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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: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
// ==========================================================================
#ifndef SEQAN_INCLUDE_SEQAN_VCF_WRITE_VCF_H_
#define SEQAN_INCLUDE_SEQAN_VCF_WRITE_VCF_H_
namespace seqan2 {
// ============================================================================
// Functions
// ============================================================================
// ----------------------------------------------------------------------------
// Function writeHeader() [VcfHeader]
// ----------------------------------------------------------------------------
template <typename TTarget, typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
inline void
writeHeader(TTarget & target,
VcfHeader const & header,
VcfIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context,
Vcf const & /*tag*/)
{
for (unsigned i = 0; i < length(header); ++i)
{
write(target, "##");
write(target, header[i].key);
writeValue(target, '=');
write(target, header[i].value);
writeValue(target, '\n');
}
write(target, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT");
for (unsigned i = 0; i < length(sampleNames(context)); ++i)
{
writeValue(target, '\t');
write(target, sampleNames(context)[i]);
}
writeValue(target, '\n');
}
// ----------------------------------------------------------------------------
// Function writeRecord() [VcfRecord]
// ----------------------------------------------------------------------------
template <typename TTarget, typename TNameStore, typename TNameStoreCache, typename TStorageSpec>
inline void
writeRecord(TTarget & target,
VcfRecord const & record,
VcfIOContext<TNameStore, TNameStoreCache, TStorageSpec> & context,
Vcf const & /*tag*/)
{
// CHROM
write(target, contigNames(context)[record.rID]);
writeValue(target, '\t');
// POS
appendNumber(target, record.beginPos + 1);
writeValue(target, '\t');
// ID
if (empty(record.id))
writeValue(target, '.');
else
write(target, record.id);
writeValue(target, '\t');
// REF
if (empty(record.ref))
writeValue(target, '.');
else
write(target, record.ref);
writeValue(target, '\t');
// ALT
if (empty(record.alt))
writeValue(target, '.');
else
write(target, record.alt);
writeValue(target, '\t');
// QUAL
if (record.qual != record.qual) // only way to test for nan
writeValue(target, '.');
else
appendNumber(target, record.qual);
// FILTER
writeValue(target, '\t');
if (empty(record.filter))
writeValue(target, '.');
else
write(target, record.filter);
writeValue(target, '\t');
// INFO
if (empty(record.info))
writeValue(target, '.');
else
write(target, record.info);
// FORMAT
writeValue(target, '\t');
if (empty(record.format))
writeValue(target, '.');
else
write(target, record.format);
// The samples.
for (unsigned i = 0; i < length(record.genotypeInfos); ++i)
{
writeValue(target, '\t');
if (empty(record.genotypeInfos[i]))
writeValue(target, '.');
else
write(target, record.genotypeInfos[i]);
}
writeValue(target, '\n');
}
} // namespace seqan2
#endif // #ifndef SEQAN_INCLUDE_SEQAN_VCF_WRITE_VCF_H_
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