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clean code

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This commit is contained in:
Haoyu Cheng
2019-12-26 02:26:24 -05:00
parent 7f9c73507d
commit 4ac9907e49
26 changed files with 1585 additions and 19325 deletions
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Levenshtein_distance.h
+58 -234
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@@ -12,152 +12,18 @@
typedef uint64_t Word;
typedef uint32_t Word_32;
typedef struct
{
/**
* vec[num_words-1], vec[num_words-2], ..., vec[1], vec[0]
* num_bits-1, num_bits-2, num_bits-3, ..., 8, 7, 6, 5, 4, 3, 2, 1, 0
**/
Word* vec;
Word num_words;
Word num_bits;
///for vec[num_words-1]
Word last_bit_mode;
Word last_bit_shift;
} bit_vectors;
inline void init_bit_vector(bit_vectors* b, Word num_bits)
{
b->num_bits = num_bits;
b->num_words = ((b->num_bits)>>6);
b->last_bit_mode = (Word)-1;
b->last_bit_shift = b->num_bits&63;
if(b->last_bit_shift != 0)
{
b->num_words++;
b->last_bit_mode = b->last_bit_mode >> (64 - b->last_bit_shift);
}
b->vec = (Word*)calloc(b->num_words, sizeof(Word));
}
inline void destory_bit_vector(bit_vectors* b, Word num_bits)
{
free(b->vec);
}
///&
inline int AND_bit_vector(bit_vectors* x, bit_vectors* y, bit_vectors* dest)
{
if(x->num_bits != y->num_bits || x->num_bits != dest->num_bits) return 0;
Word i;
for (i = 0; i < x->num_words; i++)
{
dest->vec[i] = x->vec[i] & y->vec[i];
}
if(dest->num_words > 0)
{
dest->vec[dest->num_words - 1] = dest->vec[dest->num_words - 1] & dest->last_bit_mode;
}
return 1;
}
///|
inline int OR_bit_vector(bit_vectors* x, bit_vectors* y, bit_vectors* dest)
{
if(x->num_bits != y->num_bits || x->num_bits != dest->num_bits) return 0;
Word i;
for (i = 0; i < x->num_words; i++)
{
dest->vec[i] = x->vec[i] | y->vec[i];
}
if(dest->num_words > 0)
{
dest->vec[dest->num_words - 1] = dest->vec[dest->num_words - 1] & dest->last_bit_mode;
}
return 1;
}
///^
inline int XOR_bit_vector(bit_vectors* x, bit_vectors* y, bit_vectors* dest)
{
if(x->num_bits != y->num_bits || x->num_bits != dest->num_bits) return 0;
Word i;
for (i = 0; i < x->num_words; i++)
{
dest->vec[i] = x->vec[i] ^ y->vec[i];
}
if(dest->num_words > 0)
{
dest->vec[dest->num_words - 1] = dest->vec[dest->num_words - 1] & dest->last_bit_mode;
}
return 1;
}
///~
inline int NOT_bit_vector(bit_vectors* source, bit_vectors* dest)
{
if(source->num_bits != dest->num_bits) return 0;
Word i;
for (i = 0; i < source->num_words; i++)
{
dest->vec[i] = ~(source->vec[i]);
}
if(dest->num_words > 0)
{
dest->vec[dest->num_words - 1] = dest->vec[dest->num_words - 1] & dest->last_bit_mode;
}
return 1;
}
///<< 1
inline int L_shift_1_bit_vector(bit_vectors* source, bit_vectors* dest)
{
/**
* vec[num_words-1], vec[num_words-2], ..., vec[1], vec[0]
* num_bits-1, num_bits-2, num_bits-3, ..., 8, 7, 6, 5, 4, 3, 2, 1, 0
**/
if(source->num_bits != dest->num_bits || source->num_words < 1) return 0;
Word i;
for (i = source->num_words - 1; i >= 1; i--)
{
dest->vec[i] = (source->vec[i])<<1;
dest->vec[i] = dest->vec[i] | ((source->vec[i-1])>>63);
}
dest->vec[0] = (source->vec[0])<<1;
dest->vec[dest->num_words - 1] = dest->vec[dest->num_words - 1] & dest->last_bit_mode;
return 1;
}
inline void get_error(int t_length, int errthold, int init_err, Word VP, Word VN,
unsigned int* return_err, int* back_site)
{
(*return_err) = (unsigned int)-1;
int site = t_length - 1;
int return_site = -1;
///p_length大部分情况下应该是t_length + 2 * errthold，这是i要小于last_high = 2 * errthold
///也就是p_length - t_length
///那么当p_length < t_length + 2 * errthold, available_i也应该是这个值
///in most cases, p_length should be t_length + 2 * errthold
///int available_i = p_length - t_length;
int available_i = 2 * errthold;
if ((init_err <= errthold) && (init_err <= (*return_err)))
if ((init_err <= errthold) && ((unsigned int)init_err <= (*return_err)))
{
(*return_err) = init_err;
return_site = site;
@@ -173,7 +39,7 @@ unsigned int* return_err, int* back_site)
init_err = init_err - ((VN >> i)&(Word)1);
++i;
if ((init_err <= errthold) && (init_err <= *return_err))
if ((init_err <= errthold) && ((unsigned int)init_err <= *return_err))
{
*return_err = init_err;
return_site = site + i;
@@ -188,7 +54,7 @@ unsigned int* return_err, int* back_site)
}
/****************************may have bugs********************************/
if((ungap_error<=errthold) && (ungap_error == (*return_err)))
if((ungap_error<=(unsigned int)errthold) && (ungap_error == (*return_err)))
{
return_site = site + errthold;
}
@@ -227,7 +93,7 @@ unsigned int* return_err, int* return_p_end, int* return_t_end)
///band_length = 2k + 1
for (i = 0; i<band_length; i++)
{
Peq[pattern[i]] = Peq[pattern[i]] | tmp_Peq_1;
Peq[(uint8_t)pattern[i]] = Peq[(uint8_t)pattern[i]] | tmp_Peq_1;
tmp_Peq_1 = tmp_Peq_1 << 1;
}
@@ -273,7 +139,7 @@ unsigned int* return_err, int* return_p_end, int* return_t_end)
while (i<t_length_1)
{
X = Peq[text[i]] | VN;
X = Peq[(uint8_t)text[i]] | VN;
D0 = ((VP + (X&VP)) ^ VP) | X;
@@ -308,14 +174,14 @@ unsigned int* return_err, int* return_p_end, int* return_t_end)
++i;
++i_bd;
Peq[pattern[i_bd]] = Peq[pattern[i_bd]] | Mask;
Peq[(uint8_t)pattern[i_bd]] = Peq[(uint8_t)pattern[i_bd]] | Mask;
}
X = Peq[text[i]] | VN;
X = Peq[(uint8_t)text[i]] | VN;
D0 = ((VP + (X&VP)) ^ VP) | X;
HN = VP&D0;
HP = VN | ~(VP | D0);
@@ -405,13 +271,7 @@ int* return_t_end, int* return_aligned_t_len)
/**
pattern是长的那个，是y
p_length是长的那个的长度, p_length实际没用
text是短的那个，是x
t_length是短的那个的长度
errthold是阈值
return_err是编辑距离
返回值是结束位置
pattern is the longer one, while text is the shorter one
**/
inline int Reserve_Banded_BPM
(char *pattern, int p_length, char *text, int t_length, unsigned short errthold, unsigned int* return_err)
@@ -438,7 +298,7 @@ inline int Reserve_Banded_BPM
///band_length = 2k + 1
for (i = 0; i<band_length; i++)
{
Peq[pattern[i]] = Peq[pattern[i]] | tmp_Peq_1;
Peq[(uint8_t)pattern[i]] = Peq[(uint8_t)pattern[i]] | tmp_Peq_1;
tmp_Peq_1 = tmp_Peq_1 << 1;
}
@@ -493,8 +353,7 @@ inline int Reserve_Banded_BPM
while (i<t_length_1)
{
///pattern[0]ÔÚPeq[2k], ¶øpattern[2k]ÔÚPeq[0]
X = Peq[text[i]] | VN;
X = Peq[(uint8_t)text[i]] | VN;
D0 = ((VP + (X&VP)) ^ VP) | X;
@@ -509,10 +368,8 @@ inline int Reserve_Banded_BPM
{
++err;
///¼´Ê¹È«²¿µÝ¼õ£¬Ò²¾Í¼õ2k
if ((err - last_high)>errthold)
if ((err - last_high)>(int)errthold)
{
///fprintf(stderr, "0 ######, i: %u\n", i);
return -1;
}
@@ -527,17 +384,14 @@ inline int Reserve_Banded_BPM
++i;
++i_bd;
Peq[pattern[i_bd]] = Peq[pattern[i_bd]] | Mask;
///Peq['T'] = Peq['T'] | Peq['C'];
Peq[(uint8_t)pattern[i_bd]] = Peq[(uint8_t)pattern[i_bd]] | Mask;
}
X = Peq[text[i]] | VN;
X = Peq[(uint8_t)text[i]] | VN;
D0 = ((VP + (X&VP)) ^ VP) | X;
HN = VP&D0;
HP = VN | ~(VP | D0);
@@ -560,16 +414,13 @@ inline int Reserve_Banded_BPM
///int site = p_length - last_high - 1;
int site = t_length - 1;
int return_site = -1;
///p_length大部分情况下应该是t_length + 2 * errthold，这是i要小于last_high = 2 * errthold
///也就是p_length - t_length
///那么当p_length < t_length + 2 * errthold, available_i也应该是这个值
///in most cases, p_lengthshould be t_length + 2 * errthold
int available_i = p_length - t_length;
if ((err <= errthold) && (err<=*return_err))
if ((err <= errthold) && ((unsigned int)err<=*return_err))
{
*return_err = err;
return_site = site;
}
int i_last = i;
i = 0;
/****************************may have bugs********************************/
@@ -582,14 +433,14 @@ inline int Reserve_Banded_BPM
err = err - ((VN >> i)&(Word)1);
++i;
if ((err <= errthold) && (err <= *return_err))
if ((err <= (int)errthold) && ((unsigned int)err <= *return_err))
{
*return_err = err;
return_site = site + i;
}
/****************************may have bugs********************************/
if(i == errthold)
if(i == (int)errthold)
{
ungap_error = err;
}
@@ -617,7 +468,7 @@ inline int try_cigar(char *pattern, int p_length,
{
int i = 0;
int tmp_err = 0;
///y上的起始位置
///start pos of y
int start_site = end_site - t_length + 1;
if (start_site >= 0)
@@ -626,7 +477,7 @@ inline int try_cigar(char *pattern, int p_length,
for (i = 0; i < t_length; i++)
{
///path[i] = 0;
///path倒着存
///path is saved backwards
path[t_length - i - 1] = 0;
if (text[i] != pattern[i + start_site])
{
@@ -655,8 +506,8 @@ inline int try_cigar(char *pattern, int p_length,
}
///p_length有可能不够，但是t_length总是够的
///就是p_length有可能小于t_length + 2 * errthold
///p_length might be samller than t_length + 2 * errthold
inline int Reserve_Banded_BPM_PATH
(char *pattern, int p_length, char *text, int t_length, unsigned short errthold,
unsigned int* return_err, int* return_start_site, int* return_path_length, Word* matrix_bit, char* path,
@@ -666,7 +517,6 @@ inline int Reserve_Banded_BPM_PATH
{
if (old_error == 0)
{
///fprintf(stderr, "0 error\n");
(*return_err) = old_error;
(*return_start_site) = old_end_site - t_length + 1;
return old_end_site;
@@ -675,7 +525,6 @@ inline int Reserve_Banded_BPM_PATH
if (try_cigar(pattern, p_length, text, t_length, old_end_site, path,
old_error, return_start_site, return_path_length))
{
///fprintf(stderr, "no gap error\n");
(*return_err) = old_error;
return old_end_site;
}
@@ -704,7 +553,7 @@ inline int Reserve_Banded_BPM_PATH
///band_length = 2k + 1
for (i = 0; i<band_length; i++)
{
Peq[pattern[i]] = Peq[pattern[i]] | tmp_Peq_1;
Peq[(uint8_t)pattern[i]] = Peq[(uint8_t)pattern[i]] | tmp_Peq_1;
tmp_Peq_1 = tmp_Peq_1 << 1;
}
@@ -762,7 +611,7 @@ inline int Reserve_Banded_BPM_PATH
while (i<t_length_1)
{
///pattern[0]ÔÚPeq[2k], ¶øpattern[2k]ÔÚPeq[0]
X = Peq[text[i]] | VN;
X = Peq[(uint8_t)text[i]] | VN;
D0 = ((VP + (X&VP)) ^ VP) | X;
@@ -777,7 +626,7 @@ inline int Reserve_Banded_BPM_PATH
{
++err;
if ((err - last_high)>errthold)
if ((err - last_high)>(int)errthold)
{
return -1;
}
@@ -793,7 +642,7 @@ inline int Reserve_Banded_BPM_PATH
++i;
++i_bd;
Peq[pattern[i_bd]] = Peq[pattern[i_bd]] | Mask;
Peq[(uint8_t)pattern[i_bd]] = Peq[(uint8_t)pattern[i_bd]] | Mask;
///Peq['T'] = Peq['T'] | Peq['C'];
@@ -810,7 +659,7 @@ inline int Reserve_Banded_BPM_PATH
X = Peq[text[i]] | VN;
X = Peq[(uint8_t)text[i]] | VN;
D0 = ((VP + (X&VP)) ^ VP) | X;
HN = VP&D0;
HP = VN | ~(VP | D0);
@@ -820,7 +669,7 @@ inline int Reserve_Banded_BPM_PATH
if (!(D0&err_mask))
{
++err;
if ((err - last_high)>errthold)
if ((err - last_high)>(int)errthold)
return -1;
}
@@ -846,16 +695,13 @@ inline int Reserve_Banded_BPM_PATH
unsigned int ungap_error = (unsigned int)-1;
/****************************may have bugs********************************/
///p_length大部分情况下应该是t_length + 2 * errthold，这是i要小于last_high = 2 * errthold
///也就是p_length - t_length
///那么当p_length < t_length + 2 * errthold, available_i也应该是这个值
///in most cases, p_length should be t_length + 2 * errthold
int available_i = p_length - t_length;
if ((err <= errthold) && (err<=*return_err))
if ((err <= (int)errthold) && ((unsigned int)err<=*return_err))
{
*return_err = err;
return_site = site;
}
int i_last = i;
i = 0;
while (i < available_i)
@@ -864,14 +710,14 @@ inline int Reserve_Banded_BPM_PATH
err = err - ((VN >> i)&(Word)1);
++i;
if ((err <= errthold) && (err <= *return_err))
if ((err <= (int)errthold) && ((unsigned int)err <= *return_err))
{
*return_err = err;
return_site = site + i;
}
/****************************may have bugs********************************/
if(i == errthold)
if(i == (int)errthold)
{
ungap_error = err;
}
@@ -894,24 +740,19 @@ inline int Reserve_Banded_BPM_PATH
}
/****************************may have bugs********************************/
////注意，这里p_length要矫正啊啊
///不矫正会出错
///因为p_length有可能不够
///need to correct p_length here, since p_length might be smaller than t_length + 2* err_threashlod
p_length = t_length + 2 * errthold;
///end_site是正确的
///end_site is always correct
int end_site = return_site;
int start_site = end_site;
///这个是各个bit-vector里面，end_site对应bit所在的位置
int back_track_site = band_length - (p_length - end_site);
Word v_value, h_value, delta_value, min_value, current_value;
Word direction, is_mismatch; ///0 is match, 1 is mismatch, 2 is up, 3 is left
///代表pattern到哪了，就是短的那个到哪了
///Word direction; ///0 is match, 1 is mismatch, 2 is up, 3 is left
Word direction = 0; ///0 is match, 1 is mismatch, 2 is up, 3 is left
i = t_length;
int path_length = 0;
///到0就结束了，后面的路径可以直接match
current_value = *return_err;
@@ -1044,15 +885,11 @@ inline int Reserve_Banded_BPM_PATH
(*return_start_site) = start_site;
(*return_path_length) = path_length;
return return_site;
}
////这个p_length四个是一样的
////four patterns have the same p_length
inline int Reserve_Banded_BPM_4_SSE_only(char *pattern1, char *pattern2, char *pattern3, char *pattern4, int p_length, char *text, int t_length,
int* return_sites, unsigned int* return_sites_error, unsigned short errthold, __m128i* Peq_SSE)
@@ -1076,10 +913,10 @@ inline int Reserve_Banded_BPM_4_SSE_only(char *pattern1, char *pattern2, char *p
for (i = 0; i<band_length; i++)
{
Peq[pattern1[i]][0] = Peq[pattern1[i]][0] | tmp_Peq_1;
Peq[pattern2[i]][1] = Peq[pattern2[i]][1] | tmp_Peq_1;
Peq[pattern3[i]][2] = Peq[pattern3[i]][2] | tmp_Peq_1;
Peq[pattern4[i]][3] = Peq[pattern4[i]][3] | tmp_Peq_1;
Peq[(uint8_t)pattern1[i]][0] = Peq[(uint8_t)pattern1[i]][0] | tmp_Peq_1;
Peq[(uint8_t)pattern2[i]][1] = Peq[(uint8_t)pattern2[i]][1] | tmp_Peq_1;
Peq[(uint8_t)pattern3[i]][2] = Peq[(uint8_t)pattern3[i]][2] | tmp_Peq_1;
Peq[(uint8_t)pattern4[i]][3] = Peq[(uint8_t)pattern4[i]][3] | tmp_Peq_1;
tmp_Peq_1 = tmp_Peq_1 << 1;
}
@@ -1132,7 +969,7 @@ inline int Reserve_Banded_BPM_4_SSE_only(char *pattern1, char *pattern2, char *p
while (i<t_length_1)
{
///X = Peq[text[i]] | VN;
X = _mm_or_si128(Peq_SSE[text[i]], VN);
X = _mm_or_si128(Peq_SSE[(uint8_t)text[i]], VN);
@@ -1188,17 +1025,17 @@ inline int Reserve_Banded_BPM_4_SSE_only(char *pattern1, char *pattern2, char *p
++i;
++i_bd;
Peq_SSE[pattern1[i_bd]] = _mm_or_si128(Mask1, Peq_SSE[pattern1[i_bd]]);
Peq_SSE[pattern2[i_bd]] = _mm_or_si128(Mask2, Peq_SSE[pattern2[i_bd]]);
Peq_SSE[pattern3[i_bd]] = _mm_or_si128(Mask3, Peq_SSE[pattern3[i_bd]]);
Peq_SSE[pattern4[i_bd]] = _mm_or_si128(Mask4, Peq_SSE[pattern4[i_bd]]);
Peq_SSE[(uint8_t)pattern1[i_bd]] = _mm_or_si128(Mask1, Peq_SSE[(uint8_t)pattern1[i_bd]]);
Peq_SSE[(uint8_t)pattern2[i_bd]] = _mm_or_si128(Mask2, Peq_SSE[(uint8_t)pattern2[i_bd]]);
Peq_SSE[(uint8_t)pattern3[i_bd]] = _mm_or_si128(Mask3, Peq_SSE[(uint8_t)pattern3[i_bd]]);
Peq_SSE[(uint8_t)pattern4[i_bd]] = _mm_or_si128(Mask4, Peq_SSE[(uint8_t)pattern4[i_bd]]);
///Peq_SSE['T'] = _mm_or_si128(Peq_SSE['T'], Peq_SSE['C']);
}
///X = Peq[text[i]] | VN;
X = _mm_or_si128(Peq_SSE[text[i]], VN);
X = _mm_or_si128(Peq_SSE[(uint8_t)text[i]], VN);
/*************D0 = ((VP + (X&VP)) ^ VP) | X*********************/
///X&VP
@@ -1249,22 +1086,22 @@ inline int Reserve_Banded_BPM_4_SSE_only(char *pattern1, char *pattern2, char *p
err4 = _mm_extract_epi32(Err_4, 3);
if ((err1 <= errthold) && (err1 <= return_sites_error[0]))
if ((err1 <= (int)errthold) && ((unsigned int)err1 <= return_sites_error[0]))
{
return_sites[0] = site;
return_sites_error[0] = err1;
}
if ((err2 <= errthold) && (err2 <= return_sites_error[1]))
if ((err2 <= (int)errthold) && ((unsigned int)err2 <= return_sites_error[1]))
{
return_sites[1] = site;
return_sites_error[1] = err2;
}
if ((err3 <= errthold) && (err3 <= return_sites_error[2]))
if ((err3 <= (int)errthold) && ((unsigned int)err3 <= return_sites_error[2]))
{
return_sites[2] = site;
return_sites_error[2] = err3;
}
if ((err4 <= errthold) && (err4 <= return_sites_error[3]))
if ((err4 <= (int)errthold) && ((unsigned int)err4 <= return_sites_error[3]))
{
return_sites[3] = site;
return_sites_error[3] = err4;
@@ -1281,9 +1118,7 @@ inline int Reserve_Banded_BPM_4_SSE_only(char *pattern1, char *pattern2, char *p
/****************************may have bugs********************************/
///p_length大部分情况下应该是t_length + 2 * errthold，这是i要小于last_high = 2 * errthold
///也就是p_length - t_length
///那么当p_length < t_length + 2 * errthold, available_i也应该是这个值
///in most cases, p_length should be t_length + 2 * errthold
int available_i = p_length - t_length;
while (i < available_i)
@@ -1305,29 +1140,29 @@ inline int Reserve_Banded_BPM_4_SSE_only(char *pattern1, char *pattern2, char *p
err4 = _mm_extract_epi32(Err_4, 3);
if ((err1 <= errthold) && (err1 <= return_sites_error[0]))
if ((err1 <= (int)errthold) && ((unsigned int)err1 <= return_sites_error[0]))
{
return_sites[0] = site + i;
return_sites_error[0] = err1;
}
if ((err2 <= errthold) && (err2 <= return_sites_error[1]))
if ((err2 <= (int)errthold) && ((unsigned int)err2 <= return_sites_error[1]))
{
return_sites[1] = site + i;
return_sites_error[1] = err2;
}
if ((err3 <= errthold) && (err3 <= return_sites_error[2]))
if ((err3 <= (int)errthold) && ((unsigned int)err3 <= return_sites_error[2]))
{
return_sites[2] = site + i;
return_sites_error[2] = err3;
}
if ((err4 <= errthold) && (err4 <= return_sites_error[3]))
if ((err4 <= (int)errthold) && ((unsigned int)err4 <= return_sites_error[3]))
{
return_sites[3] = site + i;
return_sites_error[3] = err4;
}
/****************************may have bugs********************************/
if(i == errthold)
if(i == (int)errthold)
{
ungap_error1 = err1;
ungap_error2 = err2;
@@ -1363,15 +1198,4 @@ inline int Reserve_Banded_BPM_4_SSE_only(char *pattern1, char *pattern2, char *p
}
void output_bit_myers(Word x, int length);
void prase_vertical(Word VP, Word VN, int length, int matrix[1000][1000], int i);
void prase_D0(Word D0, int length, int matrix[1000][1000], int i);
void prase_H(Word HP, Word HN, int length, int matrix[1000][1000], int i);
int Reserve_Banded_BPM_debug(char *pattern, int p_length, char *text, int t_length, unsigned short errthold,
unsigned int* return_err, int matrix[1000][1000]);
int Reserve_Banded_BPM_new(char *pattern,int p_length,char *text,int t_length,unsigned short errthold,
unsigned short band_down,unsigned short band_below,unsigned short band_length,int* return_err, int thread_id);
int BS_Reserve_Banded_BPM
(char *pattern, int p_length, char *text, int t_length, unsigned short errthold, unsigned int* return_err);
#endif