//! BAM reader and iterators.

pub(crate) mod query;
pub mod record;
mod records;
mod unmapped_records;

pub use self::{query::Query, records::Records, unmapped_records::UnmappedRecords};

use std::{
    ffi::CStr,
    io::{self, Read, Seek},
};

use byteorder::{LittleEndian, ReadBytesExt};
use noodles_bgzf as bgzf;
use noodles_core::{region::Interval, Region};
use noodles_csi::{binning_index::ReferenceSequenceExt, BinningIndex};
use noodles_sam::header::{ReferenceSequence, ReferenceSequences};

use self::record::read_record;
use super::{bai, Record, MAGIC_NUMBER};

/// A BAM reader.
///
/// A BAM file is an encoded and compressed version of a SAM file. While a SAM file has a header
/// and a list of records, a BAM is comprised of three parts:
///
///   1. a SAM header,
///   2. a list of reference sequences, and
///   3. a list of encoded SAM records.
///
/// The reader reads records sequentially but can use virtual positions to seek to offsets from the
/// start of a seekable stream.
///
/// # Examples
///
/// ```no_run
/// # use std::{fs::File, io};
/// use noodles_bam as bam;
///
/// let mut reader = File::open("sample.bam").map(bam::Reader::new)?;
/// reader.read_header()?;
/// reader.read_reference_sequences()?;
///
/// for result in reader.records() {
///     let record = result?;
///     println!("{:?}", record);
/// }
///
/// # Ok::<(), io::Error>(())
/// ```
pub struct Reader<R> {
    inner: R,
    buf: Vec<u8>,
}

impl<R> Reader<R>
where
    R: Read,
{
    /// Returns a reference to the underlying reader.
    ///
    /// # Examples
    ///
    /// ```
    /// use noodles_bam as bam;
    /// let data = [];
    /// let reader = bam::Reader::from(&data[..]);
    /// assert!(reader.get_ref().is_empty());
    /// ```
    pub fn get_ref(&self) -> &R {
        &self.inner
    }

    /// Returns a mutable reference to the underlying reader.
    ///
    /// # Examples
    ///
    /// ```
    /// use noodles_bam as bam;
    /// let data = [];
    /// let mut reader = bam::Reader::from(&data[..]);
    /// assert!(reader.get_mut().is_empty());
    /// ```
    pub fn get_mut(&mut self) -> &mut R {
        &mut self.inner
    }

    /// Returns the underlying reader.
    ///
    /// # Examples
    ///
    /// ```
    /// use noodles_bam as bam;
    /// let data = [];
    /// let reader = bam::Reader::from(&data[..]);
    /// assert!(reader.into_inner().is_empty());
    /// ```
    pub fn into_inner(self) -> R {
        self.inner
    }

    /// Reads the raw SAM header.
    ///
    /// The BAM magic number is also checked.
    ///
    /// The position of the stream is expected to be at the start.
    ///
    /// This returns the raw SAM header as a [`String`]. It can subsequently be parsed as a
    /// [`noodles_sam::Header`].
    ///
    /// # Examples
    ///
    /// ```no_run
    /// # use std::{fs::File, io};
    /// use noodles_bam as bam;
    /// let mut reader = File::open("sample.bam").map(bam::Reader::new)?;
    /// let header = reader.read_header()?;
    /// # Ok::<(), io::Error>(())
    /// ```
    pub fn read_header(&mut self) -> io::Result<String> {
        read_magic(&mut self.inner)?;
        read_header(&mut self.inner)
    }

    /// Reads the binary reference sequences after the SAM header.
    ///
    /// This is not the same as the `@SQ` records in the SAM header. A BAM has a list of reference
    /// sequences containing name and length tuples after the SAM header and before the list of
    /// records.
    ///
    /// The position of the stream is expected to be directly after the header.
    ///
    /// This returns a reference sequence dictionary ([`noodles_sam::header::ReferenceSequences`]),
    /// which can be used to build a minimal [`noodles_sam::Header`] if the SAM header is empty.
    ///
    /// # Examples
    ///
    /// ```no_run
    /// # use std::{fs::File, io};
    /// use noodles_bam as bam;
    /// let mut reader = File::open("sample.bam").map(bam::Reader::new)?;
    /// reader.read_header()?;
    /// let reference_sequences = reader.read_reference_sequences()?;
    /// # Ok::<(), io::Error>(())
    /// ```
    pub fn read_reference_sequences(&mut self) -> io::Result<ReferenceSequences> {
        read_reference_sequences(&mut self.inner)
    }

    /// Reads a single record.
    ///
    /// The record block size (`bs`) is read from the underlying stream, and `bs` additional bytes
    /// are read into the given record.
    ///
    /// The stream is expected to be directly after the reference sequences or at the start of
    /// another record.
    ///
    /// It is more ergonomic to read records using an iterator (see [`Self::records`] and
    /// [`Self::query`]), but using this method directly allows the reuse of a single [`Record`]
    /// buffer.
    ///
    /// If successful, the record block size is returned. If a block size of 0 is returned, the
    /// stream reached EOF.
    ///
    /// # Examples
    ///
    /// ```no_run
    /// # use std::{fs::File, io};
    /// use noodles_bam as bam;
    ///
    /// let mut reader = File::open("sample.bam").map(bam::Reader::new)?;
    /// reader.read_header()?;
    /// reader.read_reference_sequences()?;
    ///
    /// let mut record = bam::Record::default();
    /// reader.read_record(&mut record)?;
    ///
    /// # Ok::<(), io::Error>(())
    /// ```
    pub fn read_record(&mut self, record: &mut Record) -> io::Result<usize> {
        read_record(&mut self.inner, &mut self.buf, record)
    }

    /// Returns an iterator over records starting from the current stream position.
    ///
    /// The stream is expected to be directly after the reference sequences or at the start of
    /// another record.
    ///
    /// # Examples
    ///
    /// ```no_run
    /// # use std::{fs::File, io};
    /// use noodles_bam as bam;
    ///
    /// let mut reader = File::open("sample.bam").map(bam::Reader::new)?;
    /// reader.read_header()?;
    /// reader.read_reference_sequences()?;
    ///
    /// for result in reader.records() {
    ///     let record = result?;
    ///     println!("{:?}", record);
    /// }
    /// # Ok::<(), io::Error>(())
    /// ```
    pub fn records(&mut self) -> Records<'_, R> {
        Records::new(self)
    }
}

impl<R> Reader<bgzf::Reader<R>>
where
    R: Read,
{
    /// Creates a BAM reader.
    ///
    /// The given reader must be a raw BGZF stream, as the underlying reader wraps it in a decoder.
    ///
    /// # Examples
    ///
    /// ```
    /// use noodles_bam as bam;
    /// let data = [];
    /// let reader = bam::Reader::new(&data[..]);
    /// ```
    pub fn new(reader: R) -> Self {
        Self::from(bgzf::Reader::new(reader))
    }

    /// Returns the current virtual position of the underlying BGZF reader.
    ///
    /// # Examples
    ///
    /// ```
    /// # use std::io;
    /// use noodles_bam as bam;
    ///
    /// let data = Vec::new();
    /// let reader = bam::Reader::new(&data[..]);
    /// let virtual_position = reader.virtual_position();
    ///
    /// assert_eq!(virtual_position.compressed(), 0);
    /// assert_eq!(virtual_position.uncompressed(), 0);
    /// # Ok::<(), io::Error>(())
    /// ```
    pub fn virtual_position(&self) -> bgzf::VirtualPosition {
        self.inner.virtual_position()
    }
}

impl<R> Reader<bgzf::Reader<R>>
where
    R: Read + Seek,
{
    /// Seeks the underlying BGZF reader to the given virtual position.
    ///
    /// Virtual positions typically come from the associated BAM index file.
    ///
    /// # Examples
    ///
    /// ```
    /// # use std::io::{self, Cursor};
    /// use noodles_bam as bam;
    /// use noodles_bgzf as bgzf;
    /// let mut reader = bam::Reader::new(Cursor::new(Vec::new()));
    /// let virtual_position = bgzf::VirtualPosition::default();
    /// reader.seek(virtual_position)?;
    /// # Ok::<(), io::Error>(())
    /// ```
    pub fn seek(&mut self, pos: bgzf::VirtualPosition) -> io::Result<bgzf::VirtualPosition> {
        self.inner.seek(pos)
    }

    // Seeks to the first record by setting the cursor to the beginning of the stream and
    // (re)reading the header and binary reference sequences.
    fn seek_to_first_record(&mut self) -> io::Result<bgzf::VirtualPosition> {
        self.seek(bgzf::VirtualPosition::default())?;
        self.read_header()?;
        self.read_reference_sequences()?;
        Ok(self.virtual_position())
    }

    /// Returns an iterator over records that intersect the given region.
    ///
    /// # Examples
    ///
    /// ```no_run
    /// # use std::fs::File;
    /// use noodles_bam::{self as bam, bai};
    /// use noodles_core::Region;
    /// use noodles_sam as sam;
    ///
    /// let mut reader = File::open("sample.bam").map(bam::Reader::new)?;
    /// let header: sam::Header = reader.read_header()?.parse()?;
    ///
    /// let reference_sequences = header.reference_sequences();
    /// let index = bai::read("sample.bam.bai")?;
    /// let region = Region::mapped("sq0", 17711..=28657);
    /// let query = reader.query(reference_sequences, &index, &region)?;
    ///
    /// for result in query {
    ///     let record = result?;
    ///     println!("{:?}", record);
    /// }
    /// # Ok::<(), Box<dyn std::error::Error>>(())
    /// ```
    pub fn query<I, RS>(
        &mut self,
        reference_sequences: &ReferenceSequences,
        index: &I,
        region: &Region,
    ) -> io::Result<Query<'_, R>>
    where
        I: BinningIndex<RS>,
        RS: ReferenceSequenceExt,
    {
        let (reference_sequence_id, interval) = resolve_region(reference_sequences, region)?;
        let chunks = index.query(reference_sequence_id, interval)?;
        Ok(Query::new(self, chunks, reference_sequence_id, interval))
    }

    /// Returns an iterator of unmapped records after querying for the unmapped region.
    ///
    /// # Examples
    ///
    /// ```no_run
    /// # use std::{fs::File, io};
    /// use noodles_bam::{self as bam, bai};
    ///
    /// let mut reader = File::open("sample.bam").map(bam::Reader::new)?;
    /// let index = bai::read("sample.bam.bai")?;
    /// let query = reader.query_unmapped(&index)?;
    ///
    /// for result in query {
    ///     let record = result?;
    ///     println!("{:?}", record);
    /// }
    /// # Ok::<(), io::Error>(())
    /// ```
    pub fn query_unmapped(&mut self, index: &bai::Index) -> io::Result<UnmappedRecords<'_, R>> {
        if let Some(pos) = index.first_record_in_last_linear_bin_start_position() {
            self.seek(pos)?;
        } else {
            self.seek_to_first_record()?;
        }

        Ok(UnmappedRecords::new(self))
    }
}

impl<R> From<R> for Reader<R> {
    fn from(inner: R) -> Self {
        Self {
            inner,
            buf: Vec::new(),
        }
    }
}

fn read_magic<R>(reader: &mut R) -> io::Result<()>
where
    R: Read,
{
    let mut magic = [0; 4];
    reader.read_exact(&mut magic)?;

    if magic == MAGIC_NUMBER {
        Ok(())
    } else {
        Err(io::Error::new(
            io::ErrorKind::InvalidData,
            "invalid BAM header",
        ))
    }
}

fn read_header<R>(reader: &mut R) -> io::Result<String>
where
    R: Read,
{
    let l_text = reader.read_u32::<LittleEndian>().and_then(|n| {
        usize::try_from(n).map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))
    })?;

    let mut text = vec![0; l_text];
    reader.read_exact(&mut text)?;

    // § 4.2 The BAM format (2021-06-03): "Plain header text in SAM; not necessarily
    // NUL-terminated".
    bytes_with_nul_to_string(&text).or_else(|_| {
        String::from_utf8(text).map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))
    })
}

fn read_reference_sequences<R>(reader: &mut R) -> io::Result<ReferenceSequences>
where
    R: Read,
{
    let n_ref = reader.read_u32::<LittleEndian>().and_then(|n| {
        usize::try_from(n).map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))
    })?;

    let mut reference_sequences = ReferenceSequences::with_capacity(n_ref);

    for _ in 0..n_ref {
        let reference_sequence = read_reference_sequence(reader)?;
        let name = reference_sequence.name().to_string();
        reference_sequences.insert(name, reference_sequence);
    }

    Ok(reference_sequences)
}

fn read_reference_sequence<R>(reader: &mut R) -> io::Result<ReferenceSequence>
where
    R: Read,
{
    let l_name = reader.read_u32::<LittleEndian>().and_then(|n| {
        usize::try_from(n).map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))
    })?;

    let mut c_name = vec![0; l_name];
    reader.read_exact(&mut c_name)?;

    let name = bytes_with_nul_to_string(&c_name).and_then(|name| {
        name.parse()
            .map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))
    })?;

    let l_ref = reader.read_u32::<LittleEndian>().and_then(|len| {
        i32::try_from(len).map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))
    })?;

    ReferenceSequence::new(name, l_ref).map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))
}

pub(crate) fn bytes_with_nul_to_string(buf: &[u8]) -> io::Result<String> {
    CStr::from_bytes_with_nul(buf)
        .map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))
        .and_then(|c_str| {
            c_str
                .to_str()
                .map(|s| s.to_string())
                .map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))
        })
}

pub(crate) fn resolve_region(
    reference_sequences: &ReferenceSequences,
    region: &Region,
) -> io::Result<(usize, Interval)> {
    if let Some(r) = region.as_mapped() {
        let i = reference_sequences.get_index_of(r.name()).ok_or_else(|| {
            io::Error::new(
                io::ErrorKind::InvalidInput,
                format!(
                    "region reference sequence does not exist in reference sequences: {:?}",
                    region
                ),
            )
        })?;

        Ok((i, r.interval()))
    } else {
        Err(io::Error::new(
            io::ErrorKind::InvalidData,
            "region is not mapped",
        ))
    }
}

#[cfg(test)]
mod tests {
    use noodles_sam as sam;

    use super::*;

    #[test]
    fn test_read_magic() -> io::Result<()> {
        let data = b"BAM\x01";
        let mut reader = &data[..];
        assert!(read_magic(&mut reader).is_ok());

        let data = [];
        let mut reader = &data[..];
        assert!(matches!(
            read_magic(&mut reader),
            Err(ref e) if e.kind() == io::ErrorKind::UnexpectedEof
        ));

        let data = b"MThd";
        let mut reader = &data[..];
        assert!(matches!(
            read_magic(&mut reader),
            Err(ref e) if e.kind() == io::ErrorKind::InvalidData
        ));

        Ok(())
    }

    #[test]
    fn test_read_header() -> io::Result<()> {
        let expected = "@HD\tVN:1.6\n";

        let data_len = expected.len() as u32;
        let mut data = data_len.to_le_bytes().to_vec();
        data.extend(expected.as_bytes());

        let mut reader = &data[..];
        let actual = read_header(&mut reader)?;

        assert_eq!(actual, expected);

        Ok(())
    }

    #[test]
    fn test_read_reference_sequences() -> Result<(), Box<dyn std::error::Error>> {
        use sam::header::reference_sequence;

        let data = [
            0x01, 0x00, 0x00, 0x00, // n_ref = 1
            0x04, 0x00, 0x00, 0x00, // ref[0].l_name = 4
            0x73, 0x71, 0x30, 0x00, // ref[0].name = "sq0\x00"
            0x08, 0x00, 0x00, 0x00, // ref[0].l_ref = 8
        ];

        let mut reader = &data[..];
        let actual = read_reference_sequences(&mut reader)?;

        let expected: ReferenceSequences = [("sq0".parse()?, 8)]
            .into_iter()
            .map(|(name, len): (reference_sequence::Name, i32)| {
                let sn = name.to_string();
                ReferenceSequence::new(name, len).map(|rs| (sn, rs))
            })
            .collect::<Result<_, _>>()?;

        assert_eq!(actual, expected);

        Ok(())
    }
}