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/*
New style BAM writer. This file is part of Sambamba.
Copyright (C) 2017 Pjotr Prins <pjotr.prins@thebird.nl>
Sambamba 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.
Sambamba 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.std.experimental.hts.bam.writer;
import std.conv;
import core.stdc.stdio: fopen, fread, fclose;
import std.exception;
import std.file;
import std.stdio;
import std.string;
import std.typecons;
import std.bitmanip;
import bio.std.hts.bam.cigar; //depends on undead
import bio.std.hts.bam.constants;
import bio.std.experimental.hts.bgzf;
import bio.std.experimental.hts.bgzf_writer;
import bio.std.experimental.hts.constants;
import bio.std.experimental.hts.bam.header;
import bio.std.experimental.hts.bam.reader : ProcessReadBlob, Offset;
struct ModifyProcessReadBlob { // make this generic later
ProcessReadBlob _read2;
@property ubyte[] toBlob() {
return _read2.toBlob();
}
@property void set_qc_fail() {
auto data = _read2.toBlob;
// writeln(_read2._flag);
// data[Offset.flag_nc] = data[Offset.flag_nc] & 0x200;
// writeln(data[Offset.flag_nc]);
// buf.write!(T,Endian.littleEndian)(value,0);
// ushort _flag() { return fetch!ushort(Offset.flag); }
ushort flag = _read2._flag | 0x200;
// writeln("flag=",flag);
data[Offset.flag..Offset.flag+4].write!(ushort,Endian.littleEndian)(flag,0);
}
}
struct BamWriter {
BgzfWriter bgzf_writer;
this(string fn, ref BamHeader header, int compression_level = -1) {
bgzf_writer = BgzfWriter(fn,compression_level);
write_bam_header(bgzf_writer,header);
}
void push(ModifyProcessReadBlob read) {
auto mod = read;
auto blob = mod.toBlob;
// another hack for now:
bgzf_writer.write!int(cast(int)(blob.length+2*int.sizeof));
bgzf_writer.write!int(cast(int)mod._read2.raw_ref_id);
bgzf_writer.write!int(cast(int)mod._read2.raw_start_pos);
bgzf_writer.write(blob);
}
void push(ProcessReadBlob read) {
push(ModifyProcessReadBlob(read));
}
}
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