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Regarding #109 #111

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Regarding #109 #111

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1d60350
trying to add --NoMe option
vivekbhr Jan 18, 2021
8ecbb21
update
vivekbhr Jan 20, 2021
254a6ed
more attempt to fix the GCH calls
vivekbhr Jan 20, 2021
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update
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@vivekbhr
vivekbhr committed Jan 20, 2021
commit 8ecbb21855a3e260e1fea8fdf243bff1b17f6b7c
8 changes: 8 additions & 0 deletions extract.c
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Original file line number Diff line number Diff line change
Expand Up @@ -35,6 +35,13 @@ const char *TriNucleotideContexts[25] = {"CAA", "CAC", "CAG", "CAT", "CAN", \
"CTA", "CTC", "CTG", "CTT", "CTN", \
"CNA", "CNC", "CNG", "CNT", "CNN"};

const char *TriNucleotideContextsGpC[25] = {"GAA", "GAC", "GAG", "GAT", "GAN", \
"GCA", "GCC", "GCG", "GCT", "GCN", \
"GGA", "GGC", "GGG", "GGT", "GGN", \
"GTA", "GTC", "GTG", "GTT", "GTN", \
"GNA", "GNC", "GNG", "GNT", "GNN"};

// writeCall(ks[0], config, chrom, *lastPos, 1, 0, 0, (direction>0)?'C':'G', context, TriNucleotideContexts[triNucContext]);
void writeCall(kstring_t *ks, Config *config, char *chrom, int32_t pos, int32_t width, uint32_t nmethyl, uint32_t nunmethyl, char base, char *context, const char *tnc) {
char str[10000]; // I don't really like hardcoding it, but given the probability that it ever won't suffice...
char strand = (base=='C' || base=='c') ? 'F' : 'R';
Expand Down Expand Up @@ -203,6 +210,7 @@ void writeBlank(kstring_t **ks, Config *config, char *chrom, int32_t pos, uint32
if(!config->keepGCH) continue;
triNucContext = getTriNucContext(seq, *lastPos - localPos2, seqlen, direction);
context[0] = 'C'; context[1] = 'H';
fprintf(stderr, "Found GCH! triNucContext = %s \n", TriNucleotideContextsGpC[triNucContext]);
continue;
} else {
continue;
Expand Down