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/*
To run this example from this directory:
rdmd -I.. read_bam_file.d
// compile this example with
// debug version
dmd -i -I.. read_bam_file.d
// optimised version
dmd -i -O -release -inline -boundscheck=off -I.. read_bam_file.d
*/
import bio.std.hts.bam.reader;
import bio.std.hts.bam.pileup;
import std.stdio;
void main() {
auto bam = new BamReader("../test/data/ex1_header.bam");
auto reads = bam["chr2"][150 .. 160]; // region chr2:149-158
auto pileup = makePileup(reads,
false, // reads don't contain MD tags
155, 158); // specify [start, end) interval
foreach (column; pileup) {
writeln("Reference position: ", column.position);
writeln(" Coverage: ", column.coverage);
writeln(" Reads:");
foreach (read; column.reads) {
writefln("%30s\t%s\t%.2d\t%s\t%2s/%2s\t%2s/%2s\t%10s\t%s %s",
read.name,
read.current_base,
read.current_base_quality,
read.cigar_operation,
read.cigar_operation_offset + 1, read.cigar_operation.length,
read.query_offset + 1, read.sequence.length,
read.cigarString(),
read.cigar_before, read.cigar_after);
}
}
}
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