/
transcode.cpp
2313 lines (2117 loc) · 101 KB
/
transcode.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 <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/>.
*/
/*
filter_incoming_qc_fail: should we process incoming qc_fail reads?
filter_outgoing_qc_fail: should we write qc_fail reads?
inherit_qc_fail: should outgoing reads inherit qc_fail flag from incoming?
*/
#include "transcode.h"
/* TranscodingDecoder */
TranscodingDecoder::TranscodingDecoder(const Value& ontology) try :
count(0),
pf_count(0),
pf_fraction(0),
sample_classifier(NULL) {
load_sample_decoding(ontology);
load_molecular_decoding(ontology);
load_cellular_decoding(ontology);
} catch(Error& error) {
error.push("TranscodingDecoder");
throw;
};
TranscodingDecoder::~TranscodingDecoder() {
if(sample_classifier != NULL) {
delete sample_classifier;
}
if(!molecular_classifier_array.empty()) {
for(auto& classifier : molecular_classifier_array) {
delete classifier;
}
}
if(!cellular_classifier_array.empty()) {
for(auto& classifier : cellular_classifier_array) {
delete classifier;
}
}
};
void TranscodingDecoder::load_sample_decoding(const Value& ontology) {
Value::ConstMemberIterator reference = ontology.FindMember("sample");
if(reference != ontology.MemberEnd()) {
load_sample_decoder(reference->value);
}
};
void TranscodingDecoder::load_sample_decoder(const Value& value) {
Algorithm algorithm(decode_value_by_key< Algorithm >("algorithm", value));
switch(algorithm) {
case Algorithm::PAMLD: {
sample_classifier = new PamlSampleDecoder(value);
break;
};
case Algorithm::MDD: {
sample_classifier = new MdSampleDecoder(value);
break;
};
case Algorithm::PASSTHROUGH: {
sample_classifier = new Classifier< Barcode >(value);
break;
};
default:
throw ConfigurationError("unsupported sample decoder algorithm " + to_string(algorithm));
break;
}
};
void TranscodingDecoder::load_molecular_decoding(const Value& ontology) {
Value::ConstMemberIterator reference = ontology.FindMember("molecular");
if(reference != ontology.MemberEnd()) {
if(reference->value.IsObject()) {
molecular_classifier_array.reserve(1);
load_molecular_decoder(reference->value);
} else if(reference->value.IsArray()) {
molecular_classifier_array.reserve(reference->value.Size());
for(const auto& element : reference->value.GetArray()) {
load_molecular_decoder(element);
}
}
}
molecular_classifier_array.shrink_to_fit();
};
void TranscodingDecoder::load_molecular_decoder(const Value& value) {
Algorithm algorithm(decode_value_by_key< Algorithm >("algorithm", value));
switch(algorithm) {
case Algorithm::PAMLD: {
molecular_classifier_array.emplace_back(new PamlMolecularDecoder(value));
break;
};
case Algorithm::MDD: {
molecular_classifier_array.emplace_back(new MdMolecularDecoder(value));
break;
};
case Algorithm::PASSTHROUGH: {
molecular_classifier_array.emplace_back(new Classifier< Barcode >(value));
break;
};
case Algorithm::NAIVE: {
molecular_classifier_array.emplace_back(new NaiveMolecularDecoder(value));
break;
};
default:
throw ConfigurationError("unsupported molecular decoder algorithm " + to_string(algorithm));
break;
}
};
void TranscodingDecoder::load_cellular_decoding(const Value& ontology) {
Value::ConstMemberIterator reference = ontology.FindMember("cellular");
if(reference != ontology.MemberEnd()) {
if(reference->value.IsObject()) {
cellular_classifier_array.reserve(1);
load_cellular_decoder(reference->value);
} else if(reference->value.IsArray()) {
cellular_classifier_array.reserve(reference->value.Size());
for(const auto& element : reference->value.GetArray()) {
load_cellular_decoder(element);
}
}
}
cellular_classifier_array.shrink_to_fit();
};
void TranscodingDecoder::load_cellular_decoder(const Value& value) {
Algorithm algorithm(decode_value_by_key< Algorithm >("algorithm", value));
switch(algorithm) {
case Algorithm::PAMLD: {
cellular_classifier_array.emplace_back(new PamlCellularDecoder(value));
break;
};
case Algorithm::MDD: {
cellular_classifier_array.emplace_back(new MdCellularDecoder(value));
break;
};
case Algorithm::PASSTHROUGH: {
cellular_classifier_array.emplace_back(new Classifier< Barcode >(value));
break;
};
default:
throw ConfigurationError("unsupported cellular decoder algorithm " + to_string(algorithm));
break;
}
};
void TranscodingDecoder::collect(const TranscodingDecoder& other) {
count += other.count;
pf_count += other.pf_count;
if(sample_classifier != NULL) {
sample_classifier->collect(*other.sample_classifier);
}
if(!molecular_classifier_array.empty()) {
for(size_t index(0); index < molecular_classifier_array.size(); ++index) {
molecular_classifier_array[index]->collect(*other.molecular_classifier_array[index]);
}
}
if(!cellular_classifier_array.empty()) {
for(size_t index(0); index < cellular_classifier_array.size(); ++index) {
cellular_classifier_array[index]->collect(*other.cellular_classifier_array[index]);
}
}
};
void TranscodingDecoder::finalize() {
pf_fraction = double(pf_count) / double(count);
if(sample_classifier != NULL) {
sample_classifier->finalize();
}
if(!molecular_classifier_array.empty()) {
for(auto& classifier : molecular_classifier_array) {
classifier->finalize();
}
}
if(!cellular_classifier_array.empty()) {
for(auto& classifier : cellular_classifier_array) {
classifier->finalize();
}
}
};
void TranscodingDecoder::encode(Value& container, Document& document) const {
/* add the outgoing statistics to report */
if(count > 0) {
Value element(kObjectType);
encode_key_value("count", count, element, document);
encode_key_value("pf count", pf_count, element, document);
encode_key_value("pf fraction", pf_fraction, element, document);
container.AddMember("outgoing", element.Move(), document.GetAllocator());
}
if(sample_classifier != NULL) {
Value element(kObjectType);
sample_classifier->encode(element, document);
container.AddMember("sample", element.Move(), document.GetAllocator());
}
if(!molecular_classifier_array.empty()) {
Value array(kArrayType);
for(auto& classifier : molecular_classifier_array) {
Value element(kObjectType);
classifier->encode(element, document);
array.PushBack(element.Move(), document.GetAllocator());
}
container.AddMember("molecular", array.Move(), document.GetAllocator());
}
if(!cellular_classifier_array.empty()) {
Value array(kArrayType);
for(auto& classifier : cellular_classifier_array) {
Value element(kObjectType);
classifier->encode(element, document);
array.PushBack(element.Move(), document.GetAllocator());
}
container.AddMember("cellular", array.Move(), document.GetAllocator());
}
};
/* Transcode */
static int32_t compute_inheritence_depth(const string& key, const unordered_map< string, Value* >& object_by_key, Document& document) {
int32_t depth(0);
auto record = object_by_key.find(key);
if(record != object_by_key.end()) {
Value* value = record->second;
if(!decode_value_by_key("depth", depth, *value)) {
string base_key;
if(decode_value_by_key("base", base_key, *value)) {
if(base_key != key) {
depth = compute_inheritence_depth(base_key, object_by_key, document) + 1;
encode_key_value("depth", depth, *value, document);
} else { throw ConfigurationError(key + " references itself as parent"); }
} else {
encode_key_value("depth", depth, *value, document);
}
}
} else { throw ConfigurationError("referencing an unknown parent " + key); }
return depth;
};
Transcode::Transcode(Document& operation) try :
Job(operation),
count(0),
pf_count(0),
pf_fraction(0),
end_of_input(false),
decoded_nucleotide_cardinality(0),
thread_pool({NULL, 0}),
multiplexer(NULL),
transcoding_decoder(NULL) {
} catch(Error& error) {
error.push("Transcode");
throw;
};
Transcode::~Transcode() {
if(thread_pool.pool != NULL) {
hts_tpool_destroy(thread_pool.pool);
}
for(auto feed : input_feed_by_index) {
delete feed;
}
for(auto feed : output_feed_by_index) {
delete feed;
}
input_feed_by_segment.clear();
input_feed_by_index.clear();
output_feed_by_index.clear();
delete multiplexer;
delete transcoding_decoder;
};
bool Transcode::pull(Read& read) {
vector< unique_lock< mutex > > feed_locks;
feed_locks.reserve(input_feed_by_index.size());
/* acquire a pull lock for all input feeds in a fixed order */
for(const auto feed : input_feed_by_index) {
feed_locks.push_back(feed->acquire_pull_lock());
}
/* pull into input read from input feeds */
for(size_t i(0); i < read.segment_cardinality(); ++i) {
if(!input_feed_by_segment[i]->pull(read[i])) {
end_of_input = true;
}
}
/* update input counters */
if(!end_of_input) {
++count;
if(!read.qcfail()) {
++pf_count;
}
}
/* release the locks on the input feeds in reverse order */
for(auto feed_lock(feed_locks.rbegin()); feed_lock != feed_locks.rend(); ++feed_lock) {
feed_lock->unlock();
}
return !end_of_input;
};
void Transcode::collect(const TranscodingThread& transcoding_thread) {
transcoding_decoder->collect(transcoding_thread.transcoding_decoder);
multiplexer->collect(transcoding_thread.multiplexer);
};
/* assemble */
void Transcode::assemble() {
Job::assemble();
apply_inheritance();
clean_json_object(instruction, instruction);
};
void Transcode::apply_inheritance() {
/* apply inheritence between decoders defined in the repository */
apply_repository_inheritence("decoder", instruction, instruction);
/* Apply inheritence in the indivitual classification categories */
apply_topic_inheritance("sample");
apply_topic_inheritance("molecular");
apply_topic_inheritance("cellular");
if(instruction.HasMember("transform")) {
if(!instruction.HasMember("template")) {
instruction.AddMember("template", Value(kObjectType).Move(), instruction.GetAllocator());
}
if(!instruction["template"].HasMember("transform")) {
instruction["template"].AddMember("transform", Value(kObjectType).Move(), instruction.GetAllocator());
}
merge_json_value(instruction["transform"], instruction["template"]["transform"], instruction);
}
/* Remove the decoder repository, it is no longer needed in the compiled instruction */
instruction.RemoveMember("decoder");
sort_json_value(instruction, instruction);
};
void Transcode::apply_repository_inheritence(const Value::Ch* key, Value& container, Document& document) {
if(container.IsObject()) {
Value::MemberIterator reference = container.FindMember(key);
if(reference != container.MemberEnd()) {
if(reference->value.IsObject()) {
/* map each object by key */
unordered_map< string, Value* > object_by_key;
for(auto& record : reference->value.GetObject()) {
if(!record.value.IsNull()) {
record.value.RemoveMember("depth");
object_by_key.emplace(make_pair(string(record.name.GetString(), record.name.GetStringLength()), &record.value));
}
}
/* compute the inheritence depth of each object and keep track of the max depth */
int32_t max_depth(0);
for(auto& record : object_by_key) {
try {
max_depth = max(max_depth, compute_inheritence_depth(record.first, object_by_key, document));
} catch(ConfigurationError& error) {
throw CommandLineError(record.first + " is " + error.message);
}
}
/* apply object inheritence down the tree */
int32_t depth(0);
for(int32_t i(1); i <= max_depth; ++i) {
for(auto& record : object_by_key) {
Value* value = record.second;
if(decode_value_by_key("depth", depth, *value) && depth == i) {
string base;
if(decode_value_by_key< string >("base", base, *value)) {
merge_json_value(*object_by_key[base], *value, document);
value->RemoveMember("base");
}
}
}
}
for(auto& record : object_by_key) {
record.second->RemoveMember("depth");
}
}
}
}
};
void Transcode::apply_topic_inheritance(const Value::Ch* key) {
if(instruction.IsObject()) {
Value::MemberIterator reference = instruction.FindMember(key);
if(reference != instruction.MemberEnd()) {
if(!reference->value.IsNull()) {
if(reference->value.IsObject()) {
try {
apply_decoder_inheritance(reference->value);
} catch(ConfigurationError& error) {
error.message.insert(0, string(key) + " decoder : ");
throw error;
}
} else if(reference->value.IsArray()) {
int32_t index(0);
try {
for(auto& element : reference->value.GetArray()) {
apply_decoder_inheritance(element);
++index;
}
} catch(ConfigurationError& error) {
error.message.insert(0, string(key) + " decoder at " + to_string(index) + " : ");
throw error;
}
}
}
}
}
};
void Transcode::apply_decoder_inheritance(Value& value) {
if(value.IsObject()) {
string base;
Value::ConstMemberIterator reference;
const Pointer decoder_repository_query("/decoder");
if(decode_value_by_key< string >("base", base, value)) {
const Value* decoder_repository(decoder_repository_query.Get(instruction));
if(decoder_repository != NULL) {
reference = decoder_repository->FindMember(base.c_str());
if(reference != decoder_repository->MemberEnd()) {
merge_json_value(reference->value, value, instruction);
} else { throw ConfigurationError("reference to an unknown base " + base); }
}
}
value.RemoveMember("base");
clean_json_value(value, instruction);
}
};
/* compile */
void Transcode::compile() {
ontology.CopyFrom(instruction, ontology.GetAllocator());
remove_disabled_from_json_value(ontology, ontology);
clean_json_object(ontology, ontology);
/* clear computed parameters */
ontology.RemoveMember("feed");
ontology.RemoveMember("input segment cardinality");
ontology.RemoveMember("output segment cardinality");
ontology.RemoveMember("program");
/* overlay on top of the default configuration */
apply_default_ontology(ontology);
/* overlay interactive parameters on top of the configuration */
apply_interactive_ontology(ontology);
/* compile a PG SAM header ontology with details about pheniqs */
compile_PG();
ontology.AddMember("feed", Value(kObjectType).Move(), ontology.GetAllocator());
compile_input();
compile_barcode_decoding();
compile_multiplexing_decoder();
compile_output();
compile_thread_model();
clean_json_object(ontology, ontology);
validate();
};
void Transcode::compile_PG() {
Value PG(kObjectType);
string buffer;
if(decode_value_by_key< string >("application name", buffer, ontology)) {
encode_key_value("ID", buffer, PG, ontology);
}
if(decode_value_by_key< string >("application name", buffer, ontology)) {
encode_key_value("PN", buffer, PG, ontology);
}
if(decode_value_by_key< string >("full command", buffer, ontology)) {
encode_key_value("CL", buffer, PG, ontology);
}
if(decode_value_by_key< string >("previous application", buffer, ontology)) {
encode_key_value("PP", buffer, PG, ontology);
}
if(decode_value_by_key< string >("application description", buffer, ontology)) {
encode_key_value("DS", buffer, PG, ontology);
}
if(decode_value_by_key< string >("application version", buffer, ontology)) {
encode_key_value("VN", buffer, PG, ontology);
}
ontology.AddMember(Value("program", ontology.GetAllocator()).Move(), PG.Move(), ontology.GetAllocator());
};
void Transcode::compile_input() {
int32_t total_threads(decode_value_by_key< int32_t >("threads", ontology));
int32_t htslib_threads;
if(!decode_value_by_key("htslib threads", htslib_threads, ontology)) {
htslib_threads = max(1, total_threads);
encode_key_value("htslib threads", htslib_threads, ontology, ontology);
}
/* Populate the input_feed_by_index and input_feed_by_segment arrays */
standardize_url_value_by_key("base input url", ontology, ontology, IoDirection::IN);
URL base(decode_value_by_key< URL >("base input url", ontology));
standardize_url_array_by_key("input", ontology, ontology, IoDirection::IN);
relocate_url_array_by_key("input", ontology, ontology, base);
/* Collect query parameters from all reoccurring references to the same path */
unordered_map< string, URL > url_by_path;
list< URL > feed_url_by_index(decode_value_by_key< list< URL > >("input", ontology));
for(auto& url : feed_url_by_index) {
auto record = url_by_path.find(url.path());
if(record == url_by_path.end()) {
url_by_path[url.path()] = url;
} else {
record->second.override_query(url);
}
}
for(auto& url : feed_url_by_index) {
url = url_by_path[url.path()];
}
encode_key_value("input", feed_url_by_index, ontology, ontology);
if(is_sense_input_layout()) {
compile_sensed_input();
} else {
compile_explicit_input();
}
/* validate leading_segment_index */
int32_t input_segment_cardinality(decode_value_by_key< int32_t >("input segment cardinality", ontology));
int32_t leading_segment_index(decode_value_by_key< int32_t >("leading segment index", ontology));
if(leading_segment_index >= input_segment_cardinality) {
throw ConfigurationError("leading segment index " + to_string(leading_segment_index) + " references non existing input segment");
}
vector< int32_t > min_input_length(input_segment_cardinality,0);
if(decode_value_by_key< vector< int32_t > >("min input length", min_input_length, ontology)) {
if(static_cast< int32_t >(min_input_length.size()) != input_segment_cardinality) {
throw ConfigurationError (
"min input length has " +
to_string(min_input_length.size()) +
" elements. must have " +
to_string(input_segment_cardinality) +
" elements, same as the number of input segments. Use a value of 0 to skip filtering a segment by length.");
}
} else {
encode_key_value("min input length", min_input_length, ontology, ontology);
}
};
void Transcode::compile_sensed_input() {
int32_t feed_index(0);
int32_t input_segment_cardinality(0);
int32_t buffer_capacity(decode_value_by_key< int32_t >("buffer capacity", ontology));
uint8_t input_phred_offset(decode_value_by_key< uint8_t >("input phred offset", ontology));
list< URL > explicit_url_array(decode_value_by_key< list< URL > >("input", ontology));
Platform platform(decode_value_by_key< Platform >("platform", ontology));
/* create a proxy for each unique feed
feed_proxy_by_index is ordered by the first appearance of the url */
list< FeedProxy > feed_proxy_by_index;
unordered_map< URL, FeedProxy* > feed_proxy_by_url;
for(const auto& url : explicit_url_array) {
if(feed_proxy_by_url.count(url) == 0) {
Value element(kObjectType);
encode_key_value("index", feed_index, element, ontology);
encode_key_value("url", url, element, ontology);
encode_key_value("direction", IoDirection::IN, element, ontology);
encode_key_value("platform", platform, element, ontology);
encode_key_value("capacity", buffer_capacity, element, ontology);
encode_key_value("resolution", 1, element, ontology);
encode_key_value("phred offset", input_phred_offset, element, ontology);
feed_proxy_by_index.emplace_back(element);
feed_proxy_by_url.emplace(make_pair(url, &feed_proxy_by_index.back()));
++feed_index;
}
}
load_thread_pool();
/* Detect the resolution of every feed
Count the number or consecutive reads with identical read id
The resolution is the number of segments of each read interleaved into the file
the read id of all interleaved blocks from all input feeds must match.
The sum of all uniqe input feed resolutions is the input segment cardinality */
unordered_map< URL, Feed* > feed_by_url;
unordered_map< URL, string > read_id_by_url;
for(auto& proxy : feed_proxy_by_index) {
Feed* feed(NULL);
int32_t resolution(0);
proxy.open();
Segment segment;
string feed_read_id;
switch(proxy.kind()) {
case FormatKind::FASTQ: {
FastqFeed* fastq_feed = new FastqFeed(proxy);
fastq_feed->set_thread_pool(&thread_pool);
fastq_feed->initiate();
fastq_feed->replenish();
if(fastq_feed->peek(segment, resolution)) {
++resolution;
feed_read_id.assign(segment.name.s, segment.name.l);
while (
fastq_feed->peek(segment, resolution) &&
feed_read_id.size() == segment.name.l &&
strncmp(feed_read_id.c_str(), segment.name.s, segment.name.l)
) { ++resolution; }
}
fastq_feed->calibrate_resolution(resolution);
feed = fastq_feed;
break;
};
case FormatKind::HTS: {
HtsFeed* hts_feed = new HtsFeed(proxy);
hts_feed->set_thread_pool(&thread_pool);
hts_feed->initiate();
hts_feed->replenish();
if(hts_feed->peek(segment, resolution)) {
feed_read_id.assign(segment.name.s, segment.name.l);
resolution = segment.total_segments();
}
hts_feed->calibrate_resolution(resolution);
/*
const HtsHead& head = ((HtsFeed*)feed)->get_header();
for(const auto& record : head.RG_by_id) {}
*/
feed = hts_feed;
break;
};
case FormatKind::DEV_NULL: {
throw ConfigurationError("/dev/null can not be used for input");
break;
};
default: {
throw ConfigurationError("unknown input format " + string(proxy.url));
break;
};
}
read_id_by_url[proxy.url] = feed_read_id;
input_feed_by_index.push_back(feed);
feed_by_url.emplace(make_pair(proxy.url, feed));
input_segment_cardinality += resolution;
};
/* Check that the read id of all interleaved blocks from all input feeds match. */
if(input_segment_cardinality > 1) {
string anchor_read_id;
URL anchor_url;
for(auto& record : read_id_by_url) {
if(anchor_read_id.empty()) {
anchor_url = record.first;
anchor_read_id = record.second;
} else if(anchor_read_id != record.second) {
throw ConfigurationError(string(anchor_url) + " and " + string(record.second) + " are out of sync");
}
}
}
encode_key_value("input segment cardinality", input_segment_cardinality, ontology, ontology);
input_feed_by_segment.reserve(input_segment_cardinality);
for(auto& feed : input_feed_by_index) {
for(int32_t i(0); i < feed->resolution(); ++i) {
input_feed_by_segment.push_back(feed);
}
}
list< URL > feed_url_by_segment;
for(auto& feed : input_feed_by_segment) {
feed_url_by_segment.push_back(feed->url);
}
encode_key_value("input", feed_url_by_segment, ontology, ontology);
encode_key_value("input feed", input_feed_by_index, ontology["feed"], ontology);
encode_key_value("input feed by segment", input_feed_by_segment, ontology["feed"], ontology);
};
void Transcode::compile_explicit_input() {
int32_t feed_index(0);
int32_t buffer_capacity(decode_value_by_key< int32_t >("buffer capacity", ontology));
uint8_t input_phred_offset(decode_value_by_key< uint8_t >("input phred offset", ontology));
list< URL > explicit_url_array(decode_value_by_key< list< URL > >("input", ontology));
Platform platform(decode_value_by_key< Platform >("platform", ontology));
/* encode the input segment cardinality */
encode_key_value("input segment cardinality", static_cast< int32_t>(explicit_url_array.size()), ontology, ontology);
list< URL > feed_url_by_index;
map< URL, int > feed_resolution;
for(const auto& url : explicit_url_array) {
auto record = feed_resolution.find(url);
if(record == feed_resolution.end()) {
feed_resolution[url] = 1;
feed_url_by_index.push_back(url);
} else { ++(record->second); }
}
unordered_map< URL, Value > feed_ontology_by_url;
for(const auto& url : feed_url_by_index) {
Value element(kObjectType);
int resolution(feed_resolution[url]);
encode_key_value("index", feed_index, element, ontology);
encode_key_value("url", url, element, ontology);
encode_key_value("direction", IoDirection::IN, element, ontology);
encode_key_value("platform", platform, element, ontology);
encode_key_value("capacity", buffer_capacity, element, ontology);
encode_key_value("resolution", resolution, element, ontology);
encode_key_value("phred offset", input_phred_offset, element, ontology);
feed_ontology_by_url.emplace(make_pair(url, move(element)));
++feed_index;
}
Value feed_by_segment_array(kArrayType);
for(const auto& url : explicit_url_array) {
Value feed_ontology(feed_ontology_by_url[url], ontology.GetAllocator());
feed_by_segment_array.PushBack(feed_ontology.Move(), ontology.GetAllocator());
}
ontology["feed"].RemoveMember("input feed by segment");
ontology["feed"].AddMember("input feed by segment", feed_by_segment_array.Move(), ontology.GetAllocator());
Value feed_by_index_array(kArrayType);
for(const auto& url : feed_url_by_index) {
feed_by_index_array.PushBack(feed_ontology_by_url[url].Move(), ontology.GetAllocator());
}
feed_ontology_by_url.clear();
ontology["feed"].RemoveMember("input feed");
ontology["feed"].AddMember("input feed", feed_by_index_array.Move(), ontology.GetAllocator());
};
void Transcode::compile_transformation(Value& value) {
/* add the default observation if one was not specificed.
default observation will treat every token as a segment */
if(value.IsObject()) {
Value::MemberIterator reference = value.FindMember("transform");
if(reference != value.MemberEnd()) {
if(reference->value.IsObject()) {
Value& transform_element(reference->value);
reference = transform_element.FindMember("token");
if(reference != transform_element.MemberEnd()) {
if(reference->value.IsArray()) {
size_t token_cardinality(reference->value.Size());
reference = transform_element.FindMember("knit");
if(reference == transform_element.MemberEnd() || reference->value.IsNull() || (reference->value.IsArray() && reference->value.Empty())) {
Value observation(kArrayType);
for(size_t i(0); i < token_cardinality; ++i) {
string element(to_string(i));
observation.PushBack(Value(element.c_str(), element.size(),ontology.GetAllocator()).Move(), ontology.GetAllocator());
}
transform_element.RemoveMember("knit");
transform_element.AddMember(Value("knit", ontology.GetAllocator()).Move(), observation.Move(), ontology.GetAllocator());
}
} else { throw ConfigurationError("transform token element is not an array"); }
} else { throw ConfigurationError("transform element is missing a token array"); }
}
}
}
};
void Transcode::compile_barcode_decoding() {
compile_topic("sample");
compile_topic("molecular");
compile_topic("cellular");
};
void Transcode::compile_topic(const Value::Ch* key) {
Value::MemberIterator reference = ontology.FindMember(key);
if(reference != ontology.MemberEnd()) {
if(!reference->value.IsNull()) {
ClassifierType classifier_type(ClassifierType::UNKNOWN);
Value decoder_template(kObjectType);
Value barcode_template(kObjectType);
from_string(key, classifier_type);
/* aseemble a decoder template */
string decoder_projection_uri(to_string(classifier_type));
decoder_projection_uri.append(":decoder");
const Value* decoder_projection(find_projection(decoder_projection_uri));
if(decoder_projection != NULL && !decoder_projection->IsNull()) {
merge_json_value(*decoder_projection, decoder_template, ontology);
}
/* aseemble a default decoder by projecting decoder template from the ontology root */
Value default_decoder(kObjectType);
project_json_value(decoder_template, ontology, default_decoder, ontology);
/* aseemble a barcode template */
string barcode_projection_uri(to_string(classifier_type));
barcode_projection_uri.append(":barcode");
const Value* barcode_projection(find_projection(barcode_projection_uri));
if(barcode_projection != NULL && !barcode_projection->IsNull()) {
merge_json_value(*barcode_projection, barcode_template, ontology);
}
/* aseemble a default barcode by projecting barcode template from the ontology root */
Value default_barcode(kObjectType);
project_json_value(barcode_template, ontology, default_barcode, ontology);
int32_t index(0);
if(reference->value.IsObject()) {
try {
compile_decoder(reference->value, index, default_decoder, default_barcode);
} catch(ConfigurationError& error) {
error.message.insert(0, string(key) + " decoder : ");
throw error;
}
} else if(reference->value.IsArray()) {
try {
for(auto& element : reference->value.GetArray()) {
compile_decoder(element, index, default_decoder, default_barcode);
}
} catch(ConfigurationError& error) {
error.message.insert(0, string(key) + " decoder at " + to_string(index) + " : ");
throw error;
}
}
clean_json_value(reference->value, ontology);
}
}
};
void Transcode::compile_decoder_transformation(Value& value) {
if(value.HasMember("transform")) {
compile_transformation(value);
Rule rule(decode_value_by_key< Rule >("transform", value));
int32_t input_segment_cardinality(decode_value_by_key< int32_t >("input segment cardinality", ontology));
/* validate all tokens refer to an existing input segment */
for(auto& token : rule.token_array) {
if(!(token.input_segment_index < input_segment_cardinality)) {
throw ConfigurationError("invalid input feed reference " + to_string(token.input_segment_index) + " in token " + to_string(token.index));
}
if(token.empty()) {
throw ConfigurationError("token " + string(token) + " is empty");
}
if(!token.constant()) {
throw ConfigurationError("token " + string(token) + " is not fixed width");
}
}
/* annotate the decoder with cardinality information from the transfortmation */
int32_t nucleotide_cardinality(0);
vector< int32_t > barcode_length(rule.output_segment_cardinality, 0);
for(auto& transform : rule.transform_array) {
barcode_length[transform.output_segment_index] += transform.length();
nucleotide_cardinality += transform.length();
}
encode_key_value("segment cardinality", rule.output_segment_cardinality, value, ontology);
encode_key_value("nucleotide cardinality", nucleotide_cardinality, value, ontology);
encode_key_value("barcode length", barcode_length, value, ontology);
double random_barcode_probability(0);
double random_barcode_probability_lower_bound(1.0 / double(pow(4, (nucleotide_cardinality))));
if(decode_value_by_key("random barcode probability", random_barcode_probability, value)) {
if(random_barcode_probability < random_barcode_probability_lower_bound) {
throw ConfigurationError("random barcode probability is smaller than lower bound");
}
} else {
encode_key_value("random barcode probability", random_barcode_probability_lower_bound, value, ontology);
}
/* verify nucleotide cardinality and uniqueness
and annotate each barcode element with the barcode segment cardinality */
Value::MemberIterator reference = value.FindMember("undetermined");
if(reference != value.MemberEnd()) {
if(!reference->value.IsNull()) {
Value& undetermined(reference->value);
/* explicitly define a null barcode segment for the right dimension in the undetermined */
Value barcode(kArrayType);
for(size_t i(0); i < barcode_length.size(); ++i) {
string sequence(barcode_length[i], '=');
barcode.PushBack(Value(sequence.c_str(), sequence.size(), ontology.GetAllocator()).Move(), ontology.GetAllocator());
}
undetermined.RemoveMember("barcode");
undetermined.AddMember(Value("barcode", ontology.GetAllocator()).Move(), barcode.Move(), ontology.GetAllocator());
encode_key_value("segment cardinality", rule.output_segment_cardinality, undetermined, ontology);
}
}
size_t segment_index(0);
string barcode_segment;
string barcode_sequence;
set< string > unique_barcode_sequence;
reference = value.FindMember("codec");
if(reference != value.MemberEnd()) {
if(reference->value.IsObject()) {
Value& codec(reference->value);
for(auto& record : codec.GetObject()) {
reference = record.value.FindMember("barcode");
if(reference != record.value.MemberEnd()) {
if(reference->value.Size() == barcode_length.size()) {
barcode_sequence.clear();
segment_index = 0;
for(const auto& element : reference->value.GetArray()) {
barcode_segment.assign(element.GetString(), element.GetStringLength());
if(static_cast< int32_t >(barcode_segment.size()) == barcode_length[segment_index]) {
barcode_sequence.append(barcode_segment);
++segment_index;
} else {
string key(record.name.GetString(), record.name.GetStringLength());
string message;
message.append("expected ");
message.append(to_string(barcode_length[segment_index]));
message.append(" but found ");
message.append(to_string(barcode_segment.size()));
message.append(" nucleotides in segment ");
message.append(to_string(segment_index));
message.append(" of barcode ");
message.append(key);
throw ConfigurationError(message);
}
}
if(!unique_barcode_sequence.count(barcode_sequence)) {
unique_barcode_sequence.emplace(barcode_sequence);
} else {
throw ConfigurationError("duplicate barcode sequence " + barcode_sequence);
}
} else {
string key(record.name.GetString(), record.name.GetStringLength());
string message;
message.append("expected ");
message.append(to_string(barcode_length.size()));
message.append(" segments but found ");
message.append(to_string(reference->value.Size()));
message.append(" in barcode ");
message.append(key);
throw ConfigurationError(message);
}
}
encode_key_value("segment cardinality", rule.output_segment_cardinality, record.value, ontology);
}
}
}
unique_barcode_sequence.clear();
}
};
void Transcode::compile_decoder(Value& value, int32_t& index, const Value& default_decoder, const Value& default_barcode) {
if(value.IsObject()) {
encode_key_value("index", index, value, ontology);
/* overlay on top of the default decoder */
merge_json_value(default_decoder, value, ontology);
clean_json_value(value, ontology);
/* compute default barcode induced by the codec */
Value default_codec_barcode(kObjectType);
project_json_value(default_barcode, value, default_codec_barcode, ontology);
/* apply barcode default on undetermined barcode or create it from the default if one was not explicitly specified */
Value::MemberIterator reference = value.FindMember("undetermined");
if(reference != value.MemberEnd()){
merge_json_value(default_codec_barcode, reference->value, ontology);
} else {
value.AddMember (
Value("undetermined", ontology.GetAllocator()).Move(),
Value(default_codec_barcode, ontology.GetAllocator()).Move(),
ontology.GetAllocator()
);
}
compile_decoder_transformation(value);
string buffer;
int32_t barcode_index(0);
double total_concentration(0);
set< string > unique_barcode_id;
double noise(decode_value_by_key< double >("noise", value));
reference = value.FindMember("undetermined");
if(reference != value.MemberEnd()){
encode_key_value("index", barcode_index, reference->value, ontology);
infer_PU(buffer, reference->value, true);
if(infer_ID(buffer, reference->value)) {
unique_barcode_id.emplace(buffer);
}
encode_key_value("concentration", noise, reference->value, ontology);
++barcode_index;
}
reference = value.FindMember("codec");
if(reference != value.MemberEnd()){
if(reference->value.IsObject()) {
Value& codec(reference->value);
for(auto& record : codec.GetObject()) {
merge_json_value(default_codec_barcode, record.value, ontology);
encode_key_value("index", barcode_index, record.value, ontology);
infer_PU(buffer, record.value);
if(infer_ID(buffer, record.value)) {
if(!unique_barcode_id.count(buffer)) {
unique_barcode_id.emplace(buffer);
} else {
string duplicate(record.name.GetString(), record.name.GetStringLength());
throw ConfigurationError("duplicate " + duplicate + " barcode");
}
}
double concentration(decode_value_by_key< double >("concentration", record.value));