pileuphi_lib 0.9.3

High-throughput, extensible SAM/BAM pileup generation library
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use crate::errors::{Error, ErrorKind};
use rust_htslib::{bam::Record, htslib::sam_prob_realn};

const REALN_FAIL: i32 = 4;

// Method to realign record using htslib's internal realignment tools.
pub fn realign_record(r: &mut Record, ref_seq: &[u8], ref_len: i64, flag: u32) -> Result<i32, Error> {
    unsafe {
        let ptr: *const i8 = ref_seq.as_ptr() as *const i8;
        let ret = sam_prob_realn(r.inner_mut(), ptr, ref_len, flag as std::os::raw::c_int);
        if ret == REALN_FAIL {
            let readname = std::str::from_utf8(r.qname()).unwrap_or("READ QNAME INVALID UTF-8");
            Err(Error::from(ErrorKind::BAQFailed(readname.to_string())))
        } else {
            Ok(ret)
        }
    }
}