noodles_cram/io/writer/
builder.rs

1use std::{
2    fs::File,
3    io::{self, Write},
4    path::Path,
5};
6
7use noodles_fasta as fasta;
8
9use super::{Options, Writer, RECORDS_PER_CONTAINER};
10use crate::{codecs::Encoder, container::BlockContentEncoderMap, file_definition::Version};
11
12/// A CRAM writer builder.
13#[derive(Default)]
14pub struct Builder {
15    reference_sequence_repository: fasta::Repository,
16    options: Options,
17}
18
19impl Builder {
20    /// Sets the reference sequence repository.
21    ///
22    /// # Examples
23    ///
24    /// ```
25    /// use noodles_cram::io::writer::Builder;
26    /// use noodles_fasta as fasta;
27    ///
28    /// let repository = fasta::Repository::default();
29    /// let builder = Builder::default()
30    ///     .set_reference_sequence_repository(repository);
31    /// ```
32    pub fn set_reference_sequence_repository(
33        mut self,
34        reference_sequence_repository: fasta::Repository,
35    ) -> Self {
36        self.reference_sequence_repository = reference_sequence_repository;
37        self
38    }
39
40    /// Sets whether to preserve read names.
41    ///
42    /// If `false`, read names are discarded.
43    ///
44    /// The default is `true`.
45    ///
46    /// # Examples
47    ///
48    /// ```
49    /// use noodles_cram::io::writer::Builder;
50    /// let builder = Builder::default().preserve_read_names(false);
51    /// ```
52    pub fn preserve_read_names(mut self, value: bool) -> Self {
53        self.options.preserve_read_names = value;
54        self
55    }
56
57    /// Sets whether to encode alignment start positions as deltas.
58    ///
59    /// If `false`, record alignment start positions are written with their actual values.
60    ///
61    /// The default is `true`.
62    ///
63    /// # Examples
64    ///
65    /// ```
66    /// use noodles_cram::io::writer::Builder;
67    /// let builder = Builder::default()
68    ///     .encode_alignment_start_positions_as_deltas(false);
69    /// ```
70    pub fn encode_alignment_start_positions_as_deltas(mut self, value: bool) -> Self {
71        self.options.encode_alignment_start_positions_as_deltas = value;
72        self
73    }
74
75    /// Sets the block content-encoder map.
76    ///
77    /// # Examples
78    ///
79    /// ```
80    /// use noodles_cram::{container::BlockContentEncoderMap, io::writer::Builder};
81    ///
82    /// let block_content_encoder_map = BlockContentEncoderMap::default();
83    /// let builder = Builder::default()
84    ///     .set_block_content_encoder_map(block_content_encoder_map);
85    /// ```
86    pub fn set_block_content_encoder_map(mut self, map: BlockContentEncoderMap) -> Self {
87        self.options.block_content_encoder_map = map;
88        self
89    }
90
91    /// Builds a CRAM writer from a path.
92    ///
93    /// # Examples
94    ///
95    /// ```no_run
96    /// use noodles_cram::io::writer::Builder;
97    /// let writer = Builder::default().build_from_path("out.cram")?;
98    /// # Ok::<_, std::io::Error>(())
99    /// ```
100    pub fn build_from_path<P>(self, dst: P) -> io::Result<Writer<File>>
101    where
102        P: AsRef<Path>,
103    {
104        File::create(dst).map(|file| self.build_from_writer(file))
105    }
106
107    /// Builds a CRAM writer from a path.
108    #[deprecated(since = "0.68.0", note = "Use `Builder::build_from_path` instead.")]
109    pub fn build_with_path<P>(self, dst: P) -> io::Result<Writer<File>>
110    where
111        P: AsRef<Path>,
112    {
113        self.build_from_path(dst)
114    }
115
116    /// Builds a CRAM writer from a writer.
117    ///
118    /// # Examples
119    ///
120    /// ```
121    /// use noodles_cram::io::writer::Builder;
122    /// let writer = Builder::default().build_from_writer(Vec::new());
123    /// ```
124    pub fn build_from_writer<W>(mut self, writer: W) -> Writer<W>
125    where
126        W: Write,
127    {
128        if uses_cram_3_1_codecs(&self.options.block_content_encoder_map) {
129            self.options.version = Version::new(3, 1);
130        }
131
132        Writer {
133            inner: writer,
134            reference_sequence_repository: self.reference_sequence_repository,
135            options: self.options,
136            records: Vec::with_capacity(RECORDS_PER_CONTAINER),
137            record_counter: 0,
138        }
139    }
140
141    /// Builds a CRAM writer from a writer.
142    #[deprecated(since = "0.68.0", note = "Use `Builder::build_from_writer` instead.")]
143    pub fn build_with_writer<W>(self, writer: W) -> Writer<W>
144    where
145        W: Write,
146    {
147        self.build_from_writer(writer)
148    }
149}
150
151pub fn uses_cram_3_1_codecs(block_content_encoder_map: &BlockContentEncoderMap) -> bool {
152    fn is_cram_3_1_codec(encoder: &Encoder) -> bool {
153        matches!(
154            encoder,
155            Encoder::RansNx16(_) | Encoder::AdaptiveArithmeticCoding(_) | Encoder::NameTokenizer
156        )
157    }
158
159    if let Some(encoder) = block_content_encoder_map.core_data_encoder() {
160        if is_cram_3_1_codec(encoder) {
161            return true;
162        }
163    }
164
165    block_content_encoder_map
166        .data_series_encoders()
167        .iter()
168        .chain(block_content_encoder_map.tag_values_encoders().values())
169        .flatten()
170        .any(is_cram_3_1_codec)
171}
172
173#[cfg(test)]
174mod tests {
175    use super::*;
176
177    #[test]
178    fn test_uses_cram_3_1_codecs() {
179        use crate::codecs::rans_nx16::Flags;
180
181        let block_content_encoder_map = BlockContentEncoderMap::default();
182        assert!(!uses_cram_3_1_codecs(&block_content_encoder_map));
183
184        let block_content_encoder_map = BlockContentEncoderMap::builder()
185            .set_core_data_encoder(Some(Encoder::RansNx16(Flags::empty())))
186            .build();
187        assert!(uses_cram_3_1_codecs(&block_content_encoder_map));
188    }
189}
noodles_cram/io/writer/builder.rs

noodles_cram/io/writer/
builder.rs
