@@ -141,17 +141,17 @@ pub mod vcf_header {
141141 use crate :: ped:: { Disease , PedigreeByName , Sex } ;
142142
143143 /// Major VCF version to use.
144- static FILE_FORMAT_MAJOR : u32 = 4 ;
144+ pub ( crate ) const FILE_FORMAT_MAJOR : u32 = 4 ;
145145 /// Minor VCF version to use.
146- static FILE_FORMAT_MINOR : u32 = 3 ;
146+ pub ( crate ) const FILE_FORMAT_MINOR : u32 = 3 ;
147147 /// The string to write out as the source.
148- static SOURCE : & str = "mehari" ;
148+ pub ( crate ) const SOURCE : & str = "mehari" ;
149149
150150 /// Construct VCF header.
151151///
152152/// # Arguments
153153///
154- /// * `assembly` - Genome assembly to use. The canonical contigs will be taken from here.
154+ /// * `assembly` - Genome assembly to use. The canonical contigs will be taken from here.
155155/// * `pedigree` - Pedigree to use. Will write out appropriate `META`, `SAMPLE`, and
156156/// `PEDIGREE` header lines.
157157/// * `date` - Date to use for the `fileDate` header line.
@@ -514,6 +514,8 @@ pub mod vcf_header {
514514 }
515515}
516516
517+ use crate :: annotate:: strucvars:: vcf_header:: { FILE_FORMAT_MAJOR , FILE_FORMAT_MINOR } ;
518+
517519/// Writing of structural variants to VarFish TSV files.
518520struct VarFishStrucvarTsvWriter {
519521 /// The actual (compressed) text output writer.
@@ -864,8 +866,10 @@ impl AsyncAnnotatedVariantWriter for VarFishStrucvarTsvWriter {
864866 entry. gt = Some ( gt. clone ( ) ) ;
865867 }
866868 ( "GT" , Some ( sample:: Value :: Genotype ( gt) ) ) => {
867- // FIXME get file format version from header
868- let gt = genotype_string ( gt, FileFormat :: new ( 4 , 0 ) ) ;
869+ let gt = genotype_string (
870+ gt,
871+ FileFormat :: new ( FILE_FORMAT_MAJOR , FILE_FORMAT_MINOR ) ,
872+ ) ;
869873 entry. gt = Some ( gt) ;
870874 }
871875 ( "FT" , Some ( sample:: Value :: String ( ft) ) ) => {
@@ -2018,6 +2022,8 @@ mod conv {
20182022 use super :: VarFishStrucvarTsvRecord ;
20192023 use super :: VcfRecordConverter ;
20202024
2025+ use super :: vcf_header:: { FILE_FORMAT_MAJOR , FILE_FORMAT_MINOR } ;
2026+
20212027 /// Helper function that extract the CIPOS and CIEND fields from `vcf_record` into `tsv_record`.
20222028pub fn extract_standard_cis (
20232029 vcf_record : & VcfRecord ,
@@ -2097,8 +2103,10 @@ mod conv {
20972103 process_gt ( & mut entries, sample_no, gt, pedigree, tsv_record) ;
20982104 }
20992105 ( "GT" , Some ( sample:: Value :: Genotype ( gt) ) ) => {
2100- // FIXME get file format version from header
2101- let gt = genotype_string ( gt, FileFormat :: new ( 4 , 0 ) ) ;
2106+ let gt = genotype_string (
2107+ gt,
2108+ FileFormat :: new ( FILE_FORMAT_MAJOR , FILE_FORMAT_MINOR ) ,
2109+ ) ;
21022110 process_gt ( & mut entries, sample_no, & gt, pedigree, tsv_record) ;
21032111 }
21042112 // Obtain `GenotypeInfo::cn` from `FORMAT/CN`.
@@ -2183,8 +2191,10 @@ mod conv {
21832191 process_gt ( & mut entries, sample_no, gt, pedigree, tsv_record) ;
21842192 }
21852193 ( "GT" , Some ( sample:: Value :: Genotype ( gt) ) ) => {
2186- // FIXME get file format version from header
2187- let gt = genotype_string ( gt, FileFormat :: new ( 4 , 0 ) ) ;
2194+ let gt = genotype_string (
2195+ gt,
2196+ FileFormat :: new ( FILE_FORMAT_MAJOR , FILE_FORMAT_MINOR ) ,
2197+ ) ;
21882198 process_gt ( & mut entries, sample_no, & gt, pedigree, tsv_record) ;
21892199 }
21902200 // Obtain `GenotypeInfo::gq` from `FORMAT/GQ`.
@@ -2281,8 +2291,10 @@ mod conv {
22812291 process_gt ( & mut entries, sample_no, gt, pedigree, tsv_record) ;
22822292 }
22832293 ( "GT" , Some ( sample:: Value :: Genotype ( gt) ) ) => {
2284- // FIXME get file format version from header
2285- let gt = genotype_string ( gt, FileFormat :: new ( 4 , 0 ) ) ;
2294+ let gt = genotype_string (
2295+ gt,
2296+ FileFormat :: new ( FILE_FORMAT_MAJOR , FILE_FORMAT_MINOR ) ,
2297+ ) ;
22862298 process_gt ( & mut entries, sample_no, & gt, pedigree, tsv_record) ;
22872299 }
22882300 // Obtain `GenotypeInfo::pev` from `FORMAT/PE`; no pec is computed.
@@ -2403,8 +2415,10 @@ mod conv {
24032415 process_gt ( & mut entries, sample_no, gt, pedigree, tsv_record) ;
24042416 }
24052417 ( "GT" , Some ( sample:: Value :: Genotype ( gt) ) ) => {
2406- // FIXME get file format version from header
2407- let gt = genotype_string ( gt, FileFormat :: new ( 4 , 0 ) ) ;
2418+ let gt = genotype_string (
2419+ gt,
2420+ FileFormat :: new ( FILE_FORMAT_MAJOR , FILE_FORMAT_MINOR ) ,
2421+ ) ;
24082422 process_gt ( & mut entries, sample_no, & gt, pedigree, tsv_record) ;
24092423 }
24102424 // Obtain `GenotypeInfo::cn` from `FORMAT/CN`.
@@ -2471,8 +2485,10 @@ mod conv {
24712485 process_gt ( & mut entries, sample_no, gt, pedigree, tsv_record) ;
24722486 }
24732487 ( "GT" , Some ( sample:: Value :: Genotype ( gt) ) ) => {
2474- // FIXME get file format version from header
2475- let gt = genotype_string ( gt, FileFormat :: new ( 4 , 0 ) ) ;
2488+ let gt = genotype_string (
2489+ gt,
2490+ FileFormat :: new ( FILE_FORMAT_MAJOR , FILE_FORMAT_MINOR ) ,
2491+ ) ;
24762492 process_gt ( & mut entries, sample_no, & gt, pedigree, tsv_record) ;
24772493 }
24782494 // Obtain `GenotypeInfo::gq` from `FORMAT/GQ`.
@@ -2572,8 +2588,10 @@ mod conv {
25722588 process_gt ( & mut entries, sample_no, gt, pedigree, tsv_record) ;
25732589 }
25742590 ( "GT" , Some ( sample:: Value :: Genotype ( gt) ) ) => {
2575- // FIXME get file format version from header
2576- let gt = genotype_string ( gt, FileFormat :: new ( 4 , 0 ) ) ;
2591+ let gt = genotype_string (
2592+ gt,
2593+ FileFormat :: new ( FILE_FORMAT_MAJOR , FILE_FORMAT_MINOR ) ,
2594+ ) ;
25772595 process_gt ( & mut entries, sample_no, & gt, pedigree, tsv_record) ;
25782596 }
25792597 // Obtain `GenotypeInfo::gq` from `FORMAT/GL`.
@@ -2678,8 +2696,10 @@ mod conv {
26782696 process_gt ( & mut entries, sample_no, gt, pedigree, tsv_record) ;
26792697 }
26802698 ( "GT" , Some ( sample:: Value :: Genotype ( gt) ) ) => {
2681- // FIXME get file format version from header
2682- let gt = genotype_string ( gt, FileFormat :: new ( 4 , 0 ) ) ;
2699+ let gt = genotype_string (
2700+ gt,
2701+ FileFormat :: new ( FILE_FORMAT_MAJOR , FILE_FORMAT_MINOR ) ,
2702+ ) ;
26832703 process_gt ( & mut entries, sample_no, & gt, pedigree, tsv_record) ;
26842704 }
26852705 // Obtain `GenotypeInfo::gq` from `FORMAT/GQ`.
@@ -2876,8 +2896,10 @@ mod conv {
28762896 process_gt ( & mut entries, sample_no, gt, pedigree, tsv_record) ;
28772897 }
28782898 ( "GT" , Some ( sample:: Value :: Genotype ( gt) ) ) => {
2879- // FIXME get file format version from header
2880- let gt = genotype_string ( gt, FileFormat :: new ( 4 , 0 ) ) ;
2899+ let gt = genotype_string (
2900+ gt,
2901+ FileFormat :: new ( FILE_FORMAT_MAJOR , FILE_FORMAT_MINOR ) ,
2902+ ) ;
28812903 process_gt ( & mut entries, sample_no, & gt, pedigree, tsv_record) ;
28822904 }
28832905 // Obtain `GenotypeInfo::gq` from `FORMAT/GQ`.
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