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fastq.h
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fastq.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_FASTQ_H
#define PHENIQS_FASTQ_H
#include "include.h"
#include "feed.h"
KSEQ_INIT(BGZF*, bgzf_read)
class FastqRecord {
public:
FastqRecord(FastqRecord const &) = delete;
void operator=(FastqRecord const &) = delete;
kstring_t sequence;
kstring_t quality;
kstring_t name;
kstring_t comment;
FastqRecord() :
sequence({ 0, 0, NULL }),
quality({ 0, 0, NULL }),
name({ 0, 0, NULL }),
comment({ 0, 0, NULL }) {
ks_terminate(sequence);
ks_terminate(quality);
ks_terminate(name);
ks_terminate(comment);
clear();
};
~FastqRecord() {
ks_free(sequence);
ks_free(quality);
ks_free(name);
ks_free(comment);
};
inline void decode(const kseq_t* kseq, const uint8_t phred_offset) {
// read a kseq record and populate the FastqRecord
clear();
// copy from kseq_t to record
ks_put_string(kseq->name, name);
ks_put_string(kseq->comment, comment);
// decode sequence
ks_increase_to_size(sequence, kseq->seq.l + 2);
for(size_t i(0); i < kseq->seq.l; ++i) {
sequence.s[i] = AsciiToAmbiguousBam[static_cast< uint8_t >(kseq->seq.s[i])];
}
sequence.l = kseq->seq.l;
sequence.s[sequence.l] = '\0';
// decode quality
ks_increase_to_size(quality, kseq->qual.l + 2);
for(size_t i(0); i < kseq->qual.l; ++i) {
quality.s[i] = kseq->qual.s[i] - phred_offset;
}
quality.l = kseq->qual.l;
quality.s[quality.l] = '\0';
};
inline void decode(const Segment& segment) {
clear();
// copy from segment to record
ks_put_string(reinterpret_cast< char* >(segment.code), segment.length, sequence);
ks_put_string(reinterpret_cast< char* >(segment.quality), segment.length, quality);
ks_put_string(segment.name.s, segment.name.l, name);
decode_comment(segment);
};
inline void encode(Segment& segment) const {
// write the FastqRecord to Segment
segment.fill(reinterpret_cast< uint8_t* >(sequence.s), reinterpret_cast< uint8_t* >(quality.s), static_cast< int32_t >(sequence.l));
ks_put_string(name, segment.name);
ks_put_string(comment, segment.auxiliary.CO);
segment.auxiliary.FI = 0;
segment.set_qcfail(false);
#if defined(PHENIQS_ILLUMINA_CONTROL_NUMBER)
segment.auxiliary.illumina_control_number = 0;
#endif
switch (segment.platform) {
case Platform::ILLUMINA: {
/* @HWI-ST911:232:HABDFADXX:1:1101:1224:1932 1:N:0:CGATGT
name 0:1:2:3:4:5:6
0 Instrument ID HWI-ST911
1 Run count 232
2 Flowcell ID HABDFADXX
3 Lane number 1
4 Tile number 1101
5 x coordinate 1224
6 y coordinate 1932
comment 7:8:9:10
7 Segment number 1 uint8_t
8 Filtered N N|Y
9 control number 0 uint16_t
10 Barcode CGATGT char*
*/
size_t offset(0);
parse_illumina_segment_index(segment, offset);
parse_illumina_filtered(segment, offset);
parse_illumina_control(segment, offset);
parse_illumina_barcode(segment, offset);
break;
}
case Platform::CAPILLARY:
case Platform::LS454:
case Platform::HELICOS:
case Platform::ONT:
case Platform::PACBIO:
case Platform::SOLID:
case Platform::IONTORRENT:
break;
default:
break;
};
};
inline void encode(kstring_t& buffer, const uint8_t phred_offset) const {
// encode identifier
ks_put_character('@', buffer);
ks_put_string(name, buffer);
ks_put_character(' ', buffer);
ks_put_string(comment, buffer);
ks_put_character(LINE_BREAK, buffer);
// encode sequence
ks_increase_by_size(buffer, sequence.l + 2);
for(size_t i(0); i < sequence.l; ++i) {
buffer.s[buffer.l + i] = BamToAmbiguousAscii[static_cast< uint8_t >(sequence.s[i])];
}
buffer.l += sequence.l;
ks_put_character(LINE_BREAK, buffer);
// encode separator
ks_put_character('+', buffer);
ks_put_character(LINE_BREAK, buffer);
// encode quality
ks_increase_by_size(buffer, quality.l + 2);
for(size_t i(0); i < quality.l; ++i) {
buffer.s[buffer.l + i] = quality.s[i] + phred_offset;
}
buffer.l += quality.l;
ks_put_character(LINE_BREAK, buffer);
};
private:
inline void clear() {
ks_clear(sequence);
ks_clear(quality);
ks_clear(name);
ks_clear(comment);
};
inline void decode_comment(const Segment& segment) {
switch (segment.platform) {
case Platform::CAPILLARY:
// Sanger sequencing
break;
case Platform::LS454:
break;
case Platform::ILLUMINA: {
ks_put_uint32(segment.auxiliary.FI, comment);
ks_put_character(':', comment);
ks_put_character(segment.qcfail() ? 'Y' : 'N', comment);
ks_put_character(':', comment);
#if defined(PHENIQS_ILLUMINA_CONTROL_NUMBER)
ks_put_uint16(segment.auxiliary.illumina_control_number, comment);
#else
ks_put_uint16(0, comment);
#endif
ks_put_character(':', comment);
ks_put_string(segment.auxiliary.BC, comment);
break;
};
case Platform::SOLID:
break;
case Platform::HELICOS:
break;
case Platform::IONTORRENT:
break;
case Platform::ONT:
break;
case Platform::PACBIO:
break;
default:
break;
};
};
inline void parse_illumina_segment_index(Segment& segment, size_t& offset) const {
int8_t code(-1);
uint32_t value(0);
size_t position(offset);
const char* comment(segment.auxiliary.CO.s);
while (position < segment.auxiliary.CO.l) {
char c(*(comment + position));
++position;
if(c == ':') {
break;
} else {
if(code >= -1) {
if(c >= '0' && c <= '9') {
value *= 10;
value += c - '0';
code = 0;
} else {
code = -2;
}
}
}
}
if(code < 0) {
value = 1;
}
segment.auxiliary.FI = value;
offset = position;
};
inline void parse_illumina_filtered(Segment& segment, size_t& offset) const {
int8_t code(-1);
size_t position(offset);
const char* comment(segment.auxiliary.CO.s);
while (position < segment.auxiliary.CO.l) {
char c(*(comment + position));
++position;
if(c == ':') {
break;
} else {
if(code == -1) {
switch(c) {
case 'Y':
segment.set_qcfail(true);
code = 0;
break;
case 'N':
segment.set_qcfail(false);
code = 0;
break;
default:
segment.set_qcfail(false);
code = -3;
break;
}
} else {
// code equals -2 means there was more than one character to the next separator
code = -2;
}
}
}
offset = position;
};
inline void parse_illumina_control(Segment& segment, size_t& offset) const {
int8_t code(-1);
uint16_t value(0);
size_t position(offset);
const char* comment(segment.auxiliary.CO.s);
while (position < segment.auxiliary.CO.l) {
char c(*(comment + position));
++position;
if(c == ':') {
break;
} else {
if(code >= -1) {
if(c >= '0' && c <= '9') {
value *= 10;
value += c - '0';
code = 0;
} else {
code = -2;
}
}
}
}
if(code < 0) {
value = 0;
}
#if defined(PHENIQS_ILLUMINA_CONTROL_NUMBER)
segment.auxiliary.illumina_control_number = value;
#endif
offset = position;
};
inline void parse_illumina_barcode(Segment& segment, size_t& offset) const {
size_t position(offset);
const char* comment(segment.auxiliary.CO.s);
while (position < segment.auxiliary.CO.l) {
char c(*(comment + position));
++position;
if(c == ' ') {
break;
}
}
size_t length(position - offset);
if(length > 0) {
ks_put_string(comment + offset, length, segment.auxiliary.BC);
}
offset = position;
};
};
class FastqFeed : public BufferedFeed< FastqRecord > {
friend class Channel;
public:
FastqFeed(const FeedProxy& proxy) :
BufferedFeed< FastqRecord >(proxy),
bgzf_file(NULL) {
};
void open() override {
if(!opened()) {
/* from htslib bgzf.h
mode matching /[rwag][u0-9]+/: 'r' for reading, 'w' for
writing, 'a' for appending, 'g' for gzip rather than BGZF
compression (with 'w' only), and digit specifies the zlib
compression level.
Note that there is a distinction between 'u' and '0': the
first yields plain uncompressed output whereas the latter
outputs uncompressed data wrapped in the zlib format.
*/
string mode;
switch(direction) {
case IoDirection::IN: {
mode.push_back('r');
bgzf_file = bgzf_hopen(hfile, mode.c_str());
if(bgzf_file != NULL) {
kseq = kseq_init(bgzf_file);
// bgzf_thread_pool(bgzf_file, thread_pool->pool, thread_pool->qsize);
} else {
throw IOError("failed to open " + string(url.path()) + " for reading");
}
break;
};
case IoDirection::OUT: {
mode.push_back('w');
switch(url.compression()) {
case FormatCompression::GZIP: {
mode.push_back('g');
break;
};
case FormatCompression::BGZF: {
break;
};
case FormatCompression::NONE: {
mode.push_back('u');
break;
};
default: {
mode.push_back('u');
break;
};
};
if(url.compression_level() != CompressionLevel::UNKNOWN) {
mode.append(to_string(url.compression_level()));
}
bgzf_file = bgzf_hopen(hfile, mode.c_str());
if(bgzf_file != NULL) {
kseq = kseq_init(bgzf_file);
bgzf_thread_pool(bgzf_file, thread_pool->pool, thread_pool->qsize);
} else {
throw IOError("failed to open " + string(url.path()) + " for writing");
}
break;
};
default: {
break;
}
}
}
};
void close() override {
if(opened()) {
bgzf_close(bgzf_file);
bgzf_file = NULL;
kseq_destroy(kseq);
kseq = NULL;
}
};
inline bool opened() override {
return bgzf_file != NULL;
};
protected:
BGZF* bgzf_file;
kseq_t* kseq;
inline void encode(FastqRecord* record, const Segment& segment) const override {
record->decode(segment);
};
inline void decode(const FastqRecord* record, Segment& segment) override {
record->encode(segment);
};
inline void replenish_buffer() override {
while(opened() && buffer->is_not_full()) {
/* >=0 length of the sequence (normal)
-1 end-of-file
-2 truncated quality string */
if(kseq_read(kseq) < 0) {
close();
break;
} else {
buffer->vacant()->decode(kseq, phred_offset);
buffer->increment();
}
}
};
inline void flush_buffer() override {
/* encode all fastq records in the buffer to
a string buffer and write them together to the stream */
if(buffer->is_not_empty()) {
ks_clear(kbuffer);
while(buffer->is_not_empty()) {
FastqRecord* record = buffer->next();
record->encode(kbuffer, phred_offset);
buffer->decrement();
}
if(bgzf_write(bgzf_file, kbuffer.s, kbuffer.l) < 0) {
throw IOError("error writing to " + string(url.path()));
}
}
};
};
#endif /* PHENIQS_FASTQ_H */