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

// Copyright 2014 Christopher Schröder, Johannes Köster.
// Licensed under the MIT license (http://opensource.org/licenses/MIT)
// This file may not be copied, modified, or distributed
// except according to those terms.

//! Module for working with SAM files.

use std::ffi;
use std::path::Path;

use htslib;

use bam::header;
use bam::record;
use bam::HeaderView;

/// SAM writer.
#[derive(Debug)]
pub struct Writer {
    f: *mut htslib::htsFile,
    header: HeaderView,
}

/// Wrapper for opening a SAM file.
fn hts_open(path: &ffi::CStr, mode: &[u8]) -> Result<*mut htslib::htsFile, WriterError> {
    let ret = unsafe { htslib::hts_open(path.as_ptr(), ffi::CString::new(mode).unwrap().as_ptr()) };
    if ret.is_null() {
        Err(WriterError::IOError)
    } else {
        Ok(ret)
    }
}

impl Writer {
    /// Create new SAM file writer.
    ///
    /// # Arguments
    ///
    /// * `path` - the path.
    /// * `header` - header definition to use
    pub fn from_path<P: AsRef<Path>>(
        path: P,
        header: &header::Header,
    ) -> Result<Self, WriterError> {
        if let Some(p) = path.as_ref().to_str() {
            Ok(try!(Self::new(p.as_bytes(), header)))
        } else {
            Err(WriterError::IOError)
        }
    }

    /// Create a new SAM file at STDOUT.
    ///
    /// # Arguments
    ///
    /// * `header` - header definition to use
    pub fn from_stdout(header: &header::Header) -> Result<Self, WriterError> {
        Self::new(b"-", header)
    }

    fn new(path: &[u8], header: &header::Header) -> Result<Self, WriterError> {
        let f = try!(hts_open(&ffi::CString::new(path).unwrap(), b"w"));
        let header_view = HeaderView::from_header(header);

        unsafe {
            htslib::sam_hdr_write(f, &header_view.inner());
        }
        Ok(Writer {
            f: f,
            header: header_view,
        })
    }

    /// Write record to SAM.
    ///
    /// # Arguments
    ///
    /// * `record` - the record to write
    pub fn write(&mut self, record: &record::Record) -> Result<(), WriteError> {
        if unsafe { htslib::sam_write1(self.f, &self.header.inner(), record.inner) } == -1 {
            Err(WriteError::Some)
        } else {
            Ok(())
        }
    }
}

impl Drop for Writer {
    fn drop(&mut self) {
        unsafe {
            htslib::hts_close(self.f);
        }
    }
}

quick_error! {
    #[derive(Debug, Clone)]
    pub enum WriterError {
        IOError {}
    }
}

quick_error! {
    #[derive(Debug, Clone)]
    pub enum WriteError {
        Some {
            description("error writing record")
        }
    }
}

#[cfg(test)]
mod tests {
    use bam::header;
    use bam::record;
    use bam::Read;
    use bam::Reader;
    use sam::Writer;

    #[test]
    fn test_sam_writer_example() {
        fn from_bam_with_filter<'a, 'b, F>(bamfile: &'a str, samfile: &'b str, f: F) -> bool
        where
            F: Fn(&record::Record) -> Option<bool>,
        {
            let mut bam_reader = Reader::from_path(bamfile).unwrap(); // internal functions, just unwarp
            let header = header::Header::from_template(bam_reader.header());
            let mut sam_writer = Writer::from_path(samfile, &header).unwrap();
            for record in bam_reader.records() {
                if record.is_err() {
                    return false;
                }
                let parsed = record.unwrap();
                match f(&parsed) {
                    None => return true,
                    Some(false) => {}
                    Some(true) => if let Err(_) = sam_writer.write(&parsed) {
                        return false;
                    },
                }
            }
            true
        }
        use std::fs::File;
        use std::io::Read;
        let bamfile = "./test/bam2sam_test.bam";
        let samfile = "./test/bam2sam_out.sam";
        let expectedfile = "./test/bam2sam_expected.sam";
        let result = from_bam_with_filter(bamfile, samfile, |_| Some(true));
        assert!(result);
        let mut expected = Vec::new();
        let mut written = Vec::new();
        assert!(
            File::open(expectedfile)
                .unwrap()
                .read_to_end(&mut expected)
                .is_ok()
        );
        assert!(
            File::open(samfile)
                .unwrap()
                .read_to_end(&mut written)
                .is_ok()
        );
        assert_eq!(expected, written);
    }
}