#include <emmintrin.h>
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <math.h>
#include "ssw.h"
Go to the source code of this file.
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| #define | LIKELY(x) (x) |
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| #define | UNLIKELY(x) (x) |
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| #define | set_u(u, w, i, j) { int x=(i)-(w); x=x>0?x:0; (u)=(j)-x+1; } |
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| #define | set_d(u, w, i, j, p) { int x=(i)-(w); x=x>0?x:0; x=(j)-x; (u)=x*3+p; } |
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| #define | kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x)) |
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| #define | max16(m, vm) |
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| #define | max8(m, vm) |
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| __m128i * | qP_byte (const int8_t *read_num, const int8_t *mat, const int32_t readLen, const int32_t n, uint8_t bias) |
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| alignment_end * | sw_sse2_byte (const int8_t *ref, int8_t ref_dir, int32_t refLen, int32_t readLen, const uint8_t weight_gapO, const uint8_t weight_gapE, __m128i *vProfile, uint8_t terminate, uint8_t bias, int32_t maskLen) |
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| __m128i * | qP_word (const int8_t *read_num, const int8_t *mat, const int32_t readLen, const int32_t n) |
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| alignment_end * | sw_sse2_word (const int8_t *ref, int8_t ref_dir, int32_t refLen, int32_t readLen, const uint8_t weight_gapO, const uint8_t weight_gapE, __m128i *vProfile, uint16_t terminate, int32_t maskLen) |
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| cigar * | banded_sw (const int8_t *ref, const int8_t *read, int32_t refLen, int32_t readLen, int32_t score, const uint32_t weight_gapO, const uint32_t weight_gapE, int32_t band_width, const int8_t *mat, int32_t n) |
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| int8_t * | seq_reverse (const int8_t *seq, int32_t end) |
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| s_profile * | ssw_init (const int8_t *read, const int32_t readLen, const int8_t *mat, const int32_t n, const int8_t score_size) |
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| void | init_destroy (s_profile *p) |
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| s_align * | ssw_align (const s_profile *prof, const int8_t *ref, int32_t refLen, const uint8_t weight_gapO, const uint8_t weight_gapE, const uint8_t flag, const uint16_t filters, const int32_t filterd, const int32_t maskLen) |
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| void | align_destroy (s_align *a) |
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| #define kroundup32 |
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(--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x)) |
Round an integer to the next closest power-2 integer.
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| x | integer to be rounded (in place) x will be modified. |
Definition at line 64 of file ssw.cpp.
Value:(vm) = _mm_max_epu8((vm), _mm_srli_si128((vm), 8)); \
(vm) = _mm_max_epu8((vm), _mm_srli_si128((vm), 4)); \
(vm) = _mm_max_epu8((vm), _mm_srli_si128((vm), 2)); \
(vm) = _mm_max_epu8((vm), _mm_srli_si128((vm), 1)); \
(m) = _mm_extract_epi16((vm), 0)
Value:(vm) = _mm_max_epi16((vm), _mm_srli_si128((vm), 8)); \
(vm) = _mm_max_epi16((vm), _mm_srli_si128((vm), 4)); \
(vm) = _mm_max_epi16((vm), _mm_srli_si128((vm), 2)); \
(m) = _mm_extract_epi16((vm), 0)
| #define set_d |
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| { int x=(i)-(w); x=x>0?x:0; x=(j)-x; (u)=x*3+p; } |
| #define set_u |
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| #define UNLIKELY |
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Release the memory allocated by function ssw_align.
- Parameters
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| a | pointer to the alignment result structure |
Definition at line 857 of file ssw.cpp.
Release the memory allocated by function ssw_init.
- Parameters
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| p | pointer to the query profile structure |
Definition at line 764 of file ssw.cpp.
Do Striped Smith-Waterman alignment.
- Parameters
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| prof | pointer to the query profile structure |
| ref | pointer to the target sequence; the target sequence needs to be numbers and corresponding to the mat parameter of function ssw_init |
| refLen | length of the target sequence |
| weight_gapO | the absolute value of gap open penalty |
| weight_gapE | the absolute value of gap extension penalty |
| flag | bitwise FLAG; (from high to low) bit 5: when setted as 1, function ssw_align will return the best alignment beginning position; bit 6: when setted as 1, if (ref_end1 - ref_begin1 < filterd && read_end1 - read_begin1 < filterd), (whatever bit 5 is setted) the function will return the best alignment beginning position and cigar; bit 7: when setted as 1, if the best alignment score >= filters, (whatever bit 5 is setted) the function will return the best alignment beginning position and cigar; bit 8: when setted as 1, (whatever bit 5, 6 or 7 is setted) the function will always return the best alignment beginning position and cigar. When flag == 0, only the optimal and sub-optimal scores and the optimal alignment ending position will be returned. |
| filters | score filter: when bit 7 of flag is setted as 1 and bit 8 is setted as 0, filters will be used (Please check the decription of the flag parameter for detailed usage.) |
| filterd | distance filter: when bit 6 of flag is setted as 1 and bit 8 is setted as 0, filterd will be used (Please check the decription of the flag parameter for detailed usage.) |
| maskLen | The distance between the optimal and suboptimal alignment ending position >= maskLen. We suggest to use readLen/2, if you don't have special concerns. Note: maskLen has to be >= 15, otherwise this function will NOT return the suboptimal alignment information. Detailed description of maskLen: After locating the optimal alignment ending position, the suboptimal alignment score can be heuristically found by checking the second largest score in the array that contains the maximal score of each column of the SW matrix. In order to avoid picking the scores that belong to the alignments sharing the partial best alignment, SSW C library masks the reference loci nearby (mask length = maskLen) the best alignment ending position and locates the second largest score from the unmasked elements. |
- Returns
- pointer to the alignment result structure
- Note
- Whatever the parameter flag is setted, this function will at least return the optimal and sub-optimal alignment score, and the optimal alignment ending positions on target and query sequences. If both bit 6 and 7 of the flag are setted while bit 8 is not, the function will return cigar only when both criteria are fulfilled. All returned positions are 0-based coordinate.
Definition at line 770 of file ssw.cpp.
@function Create the query profile using the query sequence.
- Parameters
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| read | pointer to the query sequence; the query sequence needs to be numbers |
| readLen | length of the query sequence |
| mat | pointer to the substitution matrix; mat needs to be corresponding to the read sequence |
| n | the square root of the number of elements in mat (mat has n*n elements) |
| score_size | estimated Smith-Waterman score; if your estimated best alignment score is surely < 255 please set 0; if your estimated best alignment score >= 255, please set 1; if you don't know, please set 2 |
- Returns
- pointer to the query profile structure
- Note
- example for parameter read and mat: If the query sequence is: ACGTATC, the sequence that read points to can be: 1234142 Then if the penalty for match is 2 and for mismatch is -2, the substitution matrix of parameter mat will be: A C G T 2 -2 -2 -2 //A -2 2 -2 -2 //C -2 -2 2 -2 //G -2 -2 -2 2 //T mat is the pointer to the array {2, -2, -2, -2, -2, 2, -2, -2, -2, -2, 2, -2, -2, -2, -2, 2}
Definition at line 741 of file ssw.cpp.
1.8.4