/usr/include/pbdata/NucConversion.hpp is in libpbdata-dev 0~20151014+gitbe5d1bf-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 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 | #ifndef _BLASR_NUC_CONVERSION_HPP_
#define _BLASR_NUC_CONVERSION_HPP_
//
// Map from ascii to 2 bit representation.
//
extern int TwoBit[256];
//
// Map from charcter to 3 bit. Treat all non ACGT IUPAC as N
// IPUAC: ACGT U M R W S Y K V H D N
//
extern int ThreeBit[256];
extern int IsACTG[256];
extern int IsLowerCase[256];
extern int FourBit[256];
extern int FourBitToAscii[10];
extern int ThreeBitToAscii[6];
extern int MaskedFourBit[256];
extern unsigned char AllToUpper[256];
extern char AllToLower[256];
extern unsigned char PreserveCase[256];
extern char TwoBitToAscii[4];
extern unsigned char ReverseComplementNuc[256];
//
// HDF Column Orders: GTAC
// A - column 2; C - column 3;
// G - column 0; T - column 1;
// Ascii code:
// A=65, C=67, G=71, T=84
// a=97, c=99, g=116, t=103
//
extern int NucToHdfColumnOrder[256];
// Convert a FASTQ character to Quality.
const unsigned int FASTQ_CHAR_TO_QUALITY = 33;
#endif // _BLASR_NUC_CONVERSION_HPP_
|