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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 iterate_tags.d
import bio.bam.reader, bio.bam.tagvalue;
import std.stdio, std.datetime;
import std.conv : to;
void main() {
auto bam = new BamReader("../test/data/b7_295_chunk.bam");
auto read = bam.reads.front; // take first read
// iterating all tags
foreach (tag, value; read)
writeln(tag, ": ", value);
// taking value of tag
Value v = read["XS"];
// Usually, it will be converted to some type right away.
auto v2 = to!int(v);
// It is not necessary to know exact value type as in BAM.
// If it can be converted to specified type, that's fine.
// Otherwise, an exception will be thrown.
auto v3 = to!long(v); auto v4 = to!string(v); auto v5 = to!float(v);
// With strings and arrays there is an unsafe but faster way...
v = read["FZ"];
StopWatch sw;
// even with -O -release -inline this is slow
sw.start; auto fz1 = to!(ushort[])(v); sw.stop();
writeln(" safe conversion: ", sw.peek().usecs, "μs");
sw.reset();
// this works because v starts in memory with a union
sw.start(); auto fz2 = *(cast(ushort[]*)(&v)); sw.stop();
writeln("unsafe conversion: ", sw.peek().usecs, "μs");
assert(fz1 == fz2);
}