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DV-Kernel.cu
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DV-Kernel.cu
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/*
*
* DV-Kernel.cu
* Soap3(gpu)
*
* Copyright (C) 2011, HKU
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*
*/
#include "DV-Kernel.h"
// copied from DNACount.c
__forceinline__ __device__ uint GPUDNAOccCount ( uint * dna, uint index, char character, uint backward )
{
uint wordToCount, charToCount;
uint i;
uint sum = 0;
wordToCount = index / 32;
charToCount = index - wordToCount * 32;
dna -= backward * 4;
ulonglong2 dd;
//ulonglong2 is a 16Byte = 128bit CUDA vector
//.x is the first 8Byte while .y is the last.
dd = * ( ( ulonglong2 * ) dna );
i = 0;
if ( wordToCount > 0 ) // i = 0
{
unsigned long long d = backward ? dd.y : dd.x;
unsigned long long b = ( d >> 1 );
b ^= ( ( character & 0x2 ) ? 0 : 0xFFFFFFFFFFFFFFFF );
unsigned long long a = d ^ ( ( character & 0x1 ) ? 0 : 0xFFFFFFFFFFFFFFFF );
a &= b;
a &= 0x5555555555555555;
sum += __popcll ( a );
i = 1;
}
if ( wordToCount == 2 || charToCount > 0 )
{
if ( backward ) { i = 3 - i; }
if ( wordToCount == 2 ) { charToCount = 32; }
unsigned long long d = ( i & 1 ) ? dd.y : dd.x;
unsigned long long b = ( d >> 1 );
b ^= ( ( character & 0x2 ) ? 0 : 0xFFFFFFFFFFFFFFFF );
unsigned long long a = d ^ ( ( character & 0x1 ) ? 0 : 0xFFFFFFFFFFFFFFFF );
a &= b;
unsigned long long mask;
if ( charToCount < 16 )
{
mask = ( 0x00000000FFFFFFFF << ( 32 - charToCount * 2 ) ) & 0x00000000FFFFFFFF;
}
else
{
mask = ( 0xFFFFFFFF00000000 << ( 64 - charToCount * 2 ) ) | 0x00000000FFFFFFFF;
}
if ( backward )
{ mask = __brevll ( mask ); }
a &= ( mask & 0x5555555555555555 );
sum += __popcll ( a );
}
return sum;
}
__forceinline__ __device__ void GPUDNAAllOccCount ( uint * dna, uint index, uint backward, uint occCount[] )
{
uint wordToCount, charToCount;
uint i;
wordToCount = index / 32;
charToCount = index - wordToCount * 32;
dna -= backward * 4;
ulonglong2 dd;
dd = * ( ( ulonglong2 * ) dna );
i = 0;
if ( wordToCount > 0 ) // i = 0
{
unsigned long long d = backward ? dd.y : dd.x;
for ( int j = 0; j < ALPHABET_SIZE; ++j )
{
unsigned long long b = ( d >> 1 );
b ^= ( ( j & 0x2 ) ? 0 : 0xFFFFFFFFFFFFFFFF );
unsigned long long a = d ^ ( ( j & 0x1 ) ? 0 : 0xFFFFFFFFFFFFFFFF );
a &= b;
a &= 0x5555555555555555;
if ( backward )
{ occCount[j] -= __popcll ( a ); }
else
{ occCount[j] += __popcll ( a ); }
}
i = 1;
}
if ( wordToCount == 2 || charToCount > 0 )
{
if ( backward ) { i = 3 - i; }
if ( wordToCount == 2 ) { charToCount = 32; }
unsigned long long d = ( i & 1 ) ? dd.y : dd.x;
for ( int j = 0; j < ALPHABET_SIZE; ++j )
{
unsigned long long b = ( d >> 1 );
b ^= ( ( j & 0x2 ) ? 0 : 0xFFFFFFFFFFFFFFFF );
unsigned long long a = d ^ ( ( j & 0x1 ) ? 0 : 0xFFFFFFFFFFFFFFFF );
a &= b;
unsigned long long mask;
if ( charToCount < 16 )
{
mask = ( 0x00000000FFFFFFFF << ( 32 - charToCount * 2 ) ) & 0x00000000FFFFFFFF;
}
else
{
mask = ( 0xFFFFFFFF00000000 << ( 64 - charToCount * 2 ) ) | 0x00000000FFFFFFFF;
}
if ( backward )
{ mask = __brevll ( mask ); }
a &= ( mask & 0x5555555555555555 );
if ( backward )
{ occCount[j] -= __popcll ( a ); }
else
{ occCount[j] += __popcll ( a ); }
}
}
}
__forceinline__ __device__ uint GPUDNAOccCountWithCumu ( uint * dna, uint index, char c, uint backward, uint & cumu )
{
uint wordToCount, charToCount;
uint i;
uint sum = 0;
wordToCount = index / 32;
charToCount = index - wordToCount * 32;
dna -= backward * 4;
ulonglong2 dd;
dd = * ( ( ulonglong2 * ) dna );
i = 0;
if ( wordToCount > 0 ) // i = 0
{
unsigned long long d = backward ? dd.y : dd.x;
for ( int j = 3; j > c; --j ) // TODO hardcode
{
unsigned long long b = ( d >> 1 );
b ^= ( ( j & 0x2 ) ? 0 : 0xFFFFFFFFFFFFFFFF );
unsigned long long a = d ^ ( ( j & 0x1 ) ? 0 : 0xFFFFFFFFFFFFFFFF );
a &= b;
a &= 0x5555555555555555;
cumu += __popcll ( a );
}
{
// copy&paste for c
unsigned long long b = ( d >> 1 );
b ^= ( ( c & 0x2 ) ? 0 : 0xFFFFFFFFFFFFFFFF );
unsigned long long a = d ^ ( ( c & 0x1 ) ? 0 : 0xFFFFFFFFFFFFFFFF );
a &= b;
a &= 0x5555555555555555;
sum += __popcll ( a );
}
i = 1;
}
if ( wordToCount == 2 || charToCount > 0 )
{
if ( backward ) { i = 3 - i; }
if ( wordToCount == 2 ) { charToCount = 32; }
unsigned long long d = ( i & 1 ) ? dd.y : dd.x;
for ( int j = 3; j > c; --j ) // hardcode
{
unsigned long long b = ( d >> 1 );
b ^= ( ( j & 0x2 ) ? 0 : 0xFFFFFFFFFFFFFFFF );
unsigned long long a = d ^ ( ( j & 0x1 ) ? 0 : 0xFFFFFFFFFFFFFFFF );
a &= b;
unsigned long long mask;
if ( charToCount < 16 )
{
mask = ( 0x00000000FFFFFFFF << ( 32 - charToCount * 2 ) ) & 0x00000000FFFFFFFF;
}
else
{
mask = ( 0xFFFFFFFF00000000 << ( 64 - charToCount * 2 ) ) | 0x00000000FFFFFFFF;
}
if ( backward )
{ mask = __brevll ( mask ); }
a &= ( mask & 0x5555555555555555 );
cumu += __popcll ( a );
}
{
// copy&paste for c
unsigned long long b = ( d >> 1 );
b ^= ( ( c & 0x2 ) ? 0 : 0xFFFFFFFFFFFFFFFF );
unsigned long long a = d ^ ( ( c & 0x1 ) ? 0 : 0xFFFFFFFFFFFFFFFF );
a &= b;
unsigned long long mask;
if ( charToCount < 16 )
{
mask = ( 0x00000000FFFFFFFF << ( 32 - charToCount * 2 ) ) & 0x00000000FFFFFFFF;
}
else
{
mask = ( 0xFFFFFFFF00000000 << ( 64 - charToCount * 2 ) ) | 0x00000000FFFFFFFF;
}
if ( backward )
{ mask = __brevll ( mask ); }
a &= ( mask & 0x5555555555555555 );
sum += __popcll ( a );
}
}
return sum;
}
// copied from BWT.c
__forceinline__ __device__ uint GPUBWTOccValue ( uint * bwt, uint * occ, uint index, char c, uint inverseSa0 )
{
// $ is supposed to be positioned at inverseSa0 but it is not encoded
// therefore index is subtracted by 1 for adjustment
index -= ( index > inverseSa0 );
uint occExplicitIndex = ( index + GPU_OCC_INTERVAL / 2 - 1 ) / GPU_OCC_INTERVAL; // Bidirectional encoding
uint occIndex = occExplicitIndex * GPU_OCC_INTERVAL;
uint occValue = occ[occExplicitIndex * ALPHABET_SIZE + c];
if ( occIndex != index )
{
// __usad(x,y,z) = |x-y| + z
// GPUDNAOccCount(explicitIndex, len, character, isBackwardDirectionCount)
// - pointer to position of explicitIndex on BWT: Reference point on sampled occ
// - len: number of characters on BWT to count
// - character: the character to count
// - isBackwardDirectionCount: a boolean flag to identify backward counting
uint cnt = GPUDNAOccCount ( bwt + occIndex / CHAR_PER_WORD, __usad ( index, occIndex, 0 ), c, occIndex > index );
return occIndex > index ? occValue - cnt : occValue + cnt;
}
else
{
return occValue;
}
}
__forceinline__ __device__ void GPUBWTAllOccValue ( uint * bwt,
uint * occ,
uint inverseSa0,
uint index,
uint occCount[] )
{
// $ is supposed to be positioned at inverseSa0 but it is not encoded
// therefore index is subtracted by 1 for adjustment
index -= ( index > inverseSa0 );
uint occExplicitIndex = ( index + GPU_OCC_INTERVAL / 2 - 1 ) / GPU_OCC_INTERVAL; // Bidirectional encoding
uint occIndex = occExplicitIndex * GPU_OCC_INTERVAL;
* ( ( uint4 * ) occCount ) = * ( ( uint4 * ) ( occ + occExplicitIndex * ALPHABET_SIZE ) );
if ( occIndex != index )
{
GPUDNAAllOccCount ( bwt + occIndex / CHAR_PER_WORD, __usad ( index, occIndex, 0 ), occIndex > index, occCount );
}
}
__forceinline__ __device__ uint GPUBWTOccValueWithCumu ( uint * bwt, uint * occ, uint index, char c, uint inverseSa0, uint & cumu )
{
// $ is supposed to be positioned at inverseSa0 but it is not encoded
// therefore index is subtracted by 1 for adjustment
index -= ( index > inverseSa0 );
uint occExplicitIndex = ( index + GPU_OCC_INTERVAL / 2 - 1 ) / GPU_OCC_INTERVAL; // Bidirectional encoding
uint occIndex = occExplicitIndex * GPU_OCC_INTERVAL;
uint occValues[ALPHABET_SIZE];
* ( ( uint4 * ) occValues ) = * ( ( uint4 * ) ( occ + occExplicitIndex * ALPHABET_SIZE ) );
uint occValue = occValues[c];
cumu = 0;
for ( int j = 3; j > c; --j ) // TODO hardcode
{
cumu += occValues[j];
}
uint cum = 0;
if ( occIndex != index )
{
uint cnt = GPUDNAOccCountWithCumu ( bwt + occIndex / CHAR_PER_WORD, __usad ( index, occIndex, 0 ), c, occIndex > index, cum );
if ( occIndex > index )
{
cumu -= cum;
return occValue - cnt;
}
cumu += cum;
return occValue + cnt;
}
return occValue;
}
__forceinline__ __device__
void contBackwardSearch ( uint * query, uint start, uint len,
uint * bwt, uint * occ, uint inverseSa0,
uint saL, uint saR,
uint & saCount, uint * output,
uint maxSARangesAllowed,
uint strand, uint accumMismatches )
{
unsigned char c;
uint i;
for ( i = start + len; i > start && saL <= saR; --i )
{
// note that we use i-1 here to prevent counter overflow
c = ( query[ ( ( i - 1 ) / CHAR_PER_WORD ) * 32] >>
( ( i - 1 ) % CHAR_PER_WORD * BIT_PER_CHAR ) ) & CHAR_MASK;
saL = GPUBWTOccValue ( bwt, occ, saL, c, inverseSa0 ) + 1;
saR = GPUBWTOccValue ( bwt, occ, saR + 1, c, inverseSa0 );
}
if ( saL <= saR && saCount <= maxSARangesAllowed )
{
#ifdef BGS_OUTPUT_GENERAL_DEBUG_MESSAGE
printf ( "[Global] Address %u\n", output );
printf ( "[contBackwardSearch] Reporting of SA ranges %u %u ...", saL, saR );
#endif
if ( saCount < maxSARangesAllowed )
{
#ifdef BGS_OUTPUT_GENERAL_DEBUG_MESSAGE
printf ( "DONE\n" );
#endif
* ( output + 32 * 2 * saCount ) = saL;
* ( output + 32 * ( 2 * saCount + 1 ) ) = ( saR - saL ) + ( strand << ( BGS_GPU_ANSWER_OFFSET_LENGTH + 3 ) ) +
( accumMismatches << BGS_GPU_ANSWER_OFFSET_LENGTH );
}
else
{
#ifdef BGS_OUTPUT_GENERAL_DEBUG_MESSAGE
printf ( "FAILED\n" );
#endif
}
++saCount;
}
}
__forceinline__ __device__
void revContForwardSearch ( uint * query, uint start, uint len,
uint * revBwt, uint * revOcc, uint revInverseSa0,
uint saL, uint saR,
uint revSaL, uint revSaR,
uint & saCount, uint * output,
uint maxSARangesAllowed,
uint strand, uint accumMismatches )
{
unsigned char c;
uint i;
for ( i = start; i < start + len && saL <= saR; ++i )
{
c = ( query[ ( i / CHAR_PER_WORD ) * 32] >> ( i % CHAR_PER_WORD * BIT_PER_CHAR ) ) & CHAR_MASK;
uint start, end;
revSaL =
GPUBWTOccValueWithCumu ( revBwt, revOcc, revSaL, c, revInverseSa0, start ) + 1;
revSaR =
GPUBWTOccValueWithCumu ( revBwt, revOcc, revSaR + 1, c, revInverseSa0, end );
saR = saR + start - end;
saL = saR - ( revSaR - revSaL );
}
if ( saL <= saR && saCount <= maxSARangesAllowed )
{
#ifdef BGS_OUTPUT_GENERAL_DEBUG_MESSAGE
printf ( "[Global] Address %u\n", output );
printf ( "[revContForwardSearch] Reporting of SA ranges %u %u ...", saL, saR );
#endif
if ( saCount < maxSARangesAllowed )
{
#ifdef BGS_OUTPUT_GENERAL_DEBUG_MESSAGE
printf ( "DONE\n" );
#endif
* ( output + 32 * 2 * saCount ) = saL;
* ( output + 32 * ( 2 * saCount + 1 ) ) = ( saR - saL ) + ( strand << ( BGS_GPU_ANSWER_OFFSET_LENGTH + 3 ) ) +
( accumMismatches << BGS_GPU_ANSWER_OFFSET_LENGTH );
}
else
{
#ifdef BGS_OUTPUT_GENERAL_DEBUG_MESSAGE
printf ( "FAILED\n" );
#endif
}
++saCount;
}
}
__forceinline__ __device__
void backward1Mismatch ( uint * query, uint start, uint len,
uint * bwt, uint * occ, uint inverseSa0,
uint pl, uint pr,
uint & saCount, uint * output,
uint maxSARangesAllowed,
uint strand, uint accumMismatches )
{
uint __align__(16) occCountPStart[ALPHABET_SIZE];
uint __align__(16) occCountPEnd[ALPHABET_SIZE];
unsigned char c;
unsigned char ec;
uint i;
for ( i = start + len; i > start && pl <= pr && saCount <= maxSARangesAllowed; --i )
{
// note that we use i-1 here to prevent counter overflow
c = ( query[ ( ( i - 1 ) / CHAR_PER_WORD ) * 32] >>
( ( i - 1 ) % CHAR_PER_WORD * BIT_PER_CHAR ) ) & CHAR_MASK;
GPUBWTAllOccValue ( bwt, occ, inverseSa0, pl, occCountPStart );
GPUBWTAllOccValue ( bwt, occ, inverseSa0, pr + 1, occCountPEnd );
// Backward manner
for ( ec = c ? 0 : 1; ec < ALPHABET_SIZE && saCount <= maxSARangesAllowed; ++ec )
{
// if (c == ec) continue; // TODO optimize as before
uint mkL = occCountPStart[ec] + 1; // compute SA range if query[i] was ec
uint mkR = occCountPEnd[ec];
contBackwardSearch ( query, start, i - start - 1,
bwt, occ, inverseSa0,
mkL, mkR,
saCount, output,
maxSARangesAllowed,
strand, accumMismatches + 1 );
if ( c == ec + 1 )
{ ec = c; }
}
pl = occCountPStart[c] + 1;
pr = occCountPEnd[c];
}
}
__forceinline__ __device__
void backward1MismatchAndExact ( uint * query, uint start, uint len,
uint * bwt, uint * occ, uint inverseSa0,
uint pl, uint pr,
uint & saCount, uint * output,
uint maxSARangesAllowed,
uint strand, uint accumMismatches )
{
uint __align__(16) occCountPStart[ALPHABET_SIZE];
uint __align__(16) occCountPEnd[ALPHABET_SIZE];
unsigned char c;
unsigned char ec;
uint i;
for ( i = start + len; i > start && pl <= pr && saCount <= maxSARangesAllowed; --i )
{
// note that we use i-1 here to prevent counter overflow
c = ( query[ ( ( i - 1 ) / CHAR_PER_WORD ) * 32] >>
( ( i - 1 ) % CHAR_PER_WORD * BIT_PER_CHAR ) ) & CHAR_MASK;
GPUBWTAllOccValue ( bwt, occ, inverseSa0, pl, occCountPStart );
GPUBWTAllOccValue ( bwt, occ, inverseSa0, pr + 1, occCountPEnd );
// Backward manner
for ( ec = c ? 0 : 1; ec < ALPHABET_SIZE && saCount <= maxSARangesAllowed; ++ec )
{
// if (c == ec) continue; // TODO optimize as before
uint mkL = occCountPStart[ec] + 1; // compute SA range if query[i] was ec
uint mkR = occCountPEnd[ec];
if ( mkL <= mkR )
{
contBackwardSearch ( query, start, i - start - 1,
bwt, occ, inverseSa0,
mkL, mkR,
saCount, output,
maxSARangesAllowed, strand, accumMismatches + 1 );
}
if ( c == ec + 1 )
{ ec = c; }
}
pl = occCountPStart[c] + 1;
pr = occCountPEnd[c];
}
if ( pl <= pr && i == start && saCount <= maxSARangesAllowed )
{
#ifdef BGS_OUTPUT_GENERAL_DEBUG_MESSAGE
printf ( "[Global] Address %u\n", output );
printf ( "[backward1MismatchOrExact] Reporting of SA ranges %u %u ...", pl, pr );
#endif
if ( saCount < maxSARangesAllowed )
{
#ifdef BGS_OUTPUT_GENERAL_DEBUG_MESSAGE
printf ( "DONE\n" );
#endif
* ( output + 32 * 2 * saCount ) = pl;
* ( output + 32 * ( 2 * saCount + 1 ) ) = ( pr - pl ) + ( strand << ( BGS_GPU_ANSWER_OFFSET_LENGTH + 3 ) ) +
( accumMismatches << BGS_GPU_ANSWER_OFFSET_LENGTH );
}
else
{
#ifdef BGS_OUTPUT_GENERAL_DEBUG_MESSAGE
printf ( "FAILED\n" );
#endif
}
++saCount;
}
}
__forceinline__ __device__
void backward2Mismatch ( uint * query, uint start, uint len,
uint * bwt, uint * occ, uint inverseSa0,
uint pl, uint pr,
uint & saCount, uint * output,
uint maxSARangesAllowed,
uint strand, uint accumMismatches )
{
uint __align__(16) occCountPStart[ALPHABET_SIZE];
uint __align__(16) occCountPEnd[ALPHABET_SIZE];
unsigned char c;
unsigned char ec;
uint i;
for ( i = start + len; i > start && pl <= pr; --i )
{
// note that we use i-1 here to prevent counter overflow
c = ( query[ ( ( i - 1 ) / CHAR_PER_WORD ) * 32] >>
( ( i - 1 ) % CHAR_PER_WORD * BIT_PER_CHAR ) ) & CHAR_MASK;
GPUBWTAllOccValue ( bwt, occ, inverseSa0, pl, occCountPStart );
GPUBWTAllOccValue ( bwt, occ, inverseSa0, pr + 1, occCountPEnd );
// Backward manner
for ( ec = c ? 0 : 1; ec < ALPHABET_SIZE; ++ec )
{
// if (c == ec) continue; // TODO optimize as before
uint mkL = occCountPStart[ec] + 1; // compute SA range if query[i] was ec
uint mkR = occCountPEnd[ec];
backward1Mismatch ( query, start, i - start - 1,
bwt, occ, inverseSa0,
mkL, mkR,
saCount, output,
maxSARangesAllowed,
strand, accumMismatches + 1 );
if ( c == ec + 1 )
{ ec = c; }
}
pl = occCountPStart[c] + 1;
pr = occCountPEnd[c];
}
}
__forceinline__ __device__
void backward2MismatchAnd1Mismatch ( uint * query, uint start, uint len,
uint * bwt, uint * occ, uint inverseSa0,
uint pl, uint pr,
uint & saCount, uint * output,
uint maxSARangesAllowed,
uint strand, uint accumMismatches )
{
uint __align__(16) occCountPStart[ALPHABET_SIZE];
uint __align__(16) occCountPEnd[ALPHABET_SIZE];
unsigned char c;
unsigned char ec;
uint i;
for ( i = start + len; i > start && pl <= pr && saCount <= maxSARangesAllowed; --i )
{
// note that we use i-1 here to prevent counter overflow
c = ( query[ ( ( i - 1 ) / CHAR_PER_WORD ) * 32] >>
( ( i - 1 ) % CHAR_PER_WORD * BIT_PER_CHAR ) ) & CHAR_MASK;
GPUBWTAllOccValue ( bwt, occ, inverseSa0, pl, occCountPStart );
GPUBWTAllOccValue ( bwt, occ, inverseSa0, pr + 1, occCountPEnd );
// Backward manner
for ( ec = c ? 0 : 1; ec < ALPHABET_SIZE && saCount <= maxSARangesAllowed; ++ec )
{
// if (c == ec) continue; // TODO optimize as before
uint mkL = occCountPStart[ec] + 1; // compute SA range if query[i] was ec
uint mkR = occCountPEnd[ec];
if ( mkL <= mkR )
{
backward1MismatchAndExact ( query, start, i - start - 1,
bwt, occ, inverseSa0,
mkL, mkR,
saCount, output,
maxSARangesAllowed,
strand, accumMismatches + 1 );
}
if ( c == ec + 1 )
{ ec = c; }
}
pl = occCountPStart[c] + 1;
pr = occCountPEnd[c];
}
}
__forceinline__ __device__
void backward2MismatchAnd1MismatchAndExact ( uint * query, uint start, uint len,
uint * bwt, uint * occ, uint inverseSa0,
uint pl, uint pr,
uint & saCount, uint * output,
uint maxSARangesAllowed,
uint strand, uint accumMismatches )
{
uint __align__(16) occCountPStart[ALPHABET_SIZE];
uint __align__(16) occCountPEnd[ALPHABET_SIZE];
unsigned char c;
unsigned char ec;
uint i;
for ( i = start + len; i > start && pl <= pr && saCount <= maxSARangesAllowed; --i )
{
// note that we use i-1 here to prevent counter overflow
c = ( query[ ( ( i - 1 ) / CHAR_PER_WORD ) * 32] >>
( ( i - 1 ) % CHAR_PER_WORD * BIT_PER_CHAR ) ) & CHAR_MASK;
GPUBWTAllOccValue ( bwt, occ, inverseSa0, pl, occCountPStart );
GPUBWTAllOccValue ( bwt, occ, inverseSa0, pr + 1, occCountPEnd );
// Backward manner
for ( ec = c ? 0 : 1; ec < ALPHABET_SIZE && saCount <= maxSARangesAllowed; ++ec )
{
// if (c == ec) continue; // TODO optimize as before
uint mkL = occCountPStart[ec] + 1; // compute SA range if query[i] was ec
uint mkR = occCountPEnd[ec];
if ( mkL <= mkR )
{
backward1MismatchAndExact ( query, start, i - start - 1,
bwt, occ, inverseSa0,
mkL, mkR,
saCount, output,
maxSARangesAllowed,
strand, accumMismatches + 1 );
}
if ( c == ec + 1 )
{ ec = c; }
}
pl = occCountPStart[c] + 1;
pr = occCountPEnd[c];
}
if ( pl <= pr && i == start && saCount <= maxSARangesAllowed )
{
#ifdef BGS_OUTPUT_GENERAL_DEBUG_MESSAGE
printf ( "[Global] Address %u\n", output );
printf ( "[backward1MismatchOrExact] Reporting of SA ranges %u %u ...", pl, pr );
#endif
if ( saCount < maxSARangesAllowed )
{
#ifdef BGS_OUTPUT_GENERAL_DEBUG_MESSAGE
printf ( "DONE\n" );
#endif
* ( output + 32 * 2 * saCount ) = pl;
* ( output + 32 * ( 2 * saCount + 1 ) ) = ( pr - pl ) + ( strand << ( BGS_GPU_ANSWER_OFFSET_LENGTH + 3 ) ) +
( accumMismatches << BGS_GPU_ANSWER_OFFSET_LENGTH );
}
else
{
#ifdef BGS_OUTPUT_GENERAL_DEBUG_MESSAGE
printf ( "FAILED\n" );
#endif
}
++saCount;
}
}
__forceinline__ __device__
void backward3Mismatch ( uint * query, uint start, uint len,
uint * bwt, uint * occ, uint inverseSa0,
uint pl, uint pr,
uint & saCount, uint * output,
uint maxSARangesAllowed,
uint strand, uint accumMismatches )
{
uint __align__(16) occCountPStart[ALPHABET_SIZE];
uint __align__(16) occCountPEnd[ALPHABET_SIZE];
unsigned char c;
unsigned char ec;
uint i;
for ( i = start + len; i > start && pl <= pr; --i )
{
// note that we use i-1 here to prevent counter overflow
c = ( query[ ( ( i - 1 ) / CHAR_PER_WORD ) * 32] >>
( ( i - 1 ) % CHAR_PER_WORD * BIT_PER_CHAR ) ) & CHAR_MASK;
GPUBWTAllOccValue ( bwt, occ, inverseSa0, pl, occCountPStart );
GPUBWTAllOccValue ( bwt, occ, inverseSa0, pr + 1, occCountPEnd );
// Backward manner
for ( ec = c ? 0 : 1; ec < ALPHABET_SIZE; ++ec )
{
// if (c == ec) continue; // TODO optimize as before
uint mkL = occCountPStart[ec] + 1; // compute SA range if query[i] was ec
uint mkR = occCountPEnd[ec];
backward2Mismatch ( query, start, i - start - 1,
bwt, occ, inverseSa0,
mkL, mkR,
saCount, output,
maxSARangesAllowed,
strand, accumMismatches + 1 );
if ( c == ec + 1 )
{ ec = c; }
}
pl = occCountPStart[c] + 1;
pr = occCountPEnd[c];
}
}
__forceinline__ __device__
void backward3MismatchAnd2Mismatch ( uint * query, uint start, uint len,
uint * bwt, uint * occ, uint inverseSa0,
uint pl, uint pr,
uint & saCount, uint * output,
uint maxSARangesAllowed,
uint strand, uint accumMismatches )
{
uint __align__(16) occCountPStart[ALPHABET_SIZE];
uint __align__(16) occCountPEnd[ALPHABET_SIZE];
unsigned char c;
unsigned char ec;
uint i;
for ( i = start + len; i > start && pl <= pr && saCount <= maxSARangesAllowed; --i )
{
// note that we use i-1 here to prevent counter overflow
c = ( query[ ( ( i - 1 ) / CHAR_PER_WORD ) * 32] >>
( ( i - 1 ) % CHAR_PER_WORD * BIT_PER_CHAR ) ) & CHAR_MASK;
GPUBWTAllOccValue ( bwt, occ, inverseSa0, pl, occCountPStart );
GPUBWTAllOccValue ( bwt, occ, inverseSa0, pr + 1, occCountPEnd );
// Backward manner
for ( ec = c ? 0 : 1; ec < ALPHABET_SIZE && saCount <= maxSARangesAllowed; ++ec )
{
// if (c == ec) continue; // TODO optimize as before
uint mkL = occCountPStart[ec] + 1; // compute SA range if query[i] was ec
uint mkR = occCountPEnd[ec];
if ( mkL <= mkR )
{
backward2MismatchAnd1Mismatch ( query, start, i - start - 1,
bwt, occ, inverseSa0,
mkL, mkR,
saCount, output,
maxSARangesAllowed,
strand, accumMismatches + 1 );
}
if ( c == ec + 1 )
{ ec = c; }
}
pl = occCountPStart[c] + 1;
pr = occCountPEnd[c];
}
}
__forceinline__ __device__
void backward3MismatchAnd2MismatchAnd1MismatchAndExact ( uint * query, uint start, uint len,
uint * bwt, uint * occ, uint inverseSa0,
uint pl, uint pr,
uint & saCount, uint * output,
uint maxSARangesAllowed,
uint strand, uint accumMismatches )
{
uint __align__(16) occCountPStart[ALPHABET_SIZE];
uint __align__(16) occCountPEnd[ALPHABET_SIZE];
unsigned char c;
unsigned char ec;
uint i;
for ( i = start + len; i > start && pl <= pr && saCount <= maxSARangesAllowed; --i )
{
// note that we use i-1 here to prevent counter overflow
c = ( query[ ( ( i - 1 ) / CHAR_PER_WORD ) * 32] >>
( ( i - 1 ) % CHAR_PER_WORD * BIT_PER_CHAR ) ) & CHAR_MASK;
GPUBWTAllOccValue ( bwt, occ, inverseSa0, pl, occCountPStart );
GPUBWTAllOccValue ( bwt, occ, inverseSa0, pr + 1, occCountPEnd );
// Backward manner
for ( ec = c ? 0 : 1; ec < ALPHABET_SIZE && saCount <= maxSARangesAllowed; ++ec )
{
// if (c == ec) continue; // TODO optimize as before
uint mkL = occCountPStart[ec] + 1; // compute SA range if query[i] was ec
uint mkR = occCountPEnd[ec];
if ( mkL <= mkR )
{
backward2MismatchAnd1MismatchAndExact ( query, start, i - start - 1,
bwt, occ, inverseSa0,
mkL, mkR,
saCount, output,
maxSARangesAllowed,
strand, accumMismatches + 1 );
}
if ( c == ec + 1 )
{ ec = c; }
}
pl = occCountPStart[c] + 1;
pr = occCountPEnd[c];
}
if ( pl <= pr && i == start && saCount <= maxSARangesAllowed )
{
#ifdef BGS_OUTPUT_GENERAL_DEBUG_MESSAGE
printf ( "[Global] Address %u\n", output );
printf ( "[backward3MismatchAnd2MismatchAnd1MismatchAndExact] Reporting of SA ranges %u %u ...", pl, pr );
#endif
if ( saCount < maxSARangesAllowed )
{
#ifdef BGS_OUTPUT_GENERAL_DEBUG_MESSAGE
printf ( "DONE\n" );
#endif
* ( output + 32 * 2 * saCount ) = pl;
* ( output + 32 * ( 2 * saCount + 1 ) ) = ( pr - pl ) + ( strand << ( BGS_GPU_ANSWER_OFFSET_LENGTH + 3 ) ) +
( accumMismatches << BGS_GPU_ANSWER_OFFSET_LENGTH );
}
else
{
#ifdef BGS_OUTPUT_GENERAL_DEBUG_MESSAGE
printf ( "FAILED\n" );
#endif
}
++saCount;
}
}
__forceinline__ __device__
void backward4MismatchAnd3MismatchAnd2MismatchAnd1MismatchAndExact ( uint * query, uint start, uint len,
uint * bwt, uint * occ, uint inverseSa0,
uint pl, uint pr,
uint & saCount, uint * output,
uint maxSARangesAllowed,
uint strand, uint accumMismatches )
{
uint __align__(16) occCountPStart[ALPHABET_SIZE];
uint __align__(16) occCountPEnd[ALPHABET_SIZE];
unsigned char c;
unsigned char ec;
uint i;
for ( i = start + len; i > start && pl <= pr; --i )
{
// note that we use i-1 here to prevent counter overflow
c = ( query[ ( ( i - 1 ) / CHAR_PER_WORD ) * 32] >>
( ( i - 1 ) % CHAR_PER_WORD * BIT_PER_CHAR ) ) & CHAR_MASK;
GPUBWTAllOccValue ( bwt, occ, inverseSa0, pl, occCountPStart );
GPUBWTAllOccValue ( bwt, occ, inverseSa0, pr + 1, occCountPEnd );
// Backward manner
for ( ec = c ? 0 : 1; ec < ALPHABET_SIZE; ++ec )
{
// if (c == ec) continue; // TODO optimize as before
uint mkL = occCountPStart[ec] + 1; // compute SA range if query[i] was ec
uint mkR = occCountPEnd[ec];
backward3MismatchAnd2MismatchAnd1MismatchAndExact ( query, start, i - start - 1,
bwt, occ, inverseSa0,
mkL, mkR,
saCount, output,
maxSARangesAllowed,
strand, accumMismatches + 1 );
if ( c == ec + 1 )
{ ec = c; }
}
pl = occCountPStart[c] + 1;
pr = occCountPEnd[c];
}
if ( pl <= pr && i == start && saCount <= maxSARangesAllowed )
{
#ifdef BGS_OUTPUT_GENERAL_DEBUG_MESSAGE
printf ( "[Global] Address %u\n", output );
printf ( "[backward4MismatchAnd3MismatchAnd2MismatchAnd1MismatchAndExact] Reporting of SA ranges %u %u ...", pl, pr );
#endif
if ( saCount < maxSARangesAllowed )
{
#ifdef BGS_OUTPUT_GENERAL_DEBUG_MESSAGE
printf ( "DONE\n" );
#endif
* ( output + 32 * 2 * saCount ) = pl;
* ( output + 32 * ( 2 * saCount + 1 ) ) = ( pr - pl ) + ( strand << ( BGS_GPU_ANSWER_OFFSET_LENGTH + 3 ) ) +
( accumMismatches << BGS_GPU_ANSWER_OFFSET_LENGTH );
}
else
{
#ifdef BGS_OUTPUT_GENERAL_DEBUG_MESSAGE
printf ( "FAILED\n" );
#endif
}
++saCount;
}
}
__forceinline__ __device__
void revForward1Mismatch ( uint * query, uint start, uint len,
uint * revBwt, uint * revOcc, uint revInverseSa0,
uint pl, uint pr,
uint revPl, uint revPr,
uint & saCount, uint * output,
uint maxSARangesAllowed,
uint strand, uint accumMismatches )
{
uint mkL, mkR, revMkL, revMkR;
uint __align__(16) occCountPStart[ALPHABET_SIZE];
uint __align__(16) occCountPEnd[ALPHABET_SIZE];
uint __align__(16) occCountP[ALPHABET_SIZE];
unsigned char c;
unsigned char ec;
uint i;
for ( i = start; i < start + len && pl <= pr && saCount <= maxSARangesAllowed; ++i )
{
c = ( query[ ( i / CHAR_PER_WORD ) * 32] >> ( i % CHAR_PER_WORD * BIT_PER_CHAR ) ) & CHAR_MASK;
GPUBWTAllOccValue ( revBwt, revOcc, revInverseSa0, revPl, occCountPStart );
GPUBWTAllOccValue ( revBwt, revOcc, revInverseSa0, revPr + 1, occCountPEnd );
int k;
occCountP[ALPHABET_SIZE - 1] = 0;
for ( k = ALPHABET_SIZE - 2; k >= 0; --k )
{
occCountP[k] = occCountP[k + 1] + occCountPEnd[k + 1] - occCountPStart[k + 1];
}
// Forward manner
for ( ec = 0; ec < ALPHABET_SIZE && saCount <= maxSARangesAllowed; ++ec )
{
if ( c == ec ) { continue; } // TODO optimize as before
revMkL = occCountPStart[ec] + 1;
revMkR = occCountPEnd[ec];
mkR = pr - occCountP[ec];
mkL = mkR - ( revMkR - revMkL );
if ( mkL <= mkR )
{
revContForwardSearch ( query, i + 1, start + len - i - 1,
// search range = query[i+1, start+len)