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/*
New style BAM reader. This file is part of Sambamba.
Copyright (C) 2017,2018 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
*/
// This is a complete rewrite of Artem Tarasov's original reader.
module bio.std.experimental.hts.bam.header;
/*
import std.conv;
import core.stdc.stdio: fopen, fread, fclose;
import std.typecons;
import std.bitmanip;
import bio.bam.cigar;
*/
import std.exception;
import std.file;
import std.stdio;
import std.string;
// why import this from old bio.bam
// TODO check it depends on undead.
import bio.std.hts.bam.constants;
import bio.std.experimental.hts.bgzf;
import bio.std.experimental.hts.bgzf_writer;
// what is the difference btw these constants and the ones from bio.std.hts.bam.constants
import bio.std.experimental.hts.constants;
struct RefSequence {
size_d length;
string name;
}
struct BamHeader {
string id;
string text;
RefSequence[] refs;
@disable this(this); // disable copy semantics;
}
void fetch_bam_header(ref BamHeader header, ref BgzfStream stream) {
// stderr.writeln("Fetching BAM header");
ubyte[4] ubyte4;
stream.read(ubyte4);
enforce(ubyte4 == BAM_MAGIC,"Invalid file format: expected BAM magic number");
immutable text_size = stream.read!int();
// stderr.writeln("Text size ",text_size.sizeof," ",text_size);
immutable text = stream.read!string(text_size);
header = BamHeader(BAM_MAGIC,text);
immutable n_refs = stream.read!int();
// stderr.writeln("Fetching ",n_refs," references");
foreach(int n_ref; 0..n_refs) {
immutable l_name = stream.read!int();
// stderr.writeln("!!",l_name);
auto ref_name = stream.read!string(l_name);
immutable l_ref = stream.read!int(); // length of reference sequence (bps)
// stderr.writeln(l_name," ",ref_name," ",l_ref);
header.refs ~= RefSequence(l_ref,ref_name[0..l_name-1]); // drop zero terminator
}
}
void write_bam_header(ref BgzfWriter bw, ref BamHeader header) {
// stderr.writeln("Writing BAM header");
ubyte[4] magic = cast(ubyte[])BAM_MAGIC;
bw.write(magic);
// stderr.writeln("Text size ",int.sizeof," ",header.text.length);
bw.write!int(cast(int)header.text.length);
bw.write(header.text);
auto n_refs = cast(int)header.refs.length;
bw.write!int(cast(int)header.refs.length);
// stderr.writeln("Writing ",n_refs," references");
foreach(int n_ref; 0..n_refs) {
immutable refseq = header.refs[n_ref];
bw.write!int(cast(int)(refseq.name.length+1)); // incl. zero terminator
// stderr.writeln("!!",refseq.name.length+1);
bw.write(refseq.name);
bw.write!ubyte(cast(ubyte)'\0');
bw.write!int(cast(int)refseq.length);
// stderr.writeln(refseq.name.length+1," ",refseq.name," ",refseq.length);
}
// stderr.writeln("!!");
bw.flush_block();
}
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