mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-10-11 02:00:55 +08:00
resure alignment
This commit is contained in:
Haoyu Cheng
+90
-148
@@ -172,6 +172,10 @@ inline int Reserve_Banded_BPM
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///int site = p_length - last_high - 1;
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int site = t_length - 1;
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int return_site = -1;
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///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
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///也就是p_length - t_length
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///那么当p_length < t_length + 2 * errthold, available_i也应该是这个值
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int available_i = p_length - t_length;
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if ((err <= errthold) && (err<=*return_err))
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{
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*return_err = err;
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@@ -181,9 +185,7 @@ inline int Reserve_Banded_BPM
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i = 0;
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while (i<errthold)
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while (i < available_i)
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{
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err = err + ((VP >> i)&(Word)1);
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err = err - ((VN >> i)&(Word)1);
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@@ -196,45 +198,85 @@ inline int Reserve_Banded_BPM
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}
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}
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unsigned int ungap_err;
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ungap_err = err;
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while (i<last_high)
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{
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err = err + ((VP >> i)&(Word)1);
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err = err - ((VN >> i)&(Word)1);
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++i;
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if ((err <= errthold) && (err<=*return_err))
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{
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*return_err = err;
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return_site = site + i;
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}
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}
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if ((ungap_err <= errthold) && (ungap_err == *return_err))
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{
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return_site = site + errthold;
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}
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return return_site;
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}
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inline int try_cigar(char *pattern, int p_length,
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char *text, int t_length, int end_site, char* path,
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int error,
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int* return_start_site,
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int* return_path_length)
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{
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int i = 0;
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int tmp_err = 0;
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///y上的起始位置
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int start_site = end_site - t_length + 1;
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if (start_site >= 0)
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{
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for (i = 0; i < t_length; i++)
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{
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///path[i] = 0;
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///path倒着存
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path[t_length - i - 1] = 0;
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if (text[i] != pattern[i + start_site])
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{
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path[t_length - i - 1] = 1;
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tmp_err++;
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if (tmp_err > error)
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{
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return 0;
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}
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}
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}
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if (tmp_err == error)
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{
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(*return_path_length) = t_length;
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(*return_start_site) = start_site;
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return 6;
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}
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}
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return 0;
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}
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///p_length有可能不够，但是t_length总是够的
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///就是p_length有可能小于t_length + 2 * errthold
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inline int Reserve_Banded_BPM_PATH
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(char *pattern, int p_length, char *text, int t_length, unsigned short errthold,
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unsigned int* return_err, int* return_start_site, int* return_path_length, Word* matrix_bit, char* path)
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unsigned int* return_err, int* return_start_site, int* return_path_length, Word* matrix_bit, char* path,
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int old_error, int old_end_site)
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{
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if (old_error != -1 && old_end_site != -1)
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{
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if (old_error == 0)
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{
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///fprintf(stderr, "0 error\n");
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(*return_err) = old_error;
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(*return_start_site) = old_end_site - t_length + 1;
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return old_end_site;
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}
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if (try_cigar(pattern, p_length, text, t_length, old_end_site, path,
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old_error, return_start_site, return_path_length))
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{
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///fprintf(stderr, "no gap error\n");
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(*return_err) = old_error;
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return old_end_site;
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}
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}
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(*return_err) = (unsigned int)-1;
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Word Peq[256];
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@@ -330,10 +372,8 @@ inline int Reserve_Banded_BPM_PATH
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{
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++err;
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///¼´Ê¹È«²¿µÝ¼õ£¬Ò²¾Í¼õ2k
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if ((err - last_high)>errthold)
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{
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///fprintf(stderr, "0 ######, i: %u\n", i);
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return -1;
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}
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@@ -396,6 +436,10 @@ inline int Reserve_Banded_BPM_PATH
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///int site = p_length - last_high - 1;
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int site = t_length - 1;
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int return_site = -1;
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///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
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///也就是p_length - t_length
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///那么当p_length < t_length + 2 * errthold, available_i也应该是这个值
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int available_i = p_length - t_length;
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if ((err <= errthold) && (err<=*return_err))
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{
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*return_err = err;
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@@ -404,10 +448,7 @@ inline int Reserve_Banded_BPM_PATH
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int i_last = i;
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i = 0;
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while (i<errthold)
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while (i < available_i)
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{
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err = err + ((VP >> i)&(Word)1);
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err = err - ((VN >> i)&(Word)1);
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@@ -421,40 +462,15 @@ inline int Reserve_Banded_BPM_PATH
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}
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unsigned int ungap_err;
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ungap_err = err;
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while (i<last_high)
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{
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err = err + ((VP >> i)&(Word)1);
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err = err - ((VN >> i)&(Word)1);
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++i;
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if ((err <= errthold) && (err<=*return_err))
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{
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*return_err = err;
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return_site = site + i;
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}
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}
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if ((ungap_err <= errthold) && (ungap_err == *return_err))
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{
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return_site = site + errthold;
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}
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if ((*return_err) == (unsigned int)-1)
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{
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return return_site;
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}
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////注意，这里p_length要矫正啊啊
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///不矫正会出错
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///因为p_length有可能不够
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p_length = t_length + 2 * errthold;
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///end_site是正确的
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int end_site = return_site;
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int start_site = end_site;
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@@ -608,6 +624,8 @@ inline int Reserve_Banded_BPM_PATH
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}
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////这个p_length四个是一样的
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inline int Reserve_Banded_BPM_4_SSE_only(char *pattern1, char *pattern2, char *pattern3, char *pattern4, int p_length, char *text, int t_length,
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int* return_sites, unsigned int* return_sites_error, unsigned short errthold, __m128i* Peq_SSE)
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@@ -829,8 +847,12 @@ inline int Reserve_Banded_BPM_4_SSE_only(char *pattern1, char *pattern2, char *p
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i = 0;
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///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
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///也就是p_length - t_length
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///那么当p_length < t_length + 2 * errthold, available_i也应该是这个值
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int available_i = p_length - t_length;
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while (i<errthold)
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while (i < available_i)
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{
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///err = err + ((VP >> i)&(Word_32)1);
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tmp_process = _mm_srli_epi32(VP, i);
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@@ -871,87 +893,7 @@ inline int Reserve_Banded_BPM_4_SSE_only(char *pattern1, char *pattern2, char *p
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}
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}
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unsigned int ungap_err1;
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unsigned int ungap_err2;
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unsigned int ungap_err3;
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unsigned int ungap_err4;
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ungap_err1 = err1;
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ungap_err2 = err2;
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ungap_err3 = err3;
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ungap_err4 = err4;
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while (i<last_high)
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{
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///err = err + ((VP >> i)&(Word_32)1);
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tmp_process = _mm_srli_epi32(VP, i);
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tmp_process = _mm_and_si128(tmp_process, err_mask);
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Err_4 = _mm_add_epi32(Err_4, tmp_process);
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///err = err - ((VN >> i)&(Word_32)1);
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tmp_process1 = _mm_srli_epi32(VN, i);
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tmp_process1 = _mm_and_si128(tmp_process1, err_mask);
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Err_4 = _mm_sub_epi32(Err_4, tmp_process1);
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++i;
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err1 = _mm_extract_epi32(Err_4, 0);
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err2 = _mm_extract_epi32(Err_4, 1);
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err3 = _mm_extract_epi32(Err_4, 2);
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err4 = _mm_extract_epi32(Err_4, 3);
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if ((err1 <= errthold) && (err1 <= return_sites_error[0]))
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{
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return_sites[0] = site + i;
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return_sites_error[0] = err1;
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}
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if ((err2 <= errthold) && (err2 <= return_sites_error[1]))
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{
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return_sites[1] = site + i;
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return_sites_error[1] = err2;
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}
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if ((err3 <= errthold) && (err3 <= return_sites_error[2]))
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{
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return_sites[2] = site + i;
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return_sites_error[2] = err3;
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}
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if ((err4 <= errthold) && (err4 <= return_sites_error[3]))
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{
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return_sites[3] = site + i;
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return_sites_error[3] = err4;
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}
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}
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if ((ungap_err1 <= errthold) && ungap_err1 == return_sites_error[0])
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{
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return_sites[0] = site + errthold;
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}
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if ((ungap_err2 <= errthold) && ungap_err2 == return_sites_error[1])
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{
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return_sites[1] = site + errthold;
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}
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if ((ungap_err3 <= errthold) && ungap_err3 == return_sites_error[2])
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{
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return_sites[2] = site + errthold;
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}
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if ((ungap_err4 <= errthold) && ungap_err4 == return_sites_error[3])
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{
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return_sites[3] = site + errthold;
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}
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return 1;
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}
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