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fix bugs for overlaps of different length

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This commit is contained in:
Haoyu Cheng
2019-12-09 17:07:11 -05:00
parent fca9c8db15
commit 09603432e5
11 changed files with 1726 additions and 94 deletions
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Levenshtein_distance.h
+78
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@@ -184,6 +184,9 @@ inline int Reserve_Banded_BPM
int i_last = i;
i = 0;
/****************************may have bugs********************************/
unsigned int ungap_error = (unsigned int)-1;
/****************************may have bugs********************************/
while (i < available_i)
{
@@ -196,8 +199,22 @@ inline int Reserve_Banded_BPM
*return_err = err;
return_site = site + i;
}
/****************************may have bugs********************************/
if(i == errthold)
{
ungap_error = err;
}
/****************************may have bugs********************************/
}
/****************************may have bugs********************************/
if((ungap_error<=errthold) && (ungap_error == (*return_err)))
{
return_site = site + errthold;
}
/****************************may have bugs********************************/
return return_site;
}
@@ -436,6 +453,11 @@ inline int Reserve_Banded_BPM_PATH
///int site = p_length - last_high - 1;
int site = t_length - 1;
int return_site = -1;
/****************************may have bugs********************************/
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
@@ -459,13 +481,30 @@ inline int Reserve_Banded_BPM_PATH
*return_err = err;
return_site = site + i;
}
/****************************may have bugs********************************/
if(i == errthold)
{
ungap_error = err;
}
/****************************may have bugs********************************/
}
if ((*return_err) == (unsigned int)-1)
{
return return_site;
}
/****************************may have bugs********************************/
if((ungap_error<=errthold) && (ungap_error == (*return_err)))
{
return_site = site + errthold;
}
/****************************may have bugs********************************/
////注意，这里p_length要矫正啊啊
///不矫正会出错
@@ -846,6 +885,13 @@ inline int Reserve_Banded_BPM_4_SSE_only(char *pattern1, char *pattern2, char *p
i = 0;
/****************************may have bugs********************************/
unsigned int ungap_error1 = (unsigned int)-1;
unsigned int ungap_error2 = (unsigned int)-1;
unsigned int ungap_error3 = (unsigned int)-1;
unsigned int ungap_error4 = (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
@@ -891,8 +937,40 @@ inline int Reserve_Banded_BPM_4_SSE_only(char *pattern1, char *pattern2, char *p
return_sites[3] = site + i;
return_sites_error[3] = err4;
}
/****************************may have bugs********************************/
if(i == errthold)
{
ungap_error1 = err1;
ungap_error2 = err2;
ungap_error3 = err3;
ungap_error4 = err4;
}
/****************************may have bugs********************************/
}
/****************************may have bugs********************************/
if((ungap_error1<=errthold) && (ungap_error1 == return_sites_error[0]))
{
return_sites[0] = site + errthold;
}
if((ungap_error2<=errthold) && (ungap_error2 == return_sites_error[1]))
{
return_sites[1] = site + errthold;
}
if((ungap_error3<=errthold) && (ungap_error3 == return_sites_error[2]))
{
return_sites[2] = site + errthold;
}
if((ungap_error4<=errthold) && (ungap_error4 == return_sites_error[3]))
{
return_sites[3] = site + errthold;
}
/****************************may have bugs********************************/
return 1;
}