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Patch type mismatch in apat C library

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This commit is contained in:
Eric Coissac
2025-04-23 16:14:10 +02:00
parent c0ecaf90ab
commit 13ff892ac9
4 changed files with 15 additions and 15 deletions
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14
pkg/obiapat/obiapat.c Normal file → Executable file
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@ -149,9 +149,9 @@ char *LowerSequence(char *seq)
char *cseq; char *cseq;
for (cseq = seq ; *cseq ; cseq++) for (cseq = seq ; *cseq ; cseq++)
if (IS_UPPER(*cseq)) if (IS_UPPER(*cseq)) {
*cseq = TO_LOWER(*cseq); *cseq = TO_LOWER(*cseq);
}
return seq; return seq;
} }
@ -299,14 +299,14 @@ int32_t delete_apatseq(SeqPtr pseq,
return 1; return 1;
} }
PatternPtr buildPattern(const char *pat, int32_t error_max, uint8_t hasIndel, Pattern *buildPattern(const char *pat, int32_t error_max, uint8_t hasIndel,
int *errno, char **errmsg) int *errno, char **errmsg)
{ {
PatternPtr pattern; Pattern *pattern;
int32_t patlen; int32_t patlen;
int32_t patlen2; int32_t patlen2;
patlen = strlen(pat); patlen = (int32_t)strlen(pat);
patlen2 = lenPattern(pat); patlen2 = lenPattern(pat);
pattern = ECOMALLOC(sizeof(Pattern) + // Space for struct Pattern pattern = ECOMALLOC(sizeof(Pattern) + // Space for struct Pattern
@ -341,10 +341,10 @@ PatternPtr buildPattern(const char *pat, int32_t error_max, uint8_t hasIndel,
} }
PatternPtr complementPattern(PatternPtr pat, int *errno, Pattern *complementPattern(Pattern *pat, int *errno,
char **errmsg) char **errmsg)
{ {
PatternPtr pattern; Pattern *pattern;
pattern = ECOMALLOC(sizeof(Pattern) + pattern = ECOMALLOC(sizeof(Pattern) +
sizeof(char) * strlen(pat->cpat) + 1 + sizeof(char) * strlen(pat->cpat) + 1 +

10
pkg/obiapat/obiapat.h Normal file → Executable file
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@ -116,13 +116,13 @@ ecoseq_t *new_ecoseq_with_data( char *AC,
int32_t delete_apatseq(SeqPtr pseq, int32_t delete_apatseq(Seq *pseq,
int *errno, char **errmsg); int *errno, char **errmsg);
PatternPtr buildPattern(const char *pat, int32_t error_max, uint8_t hasIndel, int *errno, char **errmsg); Pattern *buildPattern(const char *pat, int32_t error_max, uint8_t hasIndel, int *errno, char **errmsg);
PatternPtr complementPattern(PatternPtr pat, int *errno, char **errmsg); Pattern *complementPattern(Pattern *pat, int *errno, char **errmsg);
SeqPtr new_apatseq(const char *in,int32_t circular, int32_t seqlen, Seq *new_apatseq(const char *in,int32_t circular, int32_t seqlen,
SeqPtr out, Seq *out,
int *errno, char **errmsg); int *errno, char **errmsg);
char *ecoComplementPattern(char *nucAcSeq); char *ecoComplementPattern(char *nucAcSeq);

4
pkg/obiapat/pattern.go Normal file → Executable file
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@ -26,7 +26,7 @@ var _AllocatedApaPattern = 0
// ApatPattern stores a regular pattern usable by the // ApatPattern stores a regular pattern usable by the
// Apat algorithm functions and methods // Apat algorithm functions and methods
type _ApatPattern struct { type _ApatPattern struct {
pointer *C.Pattern pointer C.PatternPtr
pattern string pattern string
} }
@ -159,7 +159,7 @@ func (pattern ApatPattern) Free() {
// Print method prints the ApatPattern to the standard output. // Print method prints the ApatPattern to the standard output.
// This is mainly a debug method. // This is mainly a debug method.
func (pattern ApatPattern) Print() { func (pattern ApatPattern) Print() {
C.PrintDebugPattern(C.PatternPtr(pattern.pointer.pointer)) C.PrintDebugPattern((*C.Pattern)(pattern.pointer.pointer))
} }
// MakeApatSequence casts an obiseq.BioSequence to an ApatSequence. // MakeApatSequence casts an obiseq.BioSequence to an ApatSequence.

2
pkg/obioptions/version.go
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@ -8,7 +8,7 @@ import (
// corresponds to the last commit, and not the one when the file will be // corresponds to the last commit, and not the one when the file will be
// commited // commited
var _Commit = "a57cfda" var _Commit = "c0ecaf9"
var _Version = "Release 4.4.0" var _Version = "Release 4.4.0"
// Version returns the version of the obitools package. // Version returns the version of the obitools package.