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// ==========================================================================
// SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2026, Knut Reinert, FU Berlin
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of Knut Reinert or the FU Berlin nor the names of
// its contributors may be used to endorse or promote products derived
// from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
// DAMAGE.
//
// ==========================================================================
// Author: David Weese <david.weese@fu-berlin.de>
// ==========================================================================
// Basic definitions for the stream module
// ==========================================================================
#ifndef SEQAN_STREAM_STREAM_BASE_
#define SEQAN_STREAM_STREAM_BASE_
namespace seqan2 {
// ============================================================================
// Forwards
// ============================================================================
// ============================================================================
// Tags, Enums
// ============================================================================
// --------------------------------------------------------------------------
// Compression Type Tags
// --------------------------------------------------------------------------
/*!
* @defgroup FileCompressionTags File Compression Tags
* @brief Tags for describing file compression formats.
*/
/*!
* @tag FileCompressionTags#GZFile
* @headerfile <seqan/stream.h>
* @brief File compression using the popular <a href="https://www.gzip.org">gzip</a> format.
* @signature typedef Tag<GZFile_> GZFile;
*/
struct GZFile_;
typedef Tag<GZFile_> GZFile;
/*!
* @tag FileCompressionTags#BgzFile
* @headerfile <seqan/stream.h>
* @signature typedef Tag<BgzfFile_> BgzfFile;
* @brief File compression using the BGZF (Block GZip Format).
*
* The file format is described in the <a href="https://samtools.github.io/hts-specs/SAMv1.pdf">SAM file format
* description</a>.
*/
struct BgzfFile_;
typedef Tag<BgzfFile_> BgzfFile;
/*!
* @tag FileCompressionTags#BZ2File
* @headerfile <seqan/stream.h>
*
* @brief File compression using the popular <a href="https://bzip.org">bzip2</a> format.
*
* @signature typedef Tag<BZ2File_> BZ2File;
*/
struct BZ2File_;
typedef Tag<BZ2File_> BZ2File;
// --------------------------------------------------------------------------
// MagicHeader
// --------------------------------------------------------------------------
template <typename T>
struct MagicHeader<GZFile, T>
{
static char const VALUE[3];
};
template <typename T>
char const MagicHeader<GZFile, T>::VALUE[3] = { 0x1f, '\x8b', 0x08 }; // gzip's magic number
template <typename T>
struct MagicHeader<BZ2File, T>
{
static char const VALUE[3];
};
template <typename T>
char const MagicHeader<BZ2File, T>::VALUE[3] = { 0x42, 0x5a, 0x68 }; // bzip2's magic number
// --------------------------------------------------------------------------
// FileExtensions
// --------------------------------------------------------------------------
template <typename T>
struct FileExtensions<GZFile, T>
{
static char const * VALUE[1];
};
template <typename T>
char const * FileExtensions<GZFile, T>::VALUE[1] =
{
".gz" // default output extension
};
template <typename T>
struct FileExtensions<BgzfFile, T>
{
static char const * VALUE[5];
};
template <typename T>
char const * FileExtensions<BgzfFile, T>::VALUE[5] =
{
".bgzf", // default output extension
".bam", // BAM files are bgzf compressed
".vcf.gz", // Compressed and indexed VCF files are bgzf compressed
".bed.gz", // Compressed and indexed BED files are bgzf compressed
".tbi" // Tabix index files are bgzf compressed
};
template <typename T>
struct FileExtensions<BZ2File, T>
{
static char const * VALUE[1];
};
template <typename T>
char const * FileExtensions<BZ2File, T>::VALUE[1] =
{
".bz2" // default output extension
};
// ============================================================================
// Functions
// ============================================================================
// --------------------------------------------------------------------------
// Function _isPipe()
// --------------------------------------------------------------------------
inline bool
_isPipe(const char * fileName)
{
#ifdef STDLIB_VS
struct _stat buf;
if (_stat(fileName, &buf) == 0)
if ((buf.st_mode & _S_IFMT) == _S_IFCHR)
return true;
#else
struct stat buf;
if (stat(fileName, &buf) == 0)
if ((buf.st_mode & S_IFMT) == S_IFIFO ||
(buf.st_mode & S_IFMT) == S_IFCHR)
return true;
#endif
return false;
}
// --------------------------------------------------------------------------
// Function guessFormat()
// --------------------------------------------------------------------------
// read first bytes of a file/stream and compare with file format's magic header
template <typename TStream, typename TFormat_>
inline bool
guessFormatFromStream(TStream &istream, Tag<TFormat_>)
{
typedef Tag<TFormat_> TFormat;
SEQAN_ASSERT(istream.good());
// For any instance of this function template, the following comparison will either be always true,
// or always false. E.g., the bzip files will always have a magic header. The "Nothing" file or
// SimpleIntervalsFile do not have a magic header, i.e. NULL.
// This could also be solved by:
// * Adding specialisations. However, this would need some forward declarations, etc.
// * if constexpr. This would require to make all VALUE static constexpr.
#if defined(__GNUC__)
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Waddress"
#endif
if ((char *)MagicHeader<TFormat>::VALUE == NULL)
return true;
#if defined(__GNUC__)
#pragma GCC diagnostic pop
#endif
bool match = true;
// check magic header
unsigned i;
for (i = 0; i != sizeof(MagicHeader<TFormat>::VALUE) / (sizeof(char)); ++i)
{
int c = (int)istream.get();
if (c != (unsigned char)MagicHeader<TFormat>::VALUE[i])
{
match = false;
if (c != EOF)
++i;
break;
}
}
// unget all read characters
for (; i > 0; --i)
istream.unget();
SEQAN_ASSERT(istream.good());
return match;
}
} // namespace seqan2
#endif // #ifndef SEQAN_STREAM_STREAM_BASE_
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