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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 calculate_gc_content_from_reference.d
import bio.bam.reader;
import bio.bam.md.reconstruct : dna;
import std.stdio, std.datetime, std.range, std.array;
void main() {
auto bam = new BamReader("../test/data/b7_295_chunk.bam");
// the sequence starts at first mapped base of first read
auto reference = dna(bam.reads);
int n_bases = 0, gc = 0;
foreach (base; reference) {
if (base == 'N') continue; // happens if coverage is zero
if (base == 'G' || base == 'C') gc += 1;
n_bases += 1;
}
writeln("total bases: ", n_bases);
writeln(" GC%: ", cast(float)gc / n_bases);
writeln(" sequence: ", reference);
writeln(" #reads: ", walkLength(bam.reads));
auto reads = array(bam.reads); // no I/O during measurements
StopWatch sw; // for a range of reads, minumum number of MD tags is parsed
sw.start(); walkLength(dna(reads)); sw.stop();
writeln("extracting reference from range of reads: ", sw.peek().usecs, "μs");
sw.reset();
sw.start(); foreach (read; reads) walkLength(dna(read)); sw.stop();
writeln("extracting reference from each read: ", sw.peek().usecs, "μs");
}