Hello DNA!

This page will teach you to familiarize with some of NVBIO's basic containers and concepts, showing you how to instantiate a PackedVector to store some DNA string. Packed vectors are useful to represent streams of symbols using a few bits per symbol. For a DNA alphabet, we'll only need 2-bits:

#include <nvbio/basic/packed_vector.h>
#include <nvbio/strings/alphabet.h>

void main()
{
    // our hello world ASCII string
    const char dna_string[] = "ACGTTGCA";
    const uint32 len = uint32( strlen( dna_string ) );

    // our DNA alphabet size, in bits
    const uint32 ALPHABET_SIZE = AlphabetTraits<DNA>::SYMBOL_SIZE;

    // instantiate a packed host vector
    nvbio::PackedVector<host_tag,ALPHABET_SIZE> h_dna( len );

    // and fill it in with the contents of our original string, converted
    // to a 2-bit DNA alphabet (i.e. A = 0, C = 1, G = 2, T = 3)
    nvbio::assign( len, nvbio::from_string<DNA>( dna_string ), h_dna.begin() );

    // copy the packed vector to the device
    nvbio::PackedVector<device_tag,ALPHABET_SIZE> d_dna( h_dna );
}

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