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 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969
//! Efficient FASTQ reading and writing
//!
use memchr::memchr;
use std::char;
use std::fs::File;
use std::io::{self, BufRead, Seek};
use std::iter;
use std::path::Path;
use std::slice;
use std::str::{self, Utf8Error};
use buffer_redux;
use super::policy::{BufPolicy, StdPolicy};
use super::*;
use std::error::Error as StdError;
type DefaultBufPolicy = StdPolicy;
const BUFSIZE: usize = 64 * 1024;
#[derive(Debug, Copy, Clone, Eq, PartialEq, Ord, PartialOrd)]
enum SearchPos {
Head,
Seq,
Sep,
Qual,
}
/// FASTQ parser.
pub struct Reader<R: io::Read, P = DefaultBufPolicy> {
buf_reader: buffer_redux::BufReader<R>,
buf_pos: BufferPosition,
search_pos: SearchPos,
position: Position,
finished: bool,
buf_policy: P,
}
impl<R> Reader<R, DefaultBufPolicy>
where
R: io::Read,
{
/// Creates a new reader with the default buffer size of 64 KiB
///
/// # Example:
///
/// ```
/// use seq_io::fastq::{Reader, Record};
/// let fastq = b"@id\nACGT\n+\nIIII";
///
/// let mut reader = Reader::new(&fastq[..]);
/// let record = reader.next().unwrap().unwrap();
/// assert_eq!(record.id(), Ok("id"))
/// ```
#[inline]
pub fn new(reader: R) -> Reader<R, StdPolicy> {
Reader::with_capacity(reader, BUFSIZE)
}
/// Creates a new reader with a given buffer capacity. The minimum allowed
/// capacity is 3.
#[inline]
pub fn with_capacity(reader: R, capacity: usize) -> Reader<R, StdPolicy> {
assert!(capacity >= 3);
Reader {
buf_reader: buffer_redux::BufReader::with_capacity(capacity, reader),
buf_pos: BufferPosition::default(),
search_pos: SearchPos::Head,
position: Position::new(1, 0),
finished: false,
buf_policy: StdPolicy,
}
}
}
impl Reader<File, DefaultBufPolicy> {
/// Creates a reader from a file path.
///
/// # Example:
///
/// ```no_run
/// use seq_io::fastq::Reader;
///
/// let mut reader = Reader::from_path("seqs.fastq").unwrap();
///
/// // (... do something with the reader)
/// ```
#[inline]
pub fn from_path<P: AsRef<Path>>(path: P) -> io::Result<Reader<File>> {
File::open(path).map(Reader::new)
}
}
impl<R, P> Reader<R, P>
where
R: io::Read,
P: BufPolicy,
{
/// Returns a reader with the given buffer policy applied
#[inline]
pub fn set_policy<T: BufPolicy>(self, policy: T) -> Reader<R, T> {
Reader {
buf_reader: self.buf_reader,
buf_pos: self.buf_pos,
position: self.position,
search_pos: self.search_pos,
finished: self.finished,
buf_policy: policy,
}
}
/// Returns the `BufPolicy` of the reader
#[inline]
pub fn policy(&self) -> &P {
&self.buf_policy
}
/// Searches the next FASTQ record and returns a [RefRecord](struct.RefRecord.html) that
/// borrows its data from the underlying buffer of this reader.
///
/// # Example:
///
/// ```no_run
/// use seq_io::fastq::{Reader, Record};
///
/// let mut reader = Reader::from_path("seqs.fastq").unwrap();
///
/// while let Some(record) = reader.next() {
/// let record = record.unwrap();
/// println!("{}", record.id().unwrap());
/// }
/// ```
#[allow(clippy::should_implement_trait)]
#[inline]
pub fn next(&mut self) -> Option<Result<RefRecord, Error>> {
if self.finished || !self.initialized() && !try_opt!(self.init()) {
return None;
}
if !self.buf_pos.is_new() {
self.next_pos();
}
if !try_opt!(self.find()) && !try_opt!(self.next_complete()) {
return None;
}
Some(Ok(RefRecord {
buffer: self.get_buf(),
buf_pos: &self.buf_pos,
}))
}
#[inline(never)]
fn init(&mut self) -> Result<bool, Error> {
let n = fill_buf(&mut self.buf_reader)?;
if n == 0 {
self.finished = true;
return Ok(false);
}
Ok(true)
}
fn initialized(&self) -> bool {
!self.get_buf().is_empty()
}
/// Updates a [RecordSet](struct.RecordSet.html) with new data. The contents of the internal
/// buffer are just copied over to the record set and the positions of all records are found.
/// Old data will be erased. Returns `None` if the input reached its end.
#[inline]
pub fn read_record_set(&mut self, rset: &mut RecordSet) -> Option<Result<(), Error>> {
if self.finished {
return None;
}
if !self.initialized() {
if !try_opt!(self.init()) {
return None;
}
if !try_opt!(self.find()) {
return Some(Ok(()));
}
} else if !try_opt!(self.next_complete()) {
return None;
};
rset.buffer.clear();
rset.buffer.extend(self.get_buf());
rset.buf_positions.clear();
rset.buf_positions.push(self.buf_pos.clone());
loop {
self.next_pos();
if !try_opt!(self.find()) {
return Some(Ok(()));
}
rset.buf_positions.push(self.buf_pos.clone());
}
}
fn get_buf(&self) -> &[u8] {
self.buf_reader.buffer()
}
// Sets starting points for next position
fn next_pos(&mut self) {
self.position.byte += (self.buf_pos.pos.1 + 1 - self.buf_pos.pos.0) as u64;
self.position.line += 4;
self.buf_pos.pos.0 = self.buf_pos.pos.1 + 1;
}
// Reads the current record and returns true if found.
// Returns false if incomplete because end of buffer reached,
// meaning that the last record may be incomplete.
// Updates self.search_pos.
fn find(&mut self) -> Result<bool, Error> {
self.buf_pos.seq = unwrap_or!(self.find_line(self.buf_pos.pos.0), {
self.search_pos = SearchPos::Head;
return Ok(false);
});
self.buf_pos.sep = unwrap_or!(self.find_line(self.buf_pos.seq), {
self.search_pos = SearchPos::Seq;
return Ok(false);
});
self.buf_pos.qual = unwrap_or!(self.find_line(self.buf_pos.sep), {
self.search_pos = SearchPos::Sep;
return Ok(false);
});
self.buf_pos.pos.1 = unwrap_or!(self.find_line(self.buf_pos.qual), {
self.search_pos = SearchPos::Qual;
return Ok(false);
}) - 1;
self.validate()?;
Ok(true)
}
// Resumes reading an incomplete record without
// re-searching positions that were already found.
// The resulting position may still be incomplete (-> false).
fn find_incomplete(&mut self) -> Result<bool, Error> {
if self.search_pos == SearchPos::Head {
self.buf_pos.seq = unwrap_or!(self.find_line(self.buf_pos.pos.0), {
self.search_pos = SearchPos::Head;
return Ok(false);
});
}
if self.search_pos <= SearchPos::Seq {
self.buf_pos.sep = unwrap_or!(self.find_line(self.buf_pos.seq), {
self.search_pos = SearchPos::Seq;
return Ok(false);
});
}
if self.search_pos <= SearchPos::Sep {
self.buf_pos.qual = unwrap_or!(self.find_line(self.buf_pos.sep), {
self.search_pos = SearchPos::Sep;
return Ok(false);
});
}
if self.search_pos <= SearchPos::Qual {
self.buf_pos.pos.1 = unwrap_or!(self.find_line(self.buf_pos.qual), {
self.search_pos = SearchPos::Qual;
return Ok(false);
}) - 1;
}
self.search_pos = SearchPos::Head;
self.validate()?;
Ok(true)
}
// should only be called on a complete BufferPosition
#[inline(always)] // has performance impact and would not be inlined otherwise
fn validate(&mut self) -> Result<(), Error> {
let start_byte = self.get_buf()[self.buf_pos.pos.0];
if start_byte != b'@' {
self.finished = true;
return Err(Error::InvalidStart {
found: start_byte,
pos: self.get_error_pos(0, false),
});
}
let sep_byte = self.get_buf()[self.buf_pos.sep];
if sep_byte != b'+' {
self.finished = true;
return Err(Error::InvalidSep {
found: sep_byte,
pos: self.get_error_pos(2, true),
});
}
let qual_len = self.buf_pos.pos.1 - self.buf_pos.qual + 1;
let seq_len = self.buf_pos.sep - self.buf_pos.seq;
if seq_len != qual_len {
self.finished = true;
return Err(Error::UnequalLengths {
seq: self.buf_pos.seq(self.get_buf()).len(),
qual: self.buf_pos.qual(self.get_buf()).len(),
pos: self.get_error_pos(0, true),
});
}
Ok(())
}
#[inline(never)]
fn get_error_pos(&self, offset: u64, parse_id: bool) -> ErrorPosition {
let id = if parse_id && self.buf_pos.seq - self.buf_pos.pos.0 > 1 {
let id = self
.buf_pos
.head(self.get_buf())
.split(|b| *b == b' ')
.next()
.unwrap();
Some(String::from_utf8_lossy(id).into())
} else {
None
};
ErrorPosition {
line: self.position.line + offset,
id,
}
}
fn find_line(&self, search_start: usize) -> Option<usize> {
memchr(b'\n', &self.get_buf()[search_start..]).map(|pos| search_start + pos + 1)
}
// To be called when the end of the buffer is reached and `next_pos` does not find
// the next record. Incomplete bytes will be moved to the start of the buffer.
// If the record still doesn't fit in, the buffer will be enlarged.
// After calling this function, the position will therefore always be 'complete'.
#[inline(never)]
fn next_complete(&mut self) -> Result<bool, Error> {
loop {
if self.get_buf().len() < self.buf_reader.capacity() {
// EOF reached, there will be no next record
return self.check_end();
} else if self.buf_pos.pos.0 == 0 {
// first record already incomplete -> buffer too small
self.grow()?;
} else {
// not the first record -> buffer may be big enough
self.make_room();
}
fill_buf(&mut self.buf_reader)?;
// self.buf_pos.pos.1 = 0;
// self.search_pos = SearchPos::HEAD;
if self.find_incomplete()? {
return Ok(true);
}
}
}
#[inline(never)]
fn check_end(&mut self) -> Result<bool, Error> {
self.finished = true;
if self.search_pos == SearchPos::Qual {
// no line ending at end of last record
self.buf_pos.pos.1 = self.get_buf().len();
self.validate()?;
return Ok(true);
}
let rest = &self.get_buf()[self.buf_pos.pos.0..];
if rest.split(|c| *c == b'\n').all(|l| trim_cr(l).is_empty()) {
// allow up to 3 newlines after last record (more will cause an Unexpected error)
return Ok(false);
}
Err(Error::UnexpectedEnd {
pos: self.get_error_pos(self.search_pos as u64, self.search_pos > SearchPos::Head),
})
}
// grow buffer based on policy
fn grow(&mut self) -> Result<(), Error> {
let cap = self.buf_reader.capacity();
let new_size = self.buf_policy.grow_to(cap).ok_or(Error::BufferLimit)?;
let additional = new_size - cap;
self.buf_reader.reserve(additional);
Ok(())
}
// move incomplete bytes to start of buffer and retry
fn make_room(&mut self) {
let consumed = self.buf_pos.pos.0;
self.buf_reader.consume(consumed);
self.buf_reader.make_room();
self.buf_pos.pos.0 = 0;
if self.search_pos >= SearchPos::Seq {
self.buf_pos.seq -= consumed;
}
if self.search_pos >= SearchPos::Sep {
self.buf_pos.sep -= consumed;
}
if self.search_pos >= SearchPos::Qual {
self.buf_pos.qual -= consumed;
}
}
/// Returns the current position (useful with `seek()`)
///
/// # Example
///
/// ```
/// # fn main() {
/// use seq_io::fastq::{Reader, Position};
///
/// let fastq = b"@id1
/// ACGT
/// +
/// IIII
/// @id2
/// TGCA
/// +
/// IIII";
///
/// let mut reader = Reader::new(&fastq[..]);
///
/// // skip one record
/// reader.next().unwrap();
/// // second position
/// reader.next().unwrap();
///
/// assert_eq!(reader.position(), &Position::new(5, 17));
/// # }
/// ```
#[inline]
pub fn position(&self) -> &Position {
&self.position
}
/// Returns a borrowed iterator over all FASTQ records. The records
/// are owned (`OwnedRecord`), this is therefore slower than using
/// `Reader::next()`.
///
/// # Example
///
/// ```
/// # fn main() {
/// use seq_io::fastq::{Reader, OwnedRecord};
///
/// let fastq = b"@id1
/// ACGT
/// +
/// IIII
/// @id2
/// TGCA
/// +
/// IIII";
///
/// let mut reader = Reader::new(&fastq[..]);
///
/// let records: Result<Vec<_>, _> = reader
/// .records()
/// .collect();
///
/// assert_eq!(records.unwrap(),
/// vec![
/// OwnedRecord {head: b"id1".to_vec(), seq: b"ACGT".to_vec(), qual: b"IIII".to_vec()},
/// OwnedRecord {head: b"id2".to_vec(), seq: b"TGCA".to_vec(), qual: b"IIII".to_vec()}
/// ]
/// );
/// # }
/// ```
#[inline]
pub fn records(&mut self) -> RecordsIter<R, P> {
RecordsIter { rdr: self }
}
/// Returns an iterator over all FASTQ records like `Reader::records()`,
/// but with the difference that it owns the underlying reader.
#[inline]
pub fn into_records(self) -> RecordsIntoIter<R, P> {
RecordsIntoIter { rdr: self }
}
}
impl<R, P> Reader<R, P>
where
R: io::Read + Seek,
P: BufPolicy,
{
/// Seeks to a specified position.
/// Keep the underyling buffer if the seek position is found within it, otherwise it has to be
/// discarded.
/// If an error was returned before, seeking to that position will return the same error.
/// The same is not always true with `None`. If there is no newline character at the end of the
/// file, the last record will be returned instead of `None`.
///
/// # Example
///
/// ```
/// # fn main() {
/// use seq_io::fastq::{Reader, Position, OwnedRecord};
/// use std::io::Cursor;
///
/// let fastq = b"@id1
/// ACGT
/// +
/// IIII
/// @id2
/// TGCA
/// +
/// IIII";
///
/// let mut cursor = Cursor::new(&fastq[..]);
/// let mut reader = Reader::new(cursor);
///
/// // read the first record and get its position
/// let record1 = reader.next().unwrap().unwrap().to_owned_record();
/// let pos1 = reader.position().to_owned();
///
/// // read the second record
/// reader.next().unwrap().unwrap();
///
/// // now seek to position of first record
/// reader.seek(&pos1);
/// assert_eq!(reader.next().unwrap().unwrap().to_owned_record(), record1);
/// # }
/// ```
#[inline]
pub fn seek(&mut self, pos: &Position) -> Result<(), Error> {
self.finished = false;
let diff = pos.byte as i64 - self.position.byte as i64;
let endpos = self.buf_pos.pos.0 as i64 + diff;
self.position = pos.clone();
if endpos >= 0 && endpos < (self.get_buf().len() as i64) {
// position reachable within buffer -> no actual seeking necessary
self.buf_pos.reset(endpos as usize); // is_new() will return true
return Ok(());
}
self.buf_reader.seek(io::SeekFrom::Start(pos.byte))?;
self.buf_pos.reset(0);
Ok(())
}
}
/// Borrowed iterator of `OwnedRecord`
pub struct RecordsIter<'a, R, P = DefaultBufPolicy>
where
P: 'a,
R: io::Read + 'a,
{
rdr: &'a mut Reader<R, P>,
}
impl<'a, R, P> Iterator for RecordsIter<'a, R, P>
where
P: BufPolicy + 'a,
R: io::Read + 'a,
{
type Item = Result<OwnedRecord, Error>;
#[inline]
fn next(&mut self) -> Option<Self::Item> {
self.rdr.next().map(|rec| rec.map(|r| r.to_owned_record()))
}
}
/// Iterator of `OwnedRecord` that owns the underlying reader
pub struct RecordsIntoIter<R: io::Read, P = DefaultBufPolicy> {
rdr: Reader<R, P>,
}
impl<R, P> Iterator for RecordsIntoIter<R, P>
where
P: BufPolicy,
R: io::Read,
{
type Item = Result<OwnedRecord, Error>;
#[inline]
fn next(&mut self) -> Option<Self::Item> {
self.rdr.next().map(|rec| rec.map(|r| r.to_owned_record()))
}
}
/// Holds line number and byte offset of a FASTQ record
#[derive(Debug, Clone, PartialEq, Eq, PartialOrd, Ord)]
pub struct Position {
line: u64,
byte: u64,
}
impl Position {
#[inline]
pub fn new(line: u64, byte: u64) -> Position {
Position { line, byte }
}
/// Line number (starting with 1)
#[inline]
pub fn line(&self) -> u64 {
self.line
}
/// Byte offset within the file
#[inline]
pub fn byte(&self) -> u64 {
self.byte
}
}
/// FASTQ parsing error
#[derive(Debug)]
pub enum Error {
Io(io::Error),
/// sequence and qualitiy lengths are not equal
UnequalLengths {
/// Length of sequence
seq: usize,
/// Length of qualities
qual: usize,
/// Position within file.
/// `ErrorPosition::line` has the position of the header, not sequence/qualities
pos: ErrorPosition,
},
/// Invalid start byte encountered (expected `@`)
InvalidStart {
/// Byte found instead.
found: u8,
/// Position within file. `ErrorPosition::id` will be `None`.
pos: ErrorPosition,
},
/// Invalid separator byte encountered (expected `+`)
InvalidSep {
/// Byte found instead.
found: u8,
/// Position within file
pos: ErrorPosition,
},
/// Truncated record found
UnexpectedEnd {
/// Position within file.
pos: ErrorPosition,
},
/// Size limit of buffer was reached, which happens if `policy::BufPolicy::grow_to()` returned
/// `None`. This does not happen with the default `struct.DoubleUntil.html` policy.
BufferLimit,
}
#[derive(Debug, Clone, PartialEq, Eq)]
pub struct ErrorPosition {
/// Line number where the error occurred (starting with 1)
pub line: u64,
/// ID of record if available
pub id: Option<String>,
}
impl fmt::Display for ErrorPosition {
#[inline]
fn fmt(&self, f: &mut fmt::Formatter) -> fmt::Result {
if let Some(id) = self.id.as_ref() {
write!(f, "record '{}' at ", id)?;
}
write!(f, "line {}", self.line)
}
}
impl fmt::Display for Error {
#[inline]
fn fmt(&self, f: &mut fmt::Formatter) -> fmt::Result {
match *self {
Error::Io(ref e) => e.fmt(f),
Error::UnequalLengths { seq, qual, ref pos } => write!(
f,
"FASTQ parse error: sequence length is {}, but quality length is {} ({}).",
seq, qual, pos
),
Error::InvalidStart { found, ref pos } => write!(
f,
"FASTQ parse error: expected '@' at record start but found '{}' ({}).",
(found as char).escape_default(),
pos
),
Error::InvalidSep { found, ref pos } => write!(
f,
"FASTQ parse error: Expected '+' separator but found '{}' ({}).",
(found as char).escape_default(),
pos
),
Error::UnexpectedEnd { ref pos } => {
write!(f, "FASTQ parse error: unexpected end of input ({}).", pos)
}
Error::BufferLimit => write!(f, "FASTQ parse error: Buffer limit reached."),
}
}
}
impl From<io::Error> for Error {
#[inline]
fn from(e: io::Error) -> Error {
Error::Io(e)
}
}
impl StdError for Error {
#[inline]
fn source(&self) -> Option<&(dyn StdError + 'static)> {
match *self {
Error::Io(ref err) => Some(err),
_ => None,
}
}
}
/// Represents the position of a record within a buffer
#[derive(Debug, Clone, Default, Serialize, Deserialize)]
struct BufferPosition {
// (start, stop), but might include \r at the end
pos: (usize, usize),
seq: usize,
sep: usize,
qual: usize,
}
impl BufferPosition {
#[inline]
fn is_new(&self) -> bool {
self.pos.1 == 0
}
#[inline]
fn reset(&mut self, start: usize) {
self.pos.0 = start;
self.pos.1 = 0;
}
#[inline]
fn head<'a>(&'a self, buffer: &'a [u8]) -> &'a [u8] {
trim_cr(&buffer[self.pos.0 + 1..self.seq - 1])
}
#[inline]
fn seq<'a>(&'a self, buffer: &'a [u8]) -> &'a [u8] {
trim_cr(&buffer[self.seq..self.sep - 1])
}
#[inline]
fn qual<'a>(&'a self, buffer: &'a [u8]) -> &'a [u8] {
trim_cr(&buffer[self.qual..self.pos.1])
}
}
/// FASTQ record trait implemented by both `RefRecord` and `OwnedRecord`
pub trait Record {
/// Return the header line of the record as byte slice
fn head(&self) -> &[u8];
/// Return the FASTQ sequence as byte slice
fn seq(&self) -> &[u8];
/// Return the FASTQ qualities as byte slice
fn qual(&self) -> &[u8];
#[inline]
fn id_bytes(&self) -> &[u8] {
self.head().split(|b| *b == b' ').next().unwrap()
}
/// Return the ID of the record (everything before an optional space) as string slice
#[inline]
fn id(&self) -> Result<&str, Utf8Error> {
str::from_utf8(self.id_bytes())
}
#[inline]
fn desc_bytes(&self) -> Option<&[u8]> {
self.head().splitn(2, |b| *b == b' ').nth(1)
}
/// Return the description of the record as string slice, if present. Otherwise, `None` is returned.
#[inline]
fn desc(&self) -> Option<Result<&str, Utf8Error>> {
self.desc_bytes().map(str::from_utf8)
}
/// Return both the ID and the description of the record (if present)
/// This should be faster than calling `id()` and `desc()` separately.
#[inline]
fn id_desc_bytes(&self) -> (&[u8], Option<&[u8]>) {
let mut h = self.head().splitn(2, |c| *c == b' ');
(h.next().unwrap(), h.next())
}
/// Return both the ID and the description of the record (if present)
/// This should be faster than calling `id()` and `desc()` separately.
#[inline]
fn id_desc(&self) -> Result<(&str, Option<&str>), Utf8Error> {
let mut h = str::from_utf8(self.head())?.splitn(2, ' ');
Ok((h.next().unwrap(), h.next()))
}
/// Writes a record to the given `io::Write` instance
#[inline]
fn write<W: io::Write>(&self, writer: W) -> io::Result<()> {
write_to(writer, self.head(), self.seq(), self.qual())
}
}
/// A FASTQ record that borrows data from a buffer
#[derive(Debug, Clone)]
pub struct RefRecord<'a> {
buffer: &'a [u8],
buf_pos: &'a BufferPosition,
}
impl<'a> Record for RefRecord<'a> {
#[inline]
fn head(&self) -> &[u8] {
self.buf_pos.head(self.buffer)
}
#[inline]
fn seq(&self) -> &[u8] {
self.buf_pos.seq(self.buffer)
}
#[inline]
fn qual(&self) -> &[u8] {
self.buf_pos.qual(self.buffer)
}
}
impl<'a> RefRecord<'a> {
#[inline]
pub fn to_owned_record(&self) -> OwnedRecord {
OwnedRecord {
head: self.head().to_vec(),
seq: self.seq().to_vec(),
qual: self.qual().to_vec(),
}
}
/// Writes a record to the given `io::Write` instance
/// by just writing the unmodified input, which is faster than `RefRecord::write`
#[inline]
pub fn write_unchanged<W: io::Write>(&self, mut writer: W) -> io::Result<()> {
let data = &self.buffer[self.buf_pos.pos.0..self.buf_pos.pos.1];
writer.write_all(data)?;
writer.write_all(b"\n")
}
}
/// A FASTQ record that ownes its data (requires allocations)
#[derive(Debug, Clone, PartialEq, Eq, Serialize, Deserialize)]
pub struct OwnedRecord {
pub head: Vec<u8>,
pub seq: Vec<u8>,
pub qual: Vec<u8>,
}
impl Record for OwnedRecord {
#[inline]
fn head(&self) -> &[u8] {
&self.head
}
#[inline]
fn seq(&self) -> &[u8] {
&self.seq
}
#[inline]
fn qual(&self) -> &[u8] {
&self.qual
}
}
/// Set of FASTQ records that owns it's buffer
/// and knows the positions of each record.
#[derive(Default, Clone, Debug, Serialize, Deserialize)]
pub struct RecordSet {
buffer: Vec<u8>,
buf_positions: Vec<BufferPosition>,
}
impl<'a> iter::IntoIterator for &'a RecordSet {
type Item = RefRecord<'a>;
type IntoIter = RecordSetIter<'a>;
#[inline]
fn into_iter(self) -> Self::IntoIter {
RecordSetIter {
buffer: &self.buffer,
pos: self.buf_positions.iter(),
}
}
}
/// Iterator over record sets
pub struct RecordSetIter<'a> {
buffer: &'a [u8],
pos: slice::Iter<'a, BufferPosition>,
}
impl<'a> Iterator for RecordSetIter<'a> {
type Item = RefRecord<'a>;
#[inline]
fn next(&mut self) -> Option<RefRecord<'a>> {
self.pos.next().map(|p| RefRecord {
buffer: self.buffer,
buf_pos: p,
})
}
}
/// Helper function for writing data (not necessarily stored in a `Record` instance)
/// to the FASTQ format
#[inline]
pub fn write_to<W: io::Write>(
mut writer: W,
head: &[u8],
seq: &[u8],
qual: &[u8],
) -> io::Result<()> {
writer.write_all(b"@")?;
writer.write_all(head)?;
writer.write_all(b"\n")?;
writer.write_all(seq)?;
writer.write_all(b"\n+\n")?;
writer.write_all(qual)?;
writer.write_all(b"\n")?;
Ok(())
}
/// Helper function for writing data (not necessarily stored in a `Record` instance)
/// to the FASTQ format. The ID and description parts of the header are supplied separately
/// instead of a whole header line
#[inline]
pub fn write_parts<W: io::Write>(
mut writer: W,
id: &[u8],
desc: Option<&[u8]>,
seq: &[u8],
qual: &[u8],
) -> io::Result<()> {
writer.write_all(b"@")?;
writer.write_all(id)?;
if let Some(d) = desc {
writer.write_all(b" ")?;
writer.write_all(d)?;
}
writer.write_all(b"\n")?;
writer.write_all(seq)?;
writer.write_all(b"\n+\n")?;
writer.write_all(qual)?;
writer.write_all(b"\n")?;
Ok(())
}