From b472ee19789146416b3e768340207914d0f049a7 Mon Sep 17 00:00:00 2001
From: Brent Pedersen <bpederse@gmail.com>
Date: Fri, 13 Dec 2024 11:14:33 -0800
Subject: [PATCH] work on writer

---
 src/writer.rs | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/src/writer.rs b/src/writer.rs
index d00e1c3..4830b7c 100644
--- a/src/writer.rs
+++ b/src/writer.rs
@@ -2,10 +2,17 @@ use crate::position::Position;
 use crate::report::{Report, ReportFragment};
 use crate::sniff::HtsFile;
 use bio::io::bed;
+<<<<<<< HEAD
 use rust_htslib::bam;
 use rust_htslib::bcf::{self, header::HeaderView};
 use rust_htslib::htslib as hts;
+=======
+use rust_htslib::bcf::{self, header::HeaderView};
+use rust_htslib::htslib as hts;
+use rust_htslib::{bam, sam};
+>>>>>>> 1daae3a (work on writer)
 use std::mem;
+use std::path::Path;
 use std::rc::Rc;
 use std::result::Result;
 use std::string::String;
@@ -252,6 +259,7 @@ impl Writer {
                             Self::add_info_field_to_vcf_record(&mut vcf_record, cr.name(), value)?;
                         }
                     }
+                    let vcf_record = record.record;
 
                     vcf_writer.write(&vcf_record).map_err(|e| {
                         std::io::Error::new(std::io::ErrorKind::InvalidData, e.to_string())
@@ -273,6 +281,7 @@ impl Writer {
                         if let Ok(value) = cr.value(fragment) {
                             br.push_aux(self.format_value(&value).as_str());
                         }
+                        writeln!(writer)?;
                     }
 
                     if let GenomicWriter::Bed(ref mut writer) = self.writer {