You can not select more than 25 topics Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
 
 
 

102 lines
3.1 KiB

/*
This file is part of BioD.
Copyright (C) 2012 Artem Tarasov <lomereiter@gmail.com>
BioD is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
BioD is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
module bio.bam.splitter;
import bio.bam.read;
import std.array;
import std.functional;
import std.range;
import std.traits;
/// Constructs range of chunks where sum { fn(read) | read in chunk }
/// does not exceed given number.
struct ReadRangeSplitter(R, alias fn)
{
this(R range, size_t threshold, bool split_by_ref) {
_range = range;
_size = threshold;
_split_by_ref = split_by_ref;
_appender = appender!(ElementType!R[])();
getNextChunk();
}
private {
R _range;
bool _empty;
bool _split_by_ref;
size_t _size;
Appender!(ElementType!R[]) _appender;
}
bool empty() @property {
return _empty;
}
ElementType!R[] front() @property {
return _appender.data.dup;
}
void popFront() {
_appender.clear();
getNextChunk();
}
private void getNextChunk() {
if (_range.empty) {
_empty = true;
return;
}
auto first_read = _range.front;
_range.popFront();
size_t total_size = first_read.size_in_bytes;
auto average_size_estimate = unaryFun!fn(first_read);
_appender.reserve(_size / average_size_estimate);
_appender.put(first_read);
while (total_size <= _size && !_range.empty) {
auto read = _range.front;
if (_split_by_ref && (read.ref_id != first_read.ref_id)) {
break;
}
total_size += unaryFun!fn(read);
_appender.put(read);
_range.popFront();
}
}
}
/// Split range in chunks where total amount of memory consumed by all reads
/// in the chunk is roughly chunk_size bytes.
///
/// Parameter $(D split_by_ref) specifies that each chunk should contain reads
/// aligned to the same reference. In most cases, this simplifies post-processing,
/// but in some cases this is not required, therefore it is optional.
auto chunksConsumingLessThan(R)(R reads, size_t size_in_bytes, bool split_by_ref=true) {
return ReadRangeSplitter!(R, "a.size_in_bytes")(reads, size_in_bytes, split_by_ref);
}
/// Split range in chunks each containing no more than N reads
auto chunksOfSize(R)(R reads, size_t N, bool split_by_ref=true) {
return ReadRangeSplitter!(R, "1")(reads, N, split_by_ref);
}