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replace stopMemset() with clearString(). #16

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replace stopMemset() with clearString(). #16

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14 changes: 7 additions & 7 deletions hmm_lib.c
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Original file line number Diff line number Diff line change
Expand Up @@ -792,13 +792,13 @@ void viterbi(HMM *hmm_ptr, char *O, char* output_buffer, char* aa_buffer,
(vpath[t]==M1_STATE || vpath[t]==M4_STATE ||
vpath[t]==M1_STATE_1 || vpath[t]==M4_STATE_1)) {

stopMemset(dna, STRINGLEN);
stopMemset(dna1, STRINGLEN);//
stopMemset(dna_f, STRINGLEN);//
stopMemset(dna_f1, STRINGLEN);//
stopMemset(protein, STRINGLEN);
stopMemset(insert, STRINGLEN);//
stopMemset(c_delete, STRINGLEN);//
clearString(dna, STRINGLEN);
clearString(dna1, STRINGLEN);
clearString(dna_f, STRINGLEN);
clearString(dna_f1, STRINGLEN);
clearString(protein, STRINGLEN);
clearString(insert, STRINGLEN);
clearString(c_delete, STRINGLEN);

insert_id = 0;
delete_id = 0;
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6 changes: 3 additions & 3 deletions run_hmm.c
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Expand Up @@ -610,9 +610,9 @@ void writeAminoAcids(FILE* aa_outfile_fp, thread_data* td, unsigned int buffer)
}

//!! Why are we clearing dna and output buff?
stopMemset(td->output_buffer[buffer][j], STRINGLEN);
stopMemset(td->aa_buffer[buffer][j], STRINGLEN);
stopMemset(td->dna_buffer[buffer][j], STRINGLEN);
clearString(td->output_buffer[buffer][j], STRINGLEN);
clearString(td->aa_buffer[buffer][j], STRINGLEN);
clearString(td->dna_buffer[buffer][j], STRINGLEN);
}
}

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11 changes: 3 additions & 8 deletions util_lib.c
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Expand Up @@ -488,12 +488,7 @@ void print_usage() {

}

void stopMemset(char* ptr, int length) {
int i;
for(i=0; i<length; i++) {
if(ptr[i] == '\0') {
return;
}
ptr[i] = '\0';
}
void clearString(char* str, int length) {
if (str != NULL && length > 0)
str[0] = '\0';
}
8 changes: 7 additions & 1 deletion util_lib.h
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Expand Up @@ -39,6 +39,12 @@ QUEUE* deq(unsigned int which);

void cutnpaste_q(QUEUE** dest, unsigned int which);

void stopMemset(char* ptr, int length);
/*
* Sets the string's first charachter to '\0', so string functions handle it
* like an empty string.
*
* NOTE: if you plan to use functions that use a given length, it's safer to use memset
*/
void clearString(char* str, int length);

#endif