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Add the possibility to look for patterns allowing indels.

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Former-commit-id: 0599c2b0ad16df086dbdb08e491503870d8904be
This commit is contained in:
Eric Coissac
2023-03-20 15:28:24 +07:00
parent 5fbe52368c
commit 27d6c60e25
14 changed files with 674 additions and 219 deletions
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4
pkg/obiapat/obiapat.c
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@@ -337,7 +337,7 @@ int32_t delete_apatseq(SeqPtr pseq,
return 1;
}
PatternPtr buildPattern(const char *pat, int32_t error_max,
PatternPtr buildPattern(const char *pat, int32_t error_max, uint8_t hasIndel,
int *errno, char **errmsg)
{
PatternPtr pattern;
@@ -355,7 +355,7 @@ PatternPtr buildPattern(const char *pat, int32_t error_max,
errno,errmsg);
pattern->ok = true;
pattern->hasIndel= false;
pattern->hasIndel= hasIndel;
pattern->maxerr = error_max;
pattern->cpat = (char*)pattern + sizeof(Pattern);