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transform.h
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transform.h
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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 <lior.galanti@nyu.edu>
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/>.
*/
#ifndef PHENIQS_TRANSFORM_H
#define PHENIQS_TRANSFORM_H
#include "include.h"
#include "read.h"
enum class LeftTokenOperator : uint8_t {
NONE,
REVERSE_COMPLEMENT,
};
ostream& operator<<(ostream& o, const LeftTokenOperator& operation);
class Token {
friend ostream& operator<<(ostream& o, const Token& token);
public:
void operator=(Token const &) = delete;
const int32_t index;
const int32_t input_segment_index;
Token(
const int32_t& index,
const int32_t& input_segment_index,
const int32_t& start,
const int32_t& end,
const bool& end_terminated);
Token(const Token& other);
virtual ~Token() = default;
inline bool empty() const {
return (end_terminated && start >= end) && ((start >= 0 && end >= 0) || (start < 0 && end < 0));
};
inline int32_t length() const {
if(constant()) {
if(end_terminated) {
return empty() ? 0 : end - start;
} else { return -start; }
} else { return -1; }
};
inline bool constant() const {
if(end_terminated) {
return (start >= 0 && end >= 0) || (start < 0 && end < 0);
} else { return start < 0; }
};
inline const int32_t absolute_end(const int32_t& length) const {
if(end_terminated) {
if(end < 0) {
int32_t value(length + end);
return (value < 0 ? 0 : value);
} else { return (end > length ? length : end); }
} else { return length; }
};
inline const int32_t absolute_start(const int32_t& length) const {
if(start < 0) {
int32_t value(length + start);
if(value < 0) {
return 0;
} else { return value; }
} else { return (start > length ? 0 : start); }
};
operator string() const;
virtual string description() const;
private:
const int32_t start;
const int32_t end;
const bool end_terminated;
};
ostream& operator<<(ostream& o, const Token& token);
template<> vector< Token > decode_value_by_key(const Value::Ch* key, const Value& container);
class Transform : public Token {
friend ostream& operator<<(ostream& o, const Transform& transform);
public:
void operator=(Transform const &) = delete;
const int32_t output_segment_index;
const LeftTokenOperator left;
Transform(
const Token& token,
const int32_t& output_segment_index,
const LeftTokenOperator& left) :
Token(token),
output_segment_index(output_segment_index),
left(left) {
};
Transform(const Transform& other);
string description() const override;
operator string() const;
};
ostream& operator<<(ostream& o, const Transform& transform);
bool encode_key_value(const string& key, const list< Transform >& value, Value& container, Document& document);
class Rule {
public:
const vector< Token > token_array;
const int32_t output_segment_cardinality;
const vector< Transform > transform_array;
Rule(
const vector< Token > token_array,
const int32_t output_segment_cardinality,
const vector< Transform > transform_array) :
token_array(token_array),
output_segment_cardinality(output_segment_cardinality),
transform_array(transform_array) {
};
Rule(const Rule& other) :
token_array(other.token_array),
output_segment_cardinality(other.output_segment_cardinality),
transform_array(other.transform_array) {
};
virtual ~Rule() {
};
inline int32_t token_cardinality() const {
return static_cast< int32_t >(token_array.size());
};
inline void apply(const Read& source, Observation& target) const {
for(auto& transform : transform_array ) {
const Segment& from = source[transform.input_segment_index];
ObservedSequence& to = target[transform.output_segment_index];
const int32_t start(transform.absolute_start(from.length));
const int32_t end(transform.absolute_end(from.length));
const int32_t size(end - start);
if(size > 0) {
to.increase_by_size(size);
switch (transform.left) {
case LeftTokenOperator::NONE: {
memcpy(to.code + to.length, from.code + start, size);
memcpy(to.quality + to.length, from.quality + start, size);
break;
};
case LeftTokenOperator::REVERSE_COMPLEMENT: {
for(int32_t i(0); i < size; ++i) {
to.code[to.length + i] = BamToReverseComplementBam[from.code[end - i - 1]];
to.quality[to.length + i] = from.quality[end - i - 1];
}
break;
};
}
to.length += size;
to.terminate();
}
}
};
};
template<> Rule decode_value_by_key(const Value::Ch* key, const Value& container);
class TemplateRule : public Rule {
public:
TemplateRule(
const vector< Token > token_array,
const int32_t output_segment_cardinality,
const vector< Transform > transform_array) :
Rule(token_array, output_segment_cardinality, transform_array) {
};
TemplateRule(const TemplateRule& other) :
Rule(other) {
};
TemplateRule(const Rule& other) :
Rule(other) {
};
~TemplateRule() override {
};
inline void apply(const Read& source, Read& target) const {
for(auto& transform : transform_array ) {
const ObservedSequence* from;
if(transform.input_segment_index == -1) {
from = &target.corrected_sample_barcode;
} else if(transform.input_segment_index == -2) {
from = &target.corrected_cellular_barcode;
} else if(transform.input_segment_index == -3) {
from = &target.corrected_molecular_barcode;
} else {
from = &source[transform.input_segment_index];
}
Segment& to = target[transform.output_segment_index];
const int32_t start(transform.absolute_start(from->length));
const int32_t end(transform.absolute_end(from->length));
const int32_t size(end - start);
if(size > 0) {
to.increase_by_size(size);
switch (transform.left) {
case LeftTokenOperator::NONE: {
memcpy(to.code + to.length, from->code + start, size);
memcpy(to.quality + to.length, from->quality + start, size);
break;
};
case LeftTokenOperator::REVERSE_COMPLEMENT: {
for(int32_t i(0); i < size; ++i) {
to.code[to.length + i] = BamToReverseComplementBam[from->code[end - i - 1]];
to.quality[to.length + i] = from->quality[end - i - 1];
}
break;
};
}
to.length += size;
to.terminate();
}
}
};
};
#endif /* PHENIQS_TRANSFORM_H */