format_error);
}
{
std::string header_str
{
"@HD\tVN:1.0\tSI:this is not a valid tag starting with S\n"
};
std::istringstream istream(header_str);
seqan3::alignment_file_input fin{istream, seqan3::format_sam{}};
EXPECT_THROW(fin.begin(), seqan3::format_error);
}
{
std::string header_str
{
"@HD\tVN:1.0\n"
"@TT\tthis is not a valid tag\n"
};
std::istringstream istream(header_str);
seqan3::alignment_file_input fin{istream, seqan3::format_sam{}};
EXPECT_THROW(fin.begin(), seqan3::format_error);
}
{
std::string header_str
{
"@HD\tVN:1.0\n"
"@PG\tID:prog\tTT:this is not a valid tag\n"
};
std::istringstream istream(header_str);
seqan3::alignment_file_input fin{istream, seqan3::format_sam{}};
EXPECT_THROW(fin.begin(), seqan3::format_error);
}
{
std::string header_str
{
"@HD\tVN:1.0\n"
"@SQ\tSN:unknown_ref\tLN:0\n"
};
std::istringstream istream(header_str);
seqan3::alignment_file_input fin{istream, this->ref_ids, this->ref_sequences, seqan3::format_sam{}};
EXPECT_THROW(fin.begin(), seqan3::format_error);
}
{
std::string header_str
{
"@HD\tVN:1.0\n"
"@SQ\tSN:ref\tLN:0\n" /*wrong length*/
};
std::istringstream istream(header_str);
seqan3::alignment_file_input fin{istream, this->ref_ids, this->ref_sequences, seqan3::format_sam{}};
EXPECT_THROW(fin.begin(), seqan3::format_error);
}
}
TEST_F(sam_format, no_hd_line_in_header)
{
// the header line (@HD) is optional
std::istringstream istream{std::string{"@SQ\tSN:ref\tLN:34\nread1\t41\tref\t1\t61\t*\tref\t10\t300\tACGT\t!##$\n"}};
seqan3::alignment_file_input fin{istream, seqan3::format_sam{}, seqan3::fields<seqan3::field::id>{}};
EXPECT_EQ(seqan3::get<seqan3::field::id>(*fin.begin()), std::string{"read1"});
}
TEST_F(sam_format, windows_file)
{
std::istringstream istream(std::string("read1\t41\tref\t1\t61\t*\tref\t10\t300\tACGT\t!##$\r\n"));
seqan3::alignment_file_input fin{istream, seqan3::format_sam{}, seqan3::fields<seqan3::field::id>{}};
EXPECT_EQ(seqan3::get<seqan3::field::id>(*fin.begin()), std::string{"read1"});
}
TEST_F(sam_format, format_error_illegal_character_in_seq)
{
std::istringstream istream(std::string("*\t0\t*\t0\t0\t*\t*\t0\t0\tAC!T\t*\n"));
seqan3::alignment_file_input fin{istream, seqan3::format_sam{}};
EXPECT_THROW(fin.begin(), seqan3::parse_error);
}
TEST_F(sam_format, format_error_invalid_arithmetic_value)
{
// invalid value
std::istringstream istream(std::string("*\t0\t*\t1abc\t0\t*\t*\t0\t0\t*\t*\n"));
{
seqan3::alignment_file_input fin{istream, seqan3::format_sam{}};
EXPECT_THROW(fin.begin(), seqan3::format_error);
}
// overflow error
{
istream = std::istringstream(std::string("*\t0\t*\t2147483650\t0\t*\t*\t0\t0\t*\t*\n"));
seqan3::alignment_file_input fin{istream, seqan3::format_sam{}};
EXPECT_THROW(fin.begin(), seqan3::format_error);
}
// negative value as ref_offset
{
istream = std::istringstream(std::string("*\t0\t*\t-3\t0\t*\t*\t0\t0\t*\t*\n"));
seqan3::alignment_file_input fin{istream, seqan3::format_sam{}};
EXPECT_THROW(fin.begin(), seqan3::format_error);
}
// negative value as mate mapping position
{
istream = std::istringstream(std::string("*\t0\t*\t0\t0\t*\t*\t-3\t0\t*\t*\n"));
seqan3::alignment_file_input fin{istream, seqan3::format_sam{}};
EXPECT_THROW(fin.begin(), seqan3::format_error);
}
}
TEST_F(sam_format, format_error_invalid_cigar)
{
// unkown operation
std::istringstream istream(std::string("*\t0\t*\t0\t0\t5Z\t*\t0\t0\t*\t*\n"));
{
seqan3::alignment_file_input fin{istream, seqan3::format_sam{}};
EXPECT_THROW(fin.begin(), seqan3::format_error);
}
// negative number as operation count
{
istream = std::istringstream(std::string("*\t0\t*\t0\t0\t-5M\t*\t0\t0\t*\t*\n"));
seqan3::alignment_file_input fin{istream, seqan3::format_sam{}};
EXPECT_THROW(fin.begin(), seqan3::format_error);
}
{
istream = std::istringstream(std::string("*\t0\t*\t0\t0\t3S4M1I-5M2D2M\t*\t0\t0\t*\t*\n"));
seqan3::alignment_file_input fin{istream, seqan3::format_sam{}};
EXPECT_THROW(fin.begin(), seqan3::format_error);
}
}
TEST_F(sam_format, format_error_invalid_sam_tag_format)
{
// type identifier is wrong
std::istringstream istream(std::string("*\t0\t*\t0\t0\t*\t*\t0\t0\t*\t*\tNM:X:3\n"));
{
seqan3::alignment_file_input fin{istream, seqan3::format_sam{}};
EXPECT_THROW(fin.begin(), seqan3::format_error);
}
// Array subtype identifier is wrong
{
istream = std::istringstream(std::string("*\t0\t*\t0\t0\t*\t*\t0\t0\t*\t*\tNM:B:x3,4\n"));
seqan3::alignment_file_input fin{istream, seqan3::format_sam{}};
EXPECT_THROW(fin.begin(), seqan3::format_error);
}
}
TEST_F(sam_format, short_cigar_string_with_softclipping)
{
using seqan3::operator""_dna5;
// The member function transfer_soft_clipping_to needs to work on 2 element cigar strings
{
std::istringstream istream("id 16 ref 0 255 10M5S * 0 0 AGAGGGGGATAACCA *\n");
seqan3::alignment_file_input fin{istream,
ref_ids,
ref_sequences,
seqan3::format_sam{},
seqan3::fields<seqan3::field::alignment>{}};
EXPECT_RANGE_EQ(std::get<1>(std::get<0>(*fin.begin())), "AGAGGGGGAT"_dna5);
}
{
std::istringstream istream("id 16 ref 0 255 5S10M * 0 0 AGAGGGGGATAACCA *\n");
seqan3::alignment_file_input fin{istream,
ref_ids,
ref_sequences,
seqan3::format_sam{},
seqan3::fields<seqan3::field::alignment>{}};
EXPECT_RANGE_EQ(std::get<1>(std::get<0>(*fin.begin())), "GGGATAACCA"_dna5);
}
}
TEST_F(sam_format, write_different_header)
{
std::ostringstream ostream;
auto write_header = [&] ()
{
seqan3::alignment_file_output fout{ostream, seqan3::format_sam{}, seqan3::fields<seqan3::field::header_ptr,
seqan3::field::ref_id,
seqan3::field::ref_offset>{}};
ASSERT_NO_THROW(fout.emplace_back(&header, this->ref_id, 0));
};
header.sorting = "unsorted";
header.grouping = "query";
write_header();
ostream.flush();
EXPECT_EQ(ostream.str(),
"@HD\tVN:1.6\tSO:unsorted\tGO:query\n@SQ\tSN:ref\tLN:34\n*\t0\tref\t1\t0\t*\t*\t0\t0\t*\t*\n");
ostream = std::ostringstream{};
header.sorting = "queryname";
header.grouping = "reference";
write_header();
ostream.flush();
EXPECT_EQ(ostream.str(),
"@HD\tVN:1.6\tSO:queryname\tGO:reference\n@SQ\tSN:ref\tLN:34\n*\t0\tref\t1\t0\t*\t*\t0\t0\t*\t*\n");
ostream = std::ostringstream{};
header.sorting = "coordinate";
header.subsorting = "query";
write_header();
ostream.flush();
EXPECT_EQ(ostream.str(),
"@HD\tVN:1.6\tSO:coordinate\tSS:query\tGO:reference\n@SQ\tSN:ref\tLN:34\n*\t0\tref\t1\t0\t*\t*\t0\t0\t*\t*\n");
}
|
