rust-htslib 0.8.0

This library provides HTSlib bindings and a high level Rust API for reading and writing BAM files.
Documentation 
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// Copyright 2014 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.


use std::slice;
use std::ffi;

use htslib;


pub type SampleSubset = Vec<i32>;


/// A BCF header.
pub struct Header {
    pub inner: *mut htslib::vcf::bcf_hdr_t,
    pub subset: Option<SampleSubset>,
}


impl Header {
    /// Create a new header.
    pub fn new() -> Self {
        Header {
            inner: unsafe { htslib::vcf::bcf_hdr_init(ffi::CString::new(&b"w"[..]).unwrap().as_ptr()) },
            subset: None,
        }
    }

    pub fn with_template(header: &HeaderView) -> Self {
        Header { inner: unsafe { htslib::vcf::bcf_hdr_dup(header.inner) }, subset: None }
    }

    pub fn subset_template(header: &HeaderView, samples: &[&[u8]]) -> Result<Self, ()> {
        let mut imap = vec![0; samples.len()];
        let names: Vec<_> = samples.iter().map(|&s| ffi::CString::new(s).unwrap()).collect();
        let name_pointers: Vec<_> = names.iter().map(|s| s.as_ptr() as *mut i8).collect();
        let inner = unsafe {
            htslib::vcf::bcf_hdr_subset(header.inner, samples.len() as i32, name_pointers.as_ptr(), imap.as_mut_ptr() as *mut i32)
        };
        if inner.is_null() {
            Err(())
        }
        else {
            Ok(Header { inner: inner, subset: Some(imap) })
        }
    }

    pub fn push_sample(&mut self, sample: &[u8]) -> &mut Self {
        unsafe { htslib::vcf::bcf_hdr_add_sample(self.inner, ffi::CString::new(sample).unwrap().as_ptr()) };
        self
    }

    /// Add a record to the header.
    pub fn push_record(&mut self, record: &[u8]) -> &mut Self {
        unsafe { htslib::vcf::bcf_hdr_append(self.inner, ffi::CString::new(record).unwrap().as_ptr()) };
        self
    }

    pub fn remove_info(&mut self, tag: &[u8]) -> &mut Self {
        unsafe {
            htslib::vcf::bcf_hdr_remove(self.inner, htslib::vcf::BCF_HL_INFO, tag.as_ptr() as *const i8);
        }
        self
    }

    pub fn remove_format(&mut self, tag: &[u8]) -> &mut Self {
        unsafe {
            htslib::vcf::bcf_hdr_remove(self.inner, htslib::vcf::BCF_HL_FMT, tag.as_ptr() as *const i8);
        }
        self
    }
}


impl Drop for Header {
    fn drop(&mut self) {
        unsafe { htslib::vcf::bcf_hdr_destroy(self.inner) };
    }
}



pub struct HeaderView {
    pub inner: *mut htslib::vcf::bcf_hdr_t,
}


impl HeaderView {
    pub fn new(inner: *mut htslib::vcf::bcf_hdr_t) -> Self {
        HeaderView { inner: inner }
    }

    #[inline]
    fn inner(&self) -> htslib::vcf::bcf_hdr_t {
        unsafe { (*self.inner) }
    }

    pub fn sample_count(&self) -> u32 {
        self.inner().n[htslib::vcf::BCF_DT_SAMPLE as usize] as u32
    }

    pub fn samples(&self) -> Vec<&[u8]> {
        let names = unsafe { slice::from_raw_parts(self.inner().samples, self.sample_count() as usize) };
        names.iter().map(|name| unsafe { ffi::CStr::from_ptr(*name).to_bytes() }).collect()
    }

    pub fn rid2name(&self, rid: u32) -> &[u8] {
        unsafe {
            let dict = self.inner().id[htslib::vcf::BCF_DT_CTG as usize];
            let ptr = (*dict.offset(rid as isize)).key;
            ffi::CStr::from_ptr(ptr).to_bytes()
        }
    }
}