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Made sequence parsing more robust (issue with arm64 systems)

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This commit is contained in:
Celine Mercier
2020-04-13 11:59:09 +02:00
parent b11748eac8
commit d7cd7e2677
1 changed files with 7 additions and 2 deletions
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9
libfasta/sequence.c
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@ -162,19 +162,24 @@ void seq_fillSeqOnlyATGC(char *seq, fastaSeqPtr seqElem, int seqLen)
{ {
char* seqTemp; char* seqTemp;
char c; char c;
int32_t index = 0, seqIndex = 0, len = strlen(seq); int32_t index = 1, seqIndex = 0, len = strlen(seq);
char* seqAlphabets = "acgtACGT"; char* seqAlphabets = "acgtACGT";
int notAllATGC = 0; int notAllATGC = 0;
int goOnParsing = 1;
seqTemp = (char*) util_malloc(seqLen*sizeof(char), __FILE__, __LINE__); seqTemp = (char*) util_malloc(seqLen*sizeof(char), __FILE__, __LINE__);
while (index < len) while (goOnParsing)
{ {
c = seq[index++]; c = seq[index++];
if (strchr(seqAlphabets, c) != NULL) if (strchr(seqAlphabets, c) != NULL)
seqTemp[seqIndex++] = tolower(c); seqTemp[seqIndex++] = tolower(c);
else if ((c == '\n') && (seq[index+1]=='\0'))
goOnParsing = 0; //End of line character terminating the sequence has been reached.
else if (c != '\n') else if (c != '\n')
notAllATGC = 1; notAllATGC = 1;
if (index == len)
goOnParsing = 0;
} }
if (notAllATGC) if (notAllATGC)