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[MISC] Update biocpp-core and biocpp-io #239

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Oct 26, 2022
Merged

[MISC] Update biocpp-core and biocpp-io #239

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6 changes: 3 additions & 3 deletions include/variant_detection/variant_output.hpp
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
#pragma once

#include <bio/io/var_io/writer.hpp>
#include <bio/io/var/writer.hpp>

#include "iGenVar.hpp" // for cmd_arguments
#include "structures/cluster.hpp" // for class Cluster
Expand All @@ -19,7 +19,7 @@ std::string transTime();
*/
void write_header(std::map<std::string, int32_t> & references_lengths,
std::string sample_name,
bio::io::var_io::header & hdr);
bio::io::var::header & hdr);

/*! \brief Detects genomic variants from junction clusters and saves them in a record vector.
*
Expand All @@ -43,7 +43,7 @@ void write_header(std::map<std::string, int32_t> & references_lengths,
void write_record(Cluster const & cluster,
cmd_arguments const & args,
bool & found_SV,
bio::io::var_io::record<> & record);
bio::io::var::record<> & record);

/*! \brief Detects genomic variants from junction clusters and prints them in output file in VCF format.
*
Expand Down
2 changes: 1 addition & 1 deletion lib/biocpp-core
Open in desktop
Submodule biocpp-core updated 13 files
+2 −2 CHANGELOG.md
+2 −2 README.md
+2 −2 doc/biocpp/api.md
+27 −14 doc/biocpp/overview.md
+9 −18 doc/core/tutorial_ranges/index.md
+1 −1 include/bio/alphabet/aminoacid/aminoacid_base.hpp
+13 −6 include/bio/alphabet/composite/tuple_base.hpp
+1 −1 include/bio/alphabet/nucleotide/nucleotide_base.hpp
+1 −1 include/bio/ranges/container/bitcompressed_vector.hpp
+4 −3 include/bio/ranges/container/small_string.hpp
+9 −9 include/bio/ranges/container/small_vector.hpp
+2 −2 include/bio/ranges/detail/inherited_iterator_base.hpp
+1 −1 include/bio/ranges/detail/random_access_iterator.hpp
2 changes: 1 addition & 1 deletion lib/biocpp-io
Open in desktop
Submodule biocpp-io updated 94 files
+8 −3 .clang-format
+2 −0 .gitignore
+7 −22 doc/main_page.md
+1 −1 doc/record_based/1_introduction.md
+20 −20 doc/record_based/2_record_faq.md
+119 −11 include/bio/io.hpp
+0 −13 include/bio/io/all.hpp
+3 −21 include/bio/io/detail/concept.hpp
+1 −1 include/bio/io/detail/in_file_iterator.hpp
+1 −1 include/bio/io/detail/magic_get.hpp
+1 −1 include/bio/io/detail/out_file_iterator.hpp
+10 −34 include/bio/io/detail/range.hpp
+1 −1 include/bio/io/detail/to_string.hpp
+4 −4 include/bio/io/detail/tuple_record.hpp
+0 −12 include/bio/io/detail/utility.hpp
+1 −1 include/bio/io/detail/writer_base.hpp
+1 −1 include/bio/io/format/all.hpp
+4 −4 include/bio/io/format/bcf.hpp
+180 −186 include/bio/io/format/bcf_input_handler.hpp
+125 −122 include/bio/io/format/bcf_output_handler.hpp
+3 −3 include/bio/io/format/fasta.hpp
+5 −5 include/bio/io/format/fasta_input_handler.hpp
+3 −3 include/bio/io/format/fastq.hpp
+6 −6 include/bio/io/format/fastq_input_handler.hpp
+5 −4 include/bio/io/format/format_input_handler.hpp
+3 −3 include/bio/io/format/format_output_handler.hpp
+4 −4 include/bio/io/format/vcf.hpp
+91 −90 include/bio/io/format/vcf_input_handler.hpp
+40 −41 include/bio/io/format/vcf_output_handler.hpp
+1 −16 include/bio/io/misc.hpp
+1 −1 include/bio/io/misc/all.hpp
+2 −2 include/bio/io/misc/char_predicate.hpp
+0 −68 include/bio/io/platform.hpp
+1 −5 include/bio/io/seq/all.hpp
+14 −15 include/bio/io/seq/reader.hpp
+13 −14 include/bio/io/seq/reader_options.hpp
+52 −52 include/bio/io/seq/record.hpp
+1 −1 include/bio/io/stream/all.hpp
+5 −4 include/bio/io/stream/compression.hpp
+1 −1 include/bio/io/stream/concept.hpp
+2 −2 include/bio/io/stream/detail/bgzf_istream.hpp
+161 −168 include/bio/io/stream/detail/buffer_queue.hpp
+2 −3 include/bio/io/stream/transparent_istream.hpp
+2 −3 include/bio/io/stream/transparent_ostream.hpp
+1 −5 include/bio/io/txt/all.hpp
+16 −13 include/bio/io/txt/misc.hpp
+51 −56 include/bio/io/txt/reader.hpp
+31 −32 include/bio/io/txt/writer.hpp
+2 −6 include/bio/io/var/all.hpp
+23 −23 include/bio/io/var/header.hpp
+69 −71 include/bio/io/var/misc.hpp
+28 −28 include/bio/io/var/reader.hpp
+14 −14 include/bio/io/var/reader_options.hpp
+262 −210 include/bio/io/var/record.hpp
+27 −27 include/bio/io/var/writer.hpp
+8 −8 include/bio/io/var/writer_options.hpp
+1 −1 test/biocpp_require_core_infrastructure.cmake
+1 −1 test/documentation/bio_doxygen_cfg.in
+1 −1 test/documentation/doc_usr/CMakeLists.txt
+4 −4 test/snippet/detail/reader_base.cpp
+13 −13 test/snippet/seq/seq_reader.cpp
+0 −0 test/snippet/seq/seq_reader.out
+6 −6 test/snippet/seq/seq_reader_options.cpp
+5 −5 test/snippet/var/var_reader.cpp
+0 −0 test/snippet/var/var_reader.out
+6 −6 test/snippet/var/var_reader_options.cpp
+0 −0 test/snippet/var/var_reader_options.out
+19 −19 test/snippet/var/var_writer.cpp
+1 −1 test/unit/detail/index_tabix_test.cpp
+6 −5 test/unit/detail/tuple_record_test.cpp
+10 −11 test/unit/format/bcf_input_test.cpp
+5 −5 test/unit/format/bcf_output_test.cpp
+3 −3 test/unit/format/fasta_input_test.cpp
+3 −3 test/unit/format/fastq_input_test.cpp
+28 −29 test/unit/format/vcf_data.hpp
+25 −26 test/unit/format/vcf_input_test.cpp
+5 −5 test/unit/format/vcf_output_test.cpp
+0 −2 test/unit/plain_io/CMakeLists.txt
+1 −0 test/unit/seq/CMakeLists.txt
+0 −0 test/unit/seq/data.hpp
+260 −0 test/unit/seq/seq_reader_test.cpp
+0 −1 test/unit/seq_io/CMakeLists.txt
+0 −260 test/unit/seq_io/seq_io_reader_test.cpp
+2 −0 test/unit/txt/CMakeLists.txt
+32 −32 test/unit/txt/txt_reader_test.cpp
+13 −13 test/unit/txt/txt_writer_test.cpp
+5 −0 test/unit/var/CMakeLists.txt
+14 −14 test/unit/var/var_header_test.cpp
+361 −0 test/unit/var/var_reader_test.cpp
+37 −0 test/unit/var/var_record_test.cpp
+96 −99 test/unit/var/var_writer_test.cpp
+4 −4 test/unit/var/var_writer_test_issue53.cpp
+0 −4 test/unit/var_io/CMakeLists.txt
+0 −367 test/unit/var_io/var_io_reader_test.cpp
20 changes: 10 additions & 10 deletions src/variant_detection/variant_output.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -22,20 +22,20 @@ std::string transTime()

void write_header(std::map<std::string, int32_t> & references_lengths,
std::string sample_name,
bio::io::var_io::header & hdr)
bio::io::var::header & hdr)
{
hdr.file_format = "VCFv4.3";
// Default:
// hdr.filters.push_back({ .id = "PASS", .description = "All filters passed"});
hdr.infos.push_back({ .id = "END", .number = 1, .type_id = bio::io::var_io::value_type_id::int32,
hdr.infos.push_back({ .id = "END", .number = 1, .type_id = bio::io::var::value_type_id::int32,
.description = "End position of SV called."});
hdr.infos.push_back({ .id = "SVLEN", .number = 1, .type_id = bio::io::var_io::value_type_id::int32,
hdr.infos.push_back({ .id = "SVLEN", .number = 1, .type_id = bio::io::var::value_type_id::int32,
.description = "Difference in length between REF and ALT alleles."});
hdr.infos.push_back({ .id = "iGenVar_SVLEN", .number = 1, .type_id = bio::io::var_io::value_type_id::int32,
hdr.infos.push_back({ .id = "iGenVar_SVLEN", .number = 1, .type_id = bio::io::var::value_type_id::int32,
.description = "Length of SV called."});
hdr.infos.push_back({ .id = "SVTYPE", .number = 1, .type_id = bio::io::var_io::value_type_id::string,
hdr.infos.push_back({ .id = "SVTYPE", .number = 1, .type_id = bio::io::var::value_type_id::string,
.description = "Type of SV called."});
hdr.formats.push_back({ .id = "GT", .number = 1, .type_id = bio::io::var_io::value_type_id::string,
hdr.formats.push_back({ .id = "GT", .number = 1, .type_id = bio::io::var::value_type_id::string,
.description = "Genotype"});

for (auto const & [id, length] : references_lengths)
Expand All @@ -52,7 +52,7 @@ void write_header(std::map<std::string, int32_t> & references_lengths,
void write_record(Cluster const & cluster,
cmd_arguments const & args,
bool & found_SV,
bio::io::var_io::record<> & record)
bio::io::var::record<> & record)
{
Breakend mate1 = cluster.get_average_mate1();
Breakend mate2 = cluster.get_average_mate2();
Expand Down Expand Up @@ -150,18 +150,18 @@ void find_and_output_variants(std::map<std::string, int32_t> & references_length
cmd_arguments const & args,
std::filesystem::path const & output_file_path)
{
bio::io::var_io::header hdr{};
bio::io::var::header hdr{};
write_header(references_lengths, args.vcf_sample_name, hdr);

bio::io::var_io::record<> record{};
bio::io::var::record<> record{};
size_t amount_SVs = 0;
bool found_SV = false;

// Sets whether the standard C++ streams are synchronized to the standard C streams after each input/output operation.
std::ios::sync_with_stdio(false);

auto writer
= output_file_path.empty() ? bio::io::var_io::writer{std::cout, bio::io::vcf{}} : bio::io::var_io::writer{output_file_path};
= output_file_path.empty() ? bio::io::var::writer{std::cout, bio::io::vcf{}} : bio::io::var::writer{output_file_path};

writer.set_header(hdr);
for (size_t i = 0; i < clusters.size(); ++i)
Expand Down