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module bio.std.sff.writer;
import bio.std.sff.constants;
import bio.std.sff.utils.roundup;
import bio.core.utils.stream;
import contrib.undead.stream;
import std.system;
/// Class for outputting SFF files
class SffWriter {
/// Create new writer.
this(string filename, string flow_order, string key_sequence)
{
_filename = filename;
_flow_order = flow_order;
_key_seq = key_sequence;
auto f = new bio.core.utils.stream.File(filename, "wb+");
auto stream = new BufferedStream(f, 1024576);
_endian_stream = new EndianStream(stream, Endian.bigEndian);
writeHeader();
}
/// Flow order
string flow_order() @property const {
return _flow_order;
}
/// Key sequence
string key_sequence() @property const {
return _key_seq;
}
/// Add a read to the end of file
void append(R)(R sff_read) {
// compute read_header_length
ushort exact_read_header_length = cast(ushort)(16 + sff_read.name.length);
ushort read_header_length = roundup(exact_read_header_length);
_endian_stream.write(read_header_length);
_endian_stream.write(cast(ushort)sff_read.name.length);
_endian_stream.write(cast(uint)sff_read.bases.length);
_endian_stream.write(sff_read.clip_qual_left);
_endian_stream.write(sff_read.clip_qual_right);
_endian_stream.write(sff_read.clip_adapter_left);
_endian_stream.write(sff_read.clip_adapter_right);
_endian_stream.writeExact(sff_read.name.ptr, sff_read.name.length);
for (size_t i = 0; i < read_header_length - exact_read_header_length; ++i)
_endian_stream.write(cast(ubyte)0);
for (size_t i = 0; i < _flow_order.length; ++i)
_endian_stream.write(sff_read.flowgram_values[i]);
auto n_bases = sff_read.bases.length;
_endian_stream.writeExact(sff_read.flow_index_per_base.ptr, n_bases);
_endian_stream.writeExact(sff_read.bases.ptr, n_bases);
_endian_stream.writeExact(sff_read.quality_scores.ptr, n_bases);
auto k = 2 * _flow_order.length + 3 * n_bases;
auto padding = roundup(k) - k;
for (size_t i = 0; i < padding; ++i)
_endian_stream.write(cast(ubyte)0);
++_n_reads;
}
/// Flush all buffers and update number of reads in the file header
void finish() {
updateNumberOfReads();
_endian_stream.close();
}
private {
string _filename;
string _flow_order;
string _key_seq;
Stream _endian_stream;
uint _n_reads;
ushort _exact_header_len() @property const {
return cast(ushort)(31 + _flow_order.length + _key_seq.length);
}
ushort _header_len() @property const {
return roundup(_exact_header_len);
}
void writeHeader() {
_endian_stream.write(SFF_MAGIC);
_endian_stream.writeExact(SFF_VERSION.ptr, 4);
_endian_stream.write(0UL);
_endian_stream.write(0U);
_endian_stream.write(_n_reads);
_endian_stream.write(_header_len);
_endian_stream.write(cast(ushort)_key_seq.length);
_endian_stream.write(cast(ushort)_flow_order.length);
_endian_stream.write(cast(ubyte)1);
_endian_stream.writeExact(_flow_order.ptr, _flow_order.length);
_endian_stream.writeExact(_key_seq.ptr, _key_seq.length);
for (size_t i = 0; i < _header_len - _exact_header_len; ++i)
_endian_stream.write(cast(ubyte)0);
}
void updateNumberOfReads() {
auto old_pos = _endian_stream.position;
_endian_stream.position = 20;
_endian_stream.write(_n_reads);
_endian_stream.position = old_pos;
}
}
}
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