/usr/include/pbdata/SeqUtilsImpl.hpp is in libpbdata-dev 0~20151014+gitbe5d1bf-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 | #include <vector>
#include <iostream>
#include <stdint.h>
#include "utils.hpp"
#include "DNASequence.hpp"
#include "NucConversion.hpp"
#include "SeqUtils.hpp"
template< typename T_Sequence>
int OnlyACTG(T_Sequence &seq) {
DNALength p;
for (p = 0; p < seq.length; p++) {
if (ThreeBit[seq.seq[p]] > 3)
return 0;
}
return 1;
}
template< typename T_Sequence>
DNALength CountMasked(T_Sequence &seq) {
DNALength p;
DNALength nMasked = 0;
for (p = 0; p < seq.length; p++) {
if ((seq.seq[p] >= 'a' and
seq.seq[p] <= 'z') or
seq.seq[p] == 'N') {
nMasked++;
}
}
return nMasked;
}
template< typename T_Sequence>
int CountNotMasked(T_Sequence &seq) {
int p;
int nUnmasked = 0;
for (p = 0; p < seq.length; p++ ) {
if (seq.seq[p] == 'A' or
seq.seq[p] == 'C' or
seq.seq[p] == 'G' or
seq.seq[p] == 'T') {
nUnmasked++;
}
}
return nUnmasked;
}
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