Commit 2e0a25ae authored by Robin Erich Muench's avatar Robin Erich Muench
Browse files

compilation fix

parent 4ae32f43
......@@ -53,7 +53,7 @@ static int print_usage()
fprintf(stderr, "Contact: Paul Costea <costea@embl.de>,\n\t Robin Muench <rmuench@embl.de>\n\n");
fprintf(stderr, "Usage: snpCall [options] <stdin.mpileup> \n");
fprintf(stderr, "Options: \n");
fprintf(stderr, " -b, TODO: list of input BAM filenames, one per line (for header) \n ");
// fprintf(stderr, " -b, TODO: list of input BAM filenames, one per line (for header) \n ");
fprintf(stderr, " -f, faidx indexed reference metagenome \n ");
fprintf(stderr, " -g, gene annotation file [NULL].\n");
fprintf(stderr, " -i, individual SNPs output file [NULL].\n\n");
......@@ -603,7 +603,7 @@ std::map<std::string, char> CodonMap(codons, codons + sizeof codons / sizeof cod
sToWrite = &s;
} else { //May be a individual variant
for (int i=1; i<=nrSamples; ++i) {
int s = getSum(map,snp,i);
int s = getSum(map,check,i);
if (s >= CALLING_THRESHOLD) {//We observe the variant "CALLING_THRESHOLD" times in one sample.
writeThis = true;
sToWrite = &indiv;
......
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