noodles-util 0.49.0

use std::{
    fs::File,
    io::{self, BufReader, Read},
    path::Path,
};

use noodles_bcf as bcf;
use noodles_bgzf as bgzf;
use noodles_csi::BinningIndex;
use noodles_vcf as vcf;

use super::IndexedReader;
use crate::variant::io::{
    reader::builder::{detect_compression_method, detect_format},
    CompressionMethod, Format,
};

/// An indexed variant reader builder.
#[derive(Default)]
pub struct Builder {
    compression_method: Option<Option<CompressionMethod>>,
    format: Option<Format>,
    index: Option<Box<dyn BinningIndex>>,
}

impl Builder {
    /// Sets the compression method of the input.
    ///
    /// By default, the compression method is autodetected on build. This can be used to override
    /// it, but note that only bgzip-compressed streams can be indexed.
    ///
    /// # Examples
    ///
    /// ```
    /// use noodles_util::variant::io::{indexed_reader::Builder, CompressionMethod};
    /// let builder = Builder::default().set_compression_method(Some(CompressionMethod::Bgzf));
    /// ```
    pub fn set_compression_method(mut self, compression_method: Option<CompressionMethod>) -> Self {
        self.compression_method = Some(compression_method);
        self
    }

    /// Sets the format of the input.
    ///
    /// By default, the format is autodetected on build. This can be used to override it.
    ///
    /// # Examples
    ///
    /// ```
    /// use noodles_util::variant::io::{indexed_reader::Builder, Format};
    /// let builder = Builder::default().set_format(Format::Vcf);
    /// ```
    pub fn set_format(mut self, format: Format) -> Self {
        self.format = Some(format);
        self
    }

    /// Sets an index.
    ///
    /// When building from a path ([`Self::build_from_path`]), an associated index at `<src>.tbi`
    /// or `<src>.csi` will attempt to be loaded. This can be used to override it if the index
    /// cannot be found or when building from a reader ([`Self::build_from_reader`]).
    ///
    /// # Examples
    ///
    /// ```
    /// use noodles_csi as csi;
    /// use noodles_util::variant::io::indexed_reader::Builder;
    ///
    /// let index = csi::Index::default();
    /// let builder = Builder::default().set_index(index);
    /// ```
    pub fn set_index<I>(mut self, index: I) -> Self
    where
        I: BinningIndex + 'static,
    {
        self.index = Some(Box::new(index));
        self
    }

    /// Builds an indexed variant reader from a path.
    ///
    /// The compression method and format will be autodetected, if not overridden. If no index is
    /// set ([`Self::set_index`]), this will attempt to load an associated index at `<src>.tbi` or
    /// `<src>.csi`.
    ///
    ///
    /// # Examples
    ///
    /// ```no_run
    /// use noodles_util::variant::io::indexed_reader::Builder;
    /// let reader = Builder::default().build_from_path("sample.vcf.gz")?;
    /// # Ok::<_, std::io::Error>(())
    /// ```
    pub fn build_from_path<P>(self, src: P) -> io::Result<IndexedReader<bgzf::Reader<File>>>
    where
        P: AsRef<Path>,
    {
        let mut reader = File::open(src.as_ref()).map(BufReader::new)?;

        let compression_method = match self.compression_method {
            Some(compression_method) => compression_method,
            None => detect_compression_method(&mut reader)?,
        };

        let format = match self.format {
            Some(format) => format,
            None => detect_format(&mut reader, compression_method)?,
        };

        match (format, compression_method) {
            (Format::Vcf, Some(CompressionMethod::Bgzf)) => {
                let mut builder = vcf::io::indexed_reader::Builder::default();

                if let Some(index) = self.index {
                    builder = builder.set_index(index);
                }

                builder.build_from_path(src).map(IndexedReader::Vcf)
            }
            (Format::Bcf, Some(CompressionMethod::Bgzf)) => {
                let mut builder = bcf::io::indexed_reader::Builder::default();

                if let Some(index) = self.index {
                    builder = builder.set_index(index);
                }

                builder.build_from_path(src).map(IndexedReader::Bcf)
            }
            (_, None) => Err(io::Error::new(
                io::ErrorKind::InvalidData,
                "source not bgzip-compressed",
            )),
        }
    }

    /// Builds an indexed variant reader from a reader.
    ///
    /// The compression method and format will be autodetected, if not overridden. An index must be
    /// set ([`Self::set_index`]). The reader must be a bgzip-compressed stream.
    ///
    /// # Examples
    ///
    /// ```
    /// # use std::io::{self, Write};
    /// use noodles_bgzf as bgzf;
    /// use noodles_csi as csi;
    /// use noodles_util::variant::io::indexed_reader::Builder;
    ///
    /// let mut writer = bgzf::Writer::new(Vec::new());
    /// writer.write_all(b"BCF")?;
    /// let data = writer.finish()?;
    ///
    /// let index = csi::Index::default();
    /// let reader = Builder::default()
    ///     .set_index(index)
    ///     .build_from_reader(&data[..])?;
    /// # Ok::<_, io::Error>(())
    /// ```
    pub fn build_from_reader<R>(
        self,
        reader: R,
    ) -> io::Result<IndexedReader<bgzf::Reader<BufReader<R>>>>
    where
        R: Read,
    {
        let mut reader = BufReader::new(reader);

        let compression = match self.compression_method {
            Some(compression) => compression,
            None => detect_compression_method(&mut reader)?,
        };

        let format = match self.format {
            Some(format) => format,
            None => detect_format(&mut reader, compression)?,
        };

        match (format, compression) {
            (Format::Vcf, Some(CompressionMethod::Bgzf)) => {
                let mut builder = vcf::io::indexed_reader::Builder::default();

                if let Some(index) = self.index {
                    builder = builder.set_index(index);
                }

                builder.build_from_reader(reader).map(IndexedReader::Vcf)
            }
            (Format::Bcf, Some(CompressionMethod::Bgzf)) => {
                let mut builder = bcf::io::indexed_reader::Builder::default();

                if let Some(index) = self.index {
                    builder = builder.set_index(index);
                }

                builder.build_from_reader(reader).map(IndexedReader::Bcf)
            }
            (_, None) => Err(io::Error::new(
                io::ErrorKind::InvalidData,
                "source not bgzip-compressed",
            )),
        }
    }
}

#[cfg(test)]
mod tests {
    use noodles_csi as csi;

    use super::*;

    #[test]
    fn test_build_from_reader() -> io::Result<()> {
        let mut writer = bcf::io::Writer::new(Vec::new());
        let header = vcf::Header::default();
        writer.write_header(&header)?;
        writer.try_finish()?;
        let data = writer.into_inner().into_inner();

        let index = csi::Index::default();

        let mut reader = Builder::default()
            .set_index(index)
            .build_from_reader(&data[..])?;

        reader.read_header()?;

        Ok(())
    }
}