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Fix buffer initialization in SD motif detection code #100

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Merged
hyattpd merged 2 commits into from
Jan 27, 2023
Merged

Fix buffer initialization in SD motif detection code #100

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7b8614d
Fix buffer initialization in SD motif detection code
althonos Jan 27, 2023
7cb28c9
Slightly refactor comparison code in `shine_dalgarno` functions
althonos Jan 27, 2023
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29 changes: 15 additions & 14 deletions sequence.c
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Original file line number Diff line number Diff line change
Expand Up @@ -663,14 +663,14 @@ int shine_dalgarno_exact(unsigned char *seq, int pos, int start, double *rwt) {
double match[6], cur_ctr, dis_flag;

limit = imin(6, start-4-pos);
for(i = limit; i < 6; i++) match[i] = -10.0;
for(i = 0; i < 6; i++) match[i] = -10.0;

/* Compare the 6-base region to AGGAGG */
for(i = 0; i < limit; i++) {
if(pos+i < 0) continue;
if(i%3 == 0 && is_a(seq, pos+i) == 1) match[i] = 2.0;
else if(i%3 != 0 && is_g(seq, pos+i) == 1) match[i] = 3.0;
else match[i] = -10.0;
if(pos + i >= 0) {
if(i%3 == 0 && is_a(seq, pos+i) == 1) match[i] = 2.0;
else if(i%3 != 0 && is_g(seq, pos+i) == 1) match[i] = 3.0;
}
}

/* Find the maximally scoring motif */
Expand Down Expand Up @@ -739,18 +739,19 @@ int shine_dalgarno_mm(unsigned char *seq, int pos, int start, double *rwt) {
double match[6], cur_ctr, dis_flag;

limit = imin(6, start-4-pos);
for(i = limit; i < 6; i++) match[i] = -10.0;
for(i = 0; i < 6; i++) match[i] = -10.0;

/* Compare the 6-base region to AGGAGG */
for(i = 0; i < limit; i++) {
if(pos+i < 0) continue;
if(i % 3 == 0) {
if(is_a(seq, pos+i) == 1) match[i] = 2.0;
else match[i] = -3.0;
}
else {
if(is_g(seq, pos+i) == 1) match[i] = 3.0;
else match[i] = -2.0;
if(pos+i >= 0) {
if(i % 3 == 0) {
if(is_a(seq, pos+i) == 1) match[i] = 2.0;
else match[i] = -3.0;
}
else {
if(is_g(seq, pos+i) == 1) match[i] = 3.0;
else match[i] = -2.0;
}
}
}

Expand Down