nvbio::bowtie2 Namespace Reference

Namespaces
	cuda

Functions
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE char	phred_to_maq (int q)

Variables
unsigned char	s_phred_to_maq []
unsigned char	s_solexa_to_phred []

Function Documentation

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE char nvbio::bowtie2::phred_to_maq

(

int

q)

Definition at line 44 of file quality_coeffs.h.

Variable Documentation

unsigned char nvbio::bowtie2::s_phred_to_maq

Initial value:

= {
        0,   0,  0,  0,  0,
        10, 10, 10, 10, 10, 10, 10, 10, 10, 10,
        20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
        30, 30, 30, 30, 30, 30, 30, 30, 30, 30,
        30, 30, 30, 30, 30, 30, 30, 30, 30, 30,
        30, 30, 30, 30, 30, 30, 30, 30, 30, 30,
        30, 30, 30, 30, 30, 30, 30, 30, 30, 30,
        30, 30, 30, 30, 30, 30, 30, 30, 30, 30,
        30, 30, 30, 30, 30, 30, 30, 30, 30, 30,
        30, 30, 30, 30, 30, 30, 30, 30, 30, 30,
        30, 30, 30, 30, 30, 30, 30, 30, 30, 30,
        30, 30, 30, 30, 30, 30, 30, 30, 30, 30,
        30, 30, 30, 30, 30, 30, 30, 30, 30, 30,
        30, 30, 30, 30, 30, 30, 30, 30, 30, 30,
        30, 30, 30, 30, 30, 30, 30, 30, 30, 30,
        30, 30, 30, 30, 30, 30, 30, 30, 30, 30,
        30, 30, 30, 30, 30, 30, 30, 30, 30, 30,
        30, 30, 30, 30, 30, 30, 30, 30, 30, 30,
        30, 30, 30, 30, 30, 30, 30, 30, 30, 30,
        30, 30, 30, 30, 30, 30, 30, 30, 30, 30,
        30, 30, 30, 30, 30, 30, 30, 30, 30, 30,
        30, 30, 30, 30, 30, 30, 30, 30, 30, 30,
        30, 30, 30, 30, 30, 30, 30, 30, 30, 30,
        30, 30, 30, 30, 30, 30, 30, 30, 30, 30,
        30, 30, 30, 30, 30, 30, 30, 30, 30, 30,
        30, 30, 30, 30, 30, 30, 30, 30, 30, 30,
        30
}

map Phred quality scores into their maq equivalents

Definition at line 35 of file quality_coeffs.cpp.

unsigned char nvbio::bowtie2::s_solexa_to_phred

Initial value:

= {
        0, 1, 1, 1, 1, 1, 1, 2, 2, 3,
        3, 4, 4, 5, 5, 6, 7, 8, 9, 10,
        10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
        20, 21, 22, 23, 24, 25, 26, 27, 28, 29,
        30, 31, 32, 33, 34, 35, 36, 37, 38, 39,
        40, 41, 42, 43, 44, 45, 46, 47, 48, 49,
        50, 51, 52, 53, 54, 55, 56, 57, 58, 59,
        60, 61, 62, 63, 64, 65, 66, 67, 68, 69,
        70, 71, 72, 73, 74, 75, 76, 77, 78, 79,
        80, 81, 82, 83, 84, 85, 86, 87, 88, 89,
        90, 91, 92, 93, 94, 95, 96, 97, 98, 99,
        100, 101, 102, 103, 104, 105, 106, 107, 108, 109,
        110, 111, 112, 113, 114, 115, 116, 117, 118, 119,
        120, 121, 122, 123, 124, 125, 126, 127, 128, 129,
        130, 131, 132, 133, 134, 135, 136, 137, 138, 139,
        140, 141, 142, 143, 144, 145, 146, 147, 148, 149,
        150, 151, 152, 153, 154, 155, 156, 157, 158, 159,
        160, 161, 162, 163, 164, 165, 166, 167, 168, 169,
        170, 171, 172, 173, 174, 175, 176, 177, 178, 179,
        180, 181, 182, 183, 184, 185, 186, 187, 188, 189,
        190, 191, 192, 193, 194, 195, 196, 197, 198, 199,
        200, 201, 202, 203, 204, 205, 206, 207, 208, 209,
        210, 211, 212, 213, 214, 215, 216, 217, 218, 219,
        220, 221, 222, 223, 224, 225, 226, 227, 228, 229,
        230, 231, 232, 233, 234, 235, 236, 237, 238, 239,
        240, 241, 242, 243, 244, 245, 246, 247, 248, 249,
        250, 251, 252, 253, 254, 255
}

map Solexa quality values to Phred scale

Definition at line 67 of file quality_coeffs.cpp.