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SeedSequencer.h
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SeedSequencer.h
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/*++
Module Name:
SeedSequencer.h
Abstract:
Code for determining the order of seeds in a read.
Authors:
Bill Bolosky, February, 2013
Environment:
User mode service.
Revision History:
Factored out of BaseAligner
--*/
#pragma once
#include "exit.h"
#include "Seed.h"
#include "Error.h"
class SeedSequencer {
public:
SeedSequencer(unsigned i_seedSize);
inline unsigned SeedOffset(unsigned wrapCount) {
_ASSERT(wrapCount < seedSize);
return offsets[wrapCount];
}
inline unsigned GetWrappedNextSeedToTest(unsigned wrapCount) {
_ASSERT(wrapCount < seedSize);
return(offsets[wrapCount]);
}
private:
unsigned seedSize;
unsigned *offsets;
};
void InitializeSeedSequencers();
unsigned GetWrappedNextSeedToTest(unsigned seedLen, unsigned wrapCount)
#if 1
; // The definition is in SeedSequencer.cpp
#else // 1 -- old style with switch/case
{
if (0 == wrapCount) {
return 0;
}
switch (seedLen) {
case 32: {
switch (wrapCount) {
case 1: return 16;
case 2: return 8;
case 3: return 24;
case 4: return 4;
case 5: return 20;
case 6: return 12;
case 7: return 28;
case 8: return 6;
case 9: return 18;
case 10: return 10;
case 11: return 26;
case 12: return 2;
case 13: return 14;
case 14: return 22;
case 15: return 30;
case 16: return 3;
case 17: return 17;
case 18: return 9;
case 19: return 23;
case 20: return 29;
case 21: return 7;
case 22: return 19;
case 23: return 27;
case 24: return 5;
case 25: return 25;
case 26: return 11;
case 27: return 21;
case 28: return 31;
case 29: return 15;
case 30: return 1;
case 31: return 13;
}
}
case 31: {
switch (wrapCount) {
case 1: return 15;
case 2: return 23;
case 3: return 8;
case 4: return 19;
case 5: return 4;
case 6: return 27;
case 7: return 11;
case 8: return 17;
case 9: return 6;
case 10: return 25;
case 11: return 2;
case 12: return 29;
case 13: return 13;
case 14: return 21;
case 15: return 9;
case 16: return 24;
case 17: return 3;
case 18: return 18;
case 19: return 10;
case 20: return 26;
case 21: return 5;
case 22: return 30;
case 23: return 14;
case 24: return 7;
case 25: return 22;
case 26: return 1;
case 27: return 16;
case 28: return 28;
case 29: return 12;
case 30: return 20;
}
}
case 25: {
switch (wrapCount) {
case 1: return 13;
case 2: return 6;
case 3: return 19;
case 4: return 3;
case 5: return 16;
case 6: return 22;
case 7: return 9;
case 8: return 11;
case 9: return 1;
case 10: return 14;
case 11: return 7;
case 12: return 20;
case 13: return 4;
case 14: return 17;
case 15: return 23;
case 16: return 2;
case 17: return 15;
case 18: return 5;
case 19: return 21;
case 20: return 8;
case 21: return 24;
case 22: return 10;
case 23: return 18;
case 24: return 12;
}
}
case 24:{
switch (wrapCount) {
case 1: return 12;
case 2: return 6;
case 3: return 18;
case 4: return 3;
case 5: return 15;
case 6: return 21;
case 7: return 9;
case 8: return 1;
case 9: return 13;
case 10: return 19;
case 11: return 7;
case 12: return 16;
case 13: return 4;
case 14: return 22;
case 15: return 10;
case 16: return 2;
case 17: return 14;
case 18: return 20;
case 19: return 5;
case 20: return 17;
case 21: return 8;
case 22: return 23;
case 23: return 11;
}
}
case 23: {
switch (wrapCount) {
case 1: return 12;
case 2: return 6;
case 3: return 17;
case 4: return 3;
case 5: return 9;
case 6: return 20;
case 7: return 14;
case 8: return 1;
case 9: return 4;
case 10: return 7;
case 11: return 10;
case 12: return 15;
case 13: return 18;
case 14: return 21;
case 15: return 4;
case 16: return 2;
case 17: return 5;
case 18: return 11;
case 19: return 16;
case 20: return 19;
case 21: return 22;
case 22: return 8;
}
}
case 22: {
switch (wrapCount) {
case 1: return 11;
case 2: return 6;
case 3: return 16;
case 4: return 3;
case 5: return 9;
case 6: return 14;
case 7: return 19;
case 8: return 2;
case 9: return 7;
case 10: return 12;
case 11: return 17;
case 12: return 20;
case 13: return 4;
case 14: return 1;
case 15: return 10;
case 16: return 13;
case 17: return 15;
case 18: return 18;
case 19: return 21;
case 20: return 5;
case 21: return 8;
default: _ASSERT(!"NOTREACHED");
}
}
case 21: {
switch (wrapCount) {
case 1: return 11;
case 2: return 6;
case 3: return 16;
case 4: return 3;
case 5: return 9;
case 6: return 13;
case 7: return 17;
case 8: return 18;
case 9: return 2;
case 10: return 5;
case 11: return 8;
case 12: return 15;
case 13: return 20;
case 14: return 1;
case 15: return 4;
case 16: return 7;
case 17: return 10;
case 18: return 12;
case 19: return 14;
case 20: return 19;
default: _ASSERT(!"NOTREACHED");
}
}
case 20: {
switch (wrapCount) {
case 1: return 10;
case 2: return 5;
case 3: return 15;
case 4: return 2;
case 5: return 7;
case 6: return 12;
case 7: return 17;
case 8: return 3;
case 9: return 9;
case 10: return 11;
case 11: return 13;
case 12: return 19;
case 13: return 1;
case 14: return 4;
case 15: return 6;
case 16: return 8;
case 17: return 14;
case 18: return 18;
case 19: return 16;
default: _ASSERT(!"NOTREACHED");
}
}
case 19: {
switch (wrapCount) {
case 1: return 10;
case 2: return 4;
case 3: return 14;
case 4: return 2;
case 5: return 6;
case 6: return 8;
case 7: return 12;
case 8: return 16;
case 9: return 18;
case 10: return 1;
case 11: return 3;
case 12: return 5;
case 13: return 7;
case 14: return 9;
case 15: return 11;
case 16: return 13;
case 17: return 15;
case 18: return 17;
default: _ASSERT(!"NOTREACHED");
}
}
case 18: {
switch (wrapCount) {
case 1: return 9;
case 2: return 4;
case 3: return 13;
case 4: return 2;
case 5: return 6;
case 6: return 11;
case 7: return 15;
case 8: return 1;
case 9: return 3;
case 10: return 5;
case 11: return 7;
case 12: return 8;
case 13: return 10;
case 14: return 12;
case 15: return 14;
case 16: return 16;
case 17: return 17;
default: _ASSERT(!"NOTREACHED");
}
}
case 17: {
switch (wrapCount) {
case 1: return 8;
case 2: return 4;
case 3: return 12;
case 4: return 2;
case 5: return 6;
case 6: return 10;
case 7: return 14;
case 8: return 1;
case 9: return 3;
case 10: return 5;
case 11: return 7;
case 12: return 9;
case 13: return 11;
case 14: return 13;
case 15: return 15;
case 16: return 16;
default: _ASSERT(!"NOTREACHED");
}
}
case 16: {
switch (wrapCount) {
case 1: return 8;
case 2: return 4;
case 3: return 12;
case 4: return 2;
case 5: return 6;
case 6: return 10;
case 7: return 14;
case 8: return 1;
case 9: return 3;
case 10: return 5;
case 11: return 7;
case 12: return 9;
case 13: return 11;
case 14: return 13;
case 15: return 15;
default: _ASSERT(!"NOTREACHED");
}
} // inner switch
default: WriteErrorMessage("SeedSequencer: Not set up to run with this seed size\n"); soft_exit(1);
} // outer switch
return 0;
}
#endif // 1