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/*
This file is part of BioD.
Copyright (C) 2012 Artem Tarasov <lomereiter@gmail.com>
Permission is hereby granted, free of charge, to any person obtaining a
copy of this software and associated documentation files (the "Software"),
to deal in the Software without restriction, including without limitation
the rights to use, copy, modify, merge, publish, distribute, sublicense,
and/or sell copies of the Software, and to permit persons to whom the
Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE.
*/
module bio.sff.reader;
public import bio.sff.index;
import bio.sff.read;
import bio.sff.readrange;
import bio.sff.constants;
import bio.core.utils.stream;
import undead.stream;
import std.system;
import std.range;
import std.exception;
/// SFF file reader
class SffReader {
/// Open file by filename
this(string filename) {
_filename = filename;
_readHeader();
}
/// Reads
auto reads() @property {
auto stream = new bio.core.utils.stream.File(filename);
Stream sff = new EndianStream(stream, Endian.bigEndian);
sff.seekSet(_header_length);
auto sff_reads = SffReadRange(sff, cast(ushort)_flow_chars.length, _index_location);
return takeExactly(sff_reads, _n_reads);
}
///
SffRead getReadAtOffset(size_t offset) {
auto stream = new bio.core.utils.stream.File(filename);
Stream sff = new EndianStream(stream, Endian.bigEndian);
sff.seekSet(offset);
auto read = SffReadRange(sff, cast(ushort)_flow_chars.length, _index_location).front;
sff.close();
return read;
}
/// File name
string filename() @property const {
return _filename;
}
/// Location of the index (if included).
IndexLocation index_location() @property const {
return _index_location;
}
///
bool has_index() @property const {
return _index_location.offset != 0 && _index_location.length != 0;
}
/// Set index location (saves new index location to the file)
void index_location(IndexLocation location) @property {
_index_location = location;
// offset spans 8 bytes (8 .. 16),
// length spans 4 bytes (16 .. 20)
auto stream = new bio.core.utils.stream.File(filename, "r+");
stream.seekSet(8);
auto endian_stream = new EndianStream(stream, Endian.bigEndian);
endian_stream.write(location.offset);
endian_stream.write(location.length);
endian_stream.close();
}
/// Nucleotides used for each flow of each read
string flow_order() @property const {
return _flow_chars;
}
/// Nucleotide bases of the key sequence used for each read
string key_sequence() @property const {
return _key_sequence;
}
private {
string _filename;
uint _magic_number;
char[4] _version;
uint _n_reads;
ushort _header_length;
string _flow_chars;
string _key_sequence;
IndexLocation _index_location;
void _readHeader() {
auto stream = new bio.core.utils.stream.File(_filename);
auto sff = new EndianStream(stream, Endian.bigEndian);
sff.read(_magic_number);
enforce(_magic_number == SFF_MAGIC, "Wrong magic number, expected 0x2E736666");
sff.readExact(_version.ptr, 4);
enforce(_version == SFF_VERSION, "Unsupported version, expected 1");
sff.read(_index_location.offset);
sff.read(_index_location.length);
sff.read(_n_reads);
sff.read(_header_length);
ushort _key_length;
ushort _number_of_flows;
ubyte _flowgram_format_code;
sff.read(_key_length);
sff.read(_number_of_flows);
sff.read(_flowgram_format_code);
enforce(_flowgram_format_code == 1,
"Flowgram format codes other than 1 are not supported");
_flow_chars = cast(string)sff.readString(_number_of_flows);
_key_sequence = cast(string)sff.readString(_key_length);
}
}
}