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added license and a couple of comments

This commit is contained in:
Heng Li 2011-05-05 15:39:04 -04:00
parent b9ba62ec2c
commit 9dcbb97e0e
2 changed files with 30 additions and 6 deletions
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34
ksw.c
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@ -1,3 +1,28 @@
/* The MIT License
Copyright (c) 2011 by Attractive Chaos <attractor@live.co.uk>
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
the following conditions:
The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
*/
#include <stdlib.h>
#include <stdint.h>
#include <emmintrin.h>
@ -17,7 +42,7 @@ struct _ksw_query_t {
__m128i *qp, *H0, *H1, *E;
};
ksw_query_t *ksw_qinit(int qlen, const uint8_t *query, int p, int m, const int8_t *mat)
ksw_query_t *ksw_qinit(int p, int qlen, const uint8_t *query, int m, const int8_t *mat)
{
ksw_query_t *q;
int8_t *t;
@ -89,7 +114,6 @@ int ksw_sse2_16(ksw_query_t *q, int tlen, const uint8_t *target, unsigned _o, un
__m128i e, h, f = zero, max = zero, *S = q->qp + target[i] * slen; // s is the 1st score vector
h = _mm_load_si128(H0 + slen - 1); // h={2,5,8,11,14,17,-1,-1} in the above example
h = _mm_slli_si128(h, 1); // h=H(i-1,-1); << instead of >> because x86 is little-endian
// for (score=0;score<16;++score)printf("%d ", ((int8_t*)&S[0])[score]);printf("\n");
for (j = 0; LIKELY(j < slen); ++j) {
// at the beginning, h=H'(i-1,j-1)
h = _mm_adds_epu8(h, S[j]);
@ -111,9 +135,9 @@ int ksw_sse2_16(ksw_query_t *q, int tlen, const uint8_t *target, unsigned _o, un
h = _mm_load_si128(H0 + j); // h=H'(i-1,j)
}
gmax = _mm_max_epu8(gmax, max); // NB: H(i,j) updated in the lazy-F loop cannot exceed max
// for (score=0;score<16;++score)printf("%d ", ((int8_t*)&gmax)[score]);printf("\n");
//for (score=0;score<16;++score)printf("%d ", ((int8_t*)&gmax)[score]);printf("\n");
// NB: we do not need to set E(i,j) as we disallow adjecent insertion and then deletion
for (k = 0; LIKELY(k < 16); ++k) {
for (k = 0; LIKELY(k < 16); ++k) { // this block mimics SWPS3
f = _mm_slli_si128(f, 1);
for (j = 0; LIKELY(j < slen); ++j) {
h = _mm_load_si128(H1 + j);
@ -196,7 +220,7 @@ int main(int argc, char *argv[])
while (kseq_read(ksq) > 0) {
ksw_query_t *q;
for (i = 0; i < ksq->seq.l; ++i) ksq->seq.s[i] = seq_nt4_table[(int)ksq->seq.s[i]];
q = ksw_qinit(ksq->seq.l, (uint8_t*)ksq->seq.s, 16, 5, mat);
q = ksw_qinit(16, ksq->seq.l, (uint8_t*)ksq->seq.s, 5, mat);
gzrewind(fpt); kseq_rewind(kst);
while (kseq_read(kst) > 0) {
int s;

2
ksw.h
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@ -8,7 +8,7 @@ typedef struct _ksw_query_t ksw_query_t;
extern "C" {
#endif
ksw_query_t *ksw_qinit(int qlen, const uint8_t *query, int p, int m, const int8_t *mat); // to free, simply call free()
ksw_query_t *ksw_qinit(int p, int qlen, const uint8_t *query, int m, const int8_t *mat); // to free, simply call free()
int ksw_sse2_16(ksw_query_t *q, int tlen, const uint8_t *target, unsigned o, unsigned e); // first gap costs -(o+e)
#ifdef __cplusplus