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// BioD depends on stream.d which is no longer included with phobos.
// To run this example from this directory,
// Clone the undead repository with
// git clone https://github.com:dlang/undeaD.git at the appropriate location and ensure
// it is available on your path
// Run example: rdmd -I.. -I../location_of_undead/src transverse_multiple_bam_files.d
import bio.bam.multireader;
import bio.bam.read : compareCoordinates;
import bio.bam.pileup;
import std.algorithm, std.conv, std.stdio;
void main() {
// multiple BAM files can be traversed simultaneously (if they can be merged)
auto bam = new MultiBamReader(["../test/data/illu_20_chunk.bam",
"../test/data/ion_20_chunk.bam"]);
auto pileup = makePileup(bam.reads, // ANY range of reads is acceptable
true, // use MD tags
32_000_083,
32_000_089);
foreach (column; pileup) {
writeln("Column position: ", column.position);
writeln(" Ref.base: ", column.reference_base); // extracted from MD tags
writeln(" Coverage: ", column.coverage);
writeln(" ", column.reads // bases from Illumina dataset
.filter!(read => to!string(read["RG"]).startsWith("ERR"))()
.map!(read => read.current_base)(),
" ", column.reads // bases from IonTorrent dataset
.filter!(read => to!string(read["RG"]).startsWith("66A0Q"))()
.map!(read => read.current_base)());
}
}