21 #if defined(SEQAN3_HAS_BZIP2)
22 #include <seqan3/contrib/stream/bz2_ostream.hpp>
24 #if defined(SEQAN3_HAS_ZLIB)
25 #include <seqan3/contrib/stream/bgzf_ostream.hpp>
26 #include <seqan3/contrib/stream/gz_ostream.hpp>
31 namespace seqan3::detail
41 template <builtin_
character
char_t>
42 inline auto make_secondary_ostream(std::basic_ostream<char_t> & primary_stream, std::filesystem::path & filename)
43 -> std::unique_ptr<std::basic_ostream<char_t>, std::function<void(std::basic_ostream<char_t>*)>>
46 constexpr
auto stream_deleter_noop = [] (std::basic_ostream<char_t> *) {};
48 [[maybe_unused]] constexpr
auto stream_deleter_default = [] (std::basic_ostream<char_t> * ptr) {
delete ptr; };
50 std::string extension = filename.extension().string();
52 if (extension ==
".gz")
54 #if defined(SEQAN3_HAS_ZLIB)
55 filename.replace_extension(
"");
56 return {
new contrib::basic_gz_ostream<char_t>{primary_stream}, stream_deleter_default};
58 throw file_open_error{
"Trying to write a gzipped file, but no ZLIB available."};
61 else if ((extension ==
".bgzf") || (extension ==
".bam"))
63 #if defined(SEQAN3_HAS_ZLIB)
64 if (extension !=
".bam")
65 filename.replace_extension(
"");
67 return {
new contrib::basic_bgzf_ostream<char_t>{primary_stream}, stream_deleter_default};
69 throw file_open_error{
"Trying to write a bgzf'ed file, but no ZLIB available."};
72 else if (extension ==
".bz2")
74 #if defined(SEQAN3_HAS_BZIP2)
75 filename.replace_extension(
"");
76 return {
new contrib::basic_bz2_ostream<char_t>{primary_stream}, stream_deleter_default};
78 throw file_open_error{
"Trying to write a bzipped file, but no libbz2 available."};
81 else if (extension ==
".zst")
83 throw file_open_error{
"Trying to write a zst'ed file, but SeqAn does not yet support this."};
86 return {&primary_stream, stream_deleter_noop};
Provides concepts for core language types and relations that don't have concepts in C++20 (yet).
This header includes C++17 filesystem support and imports it into namespace std::filesystem (independ...
Provides exceptions used in the I/O module.