bcf/writer/vcf_record: Use contig string map to find index of contig

This previously used the position of the contig in the header, but BCF allows records to override their positions using the `IDX` field, requiring a contig string map.
zaeleus · Jan 11, 2022 · 9da12e7 · 9da12e7
1 parent f1c5d59
commit 9da12e7
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Showing 3 changed files with 14 additions and 5 deletions.
diff --git a/noodles-bcf/CHANGELOG.md b/noodles-bcf/CHANGELOG.md
@@ -47,6 +47,12 @@
   * bcf/writer: `Writer::write_vcf_record` now takes `StringMaps` instead of
     `StringMap`.
 
+  * bcf/writer/vcf_record: Use contig string map to find index of contig.
+
+    This previously used the position of the contig in the header, but BCF
+    allows records to override their positions using the `IDX` field, requiring
+    a contig string map.
+
 [#64]: https://github.com/zaeleus/noodles/issues/64
 
 ### Removed

diff --git a/noodles-bcf/src/writer/vcf_record.rs b/noodles-bcf/src/writer/vcf_record.rs
@@ -58,7 +58,7 @@ mod tests {
             .add_contig(vcf::header::Contig::new("sq0"))
             .build();
 
-        let string_maps = StringMaps::default();
+        let string_maps = StringMaps::from(&header);
 
         let record = vcf::Record::builder()
             .set_chromosome("sq0".parse()?)

diff --git a/noodles-bcf/src/writer/vcf_record/site.rs b/noodles-bcf/src/writer/vcf_record/site.rs
@@ -6,7 +6,10 @@ use byteorder::{LittleEndian, WriteBytesExt};
 use noodles_vcf as vcf;
 
 use crate::{
-    header::{string_maps::StringStringMap, StringMaps},
+    header::{
+        string_maps::{ContigStringMap, StringStringMap},
+        StringMaps,
+    },
     record::value::{Float, Value},
     writer::value::write_value,
 };
@@ -24,7 +27,7 @@ pub fn write_site<W>(
 where
     W: Write,
 {
-    write_chrom(writer, header.contigs(), record.chromosome())?;
+    write_chrom(writer, string_maps.contigs(), record.chromosome())?;
     write_pos(writer, record.position())?;
 
     let end = record
@@ -56,7 +59,7 @@ where
 
 fn write_chrom<W>(
     writer: &mut W,
-    contigs: &vcf::header::Contigs,
+    contig_string_map: &ContigStringMap,
     chromosome: &vcf::record::Chromosome,
 ) -> io::Result<()>
 where
@@ -65,7 +68,7 @@ where
     use vcf::record::Chromosome;
 
     let chrom = match chromosome {
-        Chromosome::Name(name) => contigs
+        Chromosome::Name(name) => contig_string_map
             .get_index_of(name)
             .ok_or_else(|| {
                 io::Error::new(