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#include "gdna.h" |
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#include <string.h> |
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#define IUPAC_DEFS "AaCcTtGgUuMmRrWwSsYyKkVvHhDdBbNnXx-*" |
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#define IUPAC_COMP "TtGgAaCcAaKkYyWwSsRrMmBbDdHhVvNnXx-*" |
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const char* IUPAC_2BIT ="AACCTTGGTTAAAAAACCCCGGAAAAAACCAAAAAA"; |
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const char* IUPAC_2BITN ="001133223300000011112200000011000000"; |
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const char* IUPAC_DEFS ="AaCcTtGgUuMmRrWwSsYyKkVvHhDdBbNnXx-*"; |
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const char* IUPAC_COMP ="TtGgAaCcAaKkYyWwSsRrMmBbDdHhVvNnXx-*"; |
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#define A_2BIT 0 // 00 |
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#define C_2BIT 1 // 01 |
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#define G_2BIT 2 // 10 |
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#define T_2BIT 3 // 11 |
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static byte ntCompTable[256]; |
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static byte nt2bit[256]; //maps any character to a 2bit base value (with N = A) |
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static char v_2bit2nt[4] = {'A','C','G','T'}; |
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//---------------------- |
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static bool gdna_Ready=gDnaInit(); |
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//---------------------- |
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byte gdna2bit(char* &nt, int n) { |
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// Pack n bases into a byte (n can be 1..4) |
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byte out = 0; |
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while (n && *nt) { |
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n--; |
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out <<= 2; |
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out += nt2bit[(int)*nt]; |
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nt++; |
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} |
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return out; |
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} |
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unsigned char ntCompTable[256]; |
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static bool gdna_ntCompTableReady=ntCompTableInit(); |
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char ntComplement(char c) { |
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return ntCompTable[(int)c]; |
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} |
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char g2bit2base(byte v2bit) { |
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return v_2bit2nt[v2bit & 0x03 ]; |
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} |
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//in place reverse complement of nucleotide (sub)sequence |
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char* reverseComplement(char* seq, int slen) { |
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if (slen==0) slen=strlen(seq); |
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return seq; |
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} |
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bool ntCompTableInit() { |
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//if (gdna_ntCompTableReady) return true; |
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char n[]=IUPAC_DEFS; |
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char c[]=IUPAC_COMP; |
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bool gDnaInit() { |
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if (gdna_Ready) return true; |
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int l=strlen(IUPAC_DEFS); |
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ntCompTable[0]=0; |
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nt2bit[0]=0; |
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for (int ch=1;ch<256;ch++) { |
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ntCompTable[ch]=0; |
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nt2bit[ch]=0; |
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for (int i=0;i<l;i++) |
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if (ch==n[i]) { |
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ntCompTable[ch]=c[i]; |
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if (ch==IUPAC_DEFS[i]) { |
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ntCompTable[ch]=IUPAC_COMP[i]; |
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nt2bit[ch] = IUPAC_2BITN[i]-'0'; |
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break; |
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} |
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if (ntCompTable[ch]==0) |
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if (ntCompTable[ch]==0) { |
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ntCompTable[ch]='N'; |
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} |
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} |
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//gdna_ntCompTableReady=true; |
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gdna_Ready=true; |
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return true; |
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} |
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