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sequence.cpp
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/*
Pheniqs : PHilology ENcoder wIth Quality Statistics
Copyright (C) 2018 Lior Galanti
NYU Center for Genetics and System Biology
Author: Lior Galanti <[email protected]>
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as
published by the Free Software Foundation, either version 3 of the
License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Affero General Public License for more details.
You should have received a copy of the GNU Affero General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#include "sequence.h"
bool operator<(const Sequence& left, const Sequence& right) {
int32_t position(0);
while(position < left.length && position < right.length) {
if(left.code[position] == right.code[position]) {
++position;
} else {
if(left.code[position] < right.code[position]) {
return true;
} else {
return false;
}
}
}
return false;
};
bool operator>(const Sequence& left, const Sequence& right) {
int32_t position(0);
while(position < left.length && position < right.length) {
if(left.code[position] == right.code[position]) {
++position;
} else {
if(left.code[position] > right.code[position]) {
return true;
} else {
return false;
}
}
}
return false;
};
void encode_value(const Sequence& value, Value& container, Document& document) {
if(!value.empty()) {
kstring_t buffer({ 0, 0, NULL });
value.encode_iupac_ambiguity(buffer);
container.PushBack(Value(buffer.s, buffer.l, document.GetAllocator()).Move(), document.GetAllocator());
ks_free(buffer);
}
};
ostream& operator<<(ostream& o, const Sequence& sequence) {
if(!sequence.empty()) {
kstring_t buffer({ 0, 0, NULL });
sequence.encode_iupac_ambiguity(buffer);
o << buffer.s;
ks_free(buffer);
}
return o;
};
ostream& operator<<(ostream& o, const ObservedSequence& sequence) {
if(!sequence.empty()) {
kstring_t buffer({ 0, 0, NULL });
sequence.encode_iupac_ambiguity(buffer);
ks_put_character('/', buffer);
sequence.encode_phred_quality(buffer, SAM_PHRED_DECODING_OFFSET);
o << buffer.s;
ks_free(buffer);
}
return o;
};
ostream& operator<<(ostream& o, const Observation& observation) {
if(!observation.empty()) {
kstring_t buffer({ 0, 0, NULL });
observation.encode_iupac_ambiguity(buffer);
ks_put_character('/', buffer);
observation.encode_phred_quality(buffer, SAM_PHRED_DECODING_OFFSET);
o << buffer.s;
ks_free(buffer);
}
return o;
}