@@ -557,7 +557,7 @@ pub struct GenotypeInfo {
557557 pub amq : Option < i32 > ,
558558 /// Copy number.
559559#[ serde( default , skip_serializing_if = "Option::is_none" ) ]
560- pub cn : Option < i32 > ,
560+ pub cn : Option < f32 > ,
561561 /// Average normalized coverage.
562562#[ serde( default , skip_serializing_if = "Option::is_none" ) ]
563563 pub anc : Option < f32 > ,
@@ -887,7 +887,7 @@ impl AsyncAnnotatedVariantWriter for VarFishStrucvarTsvWriter {
887887 entry. src = Some ( * src) ;
888888 }
889889 // amq
890- ( "CN" , Some ( sample:: Value :: Integer ( cn) ) ) => {
890+ ( "CN" , Some ( sample:: Value :: Float ( cn) ) ) => {
891891 entry. cn = Some ( * cn) ;
892892 }
893893 // anc
@@ -1403,7 +1403,7 @@ impl TryInto<VcfRecord> for VarFishStrucvarTsvRecord {
14031403 . amq
14041404 . as_ref( )
14051405 . map( |amq| sample:: Value :: Integer ( * amq) ) ,
1406- genotype. cn. as_ref( ) . map( |cn| sample:: Value :: Integer ( * cn) ) ,
1406+ genotype. cn. as_ref( ) . map( |cn| sample:: Value :: Float ( * cn) ) ,
14071407 genotype. anc. as_ref( ) . map( |anc| sample:: Value :: Float ( * anc) ) ,
14081408 genotype. pc. as_ref( ) . map( |pc| sample:: Value :: Integer ( * pc) ) ,
14091409 ] ) ;
@@ -2102,9 +2102,12 @@ mod conv {
21022102 process_gt ( & mut entries, sample_no, & gt, pedigree, tsv_record) ;
21032103 }
21042104 // Obtain `GenotypeInfo::cn` from `FORMAT/CN`.
2105- ( "CN" , Some ( sample:: Value :: Integer ( cn) ) ) => {
2105+ ( "CN" , Some ( sample:: Value :: Float ( cn) ) ) => {
21062106 entries[ sample_no] . cn = Some ( * cn) ;
21072107 }
2108+ ( "CN" , Some ( sample:: Value :: Integer ( cn) ) ) => {
2109+ entries[ sample_no] . cn = Some ( * cn as f32 ) ;
2110+ }
21082111 // Obtain `GenotypeInfo::gq` from `FORMAT/GQ`.
21092112 ( "GQ" , Some ( sample:: Value :: Integer ( gq) ) ) => {
21102113 entries[ sample_no] . gq = Some ( * gq) ;
@@ -2287,9 +2290,12 @@ mod conv {
22872290 entries[ sample_no] . pev = Some ( * pe) ;
22882291 }
22892292 // Obtain `GenotypeInfo::cn` from `FORMAT/CN`.
2290- ( "CN" , Some ( sample:: Value :: Integer ( cn) ) ) => {
2293+ ( "CN" , Some ( sample:: Value :: Float ( cn) ) ) => {
22912294 entries[ sample_no] . cn = Some ( * cn) ;
22922295 }
2296+ ( "CN" , Some ( sample:: Value :: Integer ( cn) ) ) => {
2297+ entries[ sample_no] . cn = Some ( * cn as f32 ) ;
2298+ }
22932299 // Obtain `GenotypeInfo::pc` from `FORMAT/BC`.
22942300 ( "BC" , Some ( sample:: Value :: Integer ( bc) ) ) => {
22952301 entries[ sample_no] . pc = Some ( * bc) ;
@@ -2402,9 +2408,12 @@ mod conv {
24022408 process_gt ( & mut entries, sample_no, & gt, pedigree, tsv_record) ;
24032409 }
24042410 // Obtain `GenotypeInfo::cn` from `FORMAT/CN`.
2405- ( "CN" , Some ( sample:: Value :: Integer ( cn) ) ) => {
2411+ ( "CN" , Some ( sample:: Value :: Float ( cn) ) ) => {
24062412 entries[ sample_no] . cn = Some ( * cn) ;
24072413 }
2414+ ( "CN" , Some ( sample:: Value :: Integer ( cn) ) ) => {
2415+ entries[ sample_no] . cn = Some ( * cn as f32 ) ;
2416+ }
24082417 // Obtain `GenotypeInfo::pc` from `FORMAT/NP`.
24092418 ( "NP" , Some ( sample:: Value :: Integer ( np) ) ) => {
24102419 entries[ sample_no] . pc = Some ( * np) ;
@@ -2780,15 +2789,24 @@ mod conv {
27802789 . unwrap_or_else ( || panic ! ( "sample must be in pedigree: {:?}" , & entry. name) )
27812790 . sex ;
27822791 let expected_cn = match ( sex, is_chr_x, is_chr_y) {
2783- ( _, false , false ) => Some ( 2 ) ,
2784- ( Sex :: Male , false , true ) | ( Sex :: Male , true , false ) => Some ( 1 ) ,
2785- ( Sex :: Female , true , false ) => Some ( 2 ) ,
2792+ ( _, false , false ) => Some ( 2. ) ,
2793+ ( Sex :: Male , false , true ) | ( Sex :: Male , true , false ) => Some ( 1. ) ,
2794+ ( Sex :: Female , true , false ) => Some ( 2. ) ,
27862795 // do not count, sex missing or conflicting chromosome
27872796 _ => None ,
27882797 } ;
27892798 if let ( Some ( cn) , Some ( expected_cn) ) = ( entry. cn , expected_cn) {
27902799 let delta = ( cn - expected_cn) . abs ( ) ;
2791- if expected_cn == 1 {
2800+ if delta. round ( ) != delta {
2801+ tracing:: warn!(
2802+ "Fractional CN value: {} and expected {} for sample {}, rounding." ,
2803+ cn,
2804+ expected_cn,
2805+ entry. name,
2806+ ) ;
2807+ }
2808+ let delta = delta. round ( ) as i32 ;
2809+ if expected_cn == 1. {
27922810 tsv_record. num_hemi_alt += delta;
27932811 } else if delta == 0 {
27942812 tsv_record. num_hom_ref += 1 ;
@@ -3988,7 +4006,7 @@ mod test {
39884006 src: Some ( 143 ) ,
39894007 srv: Some ( 43 ) ,
39904008 amq: Some ( 99 ) ,
3991- cn: Some ( 1 ) ,
4009+ cn: Some ( 1. ) ,
39924010 anc: Some ( 0.5 ) ,
39934011 pc: Some ( 10 ) ,
39944012 } ,
@@ -4002,7 +4020,7 @@ mod test {
40024020 src: Some ( 44 ) ,
40034021 srv: Some ( 0 ) ,
40044022 amq: Some ( 98 ) ,
4005- cn: Some ( 2 ) ,
4023+ cn: Some ( 2. ) ,
40064024 anc: Some ( 1.0 ) ,
40074025 pc: Some ( 10 ) ,
40084026 } ,
@@ -4016,7 +4034,7 @@ mod test {
40164034 src: Some ( 33 ) ,
40174035 srv: Some ( 0 ) ,
40184036 amq: Some ( 97 ) ,
4019- cn: Some ( 2 ) ,
4037+ cn: Some ( 2. ) ,
40204038 anc: Some ( 1.0 ) ,
40214039 pc: Some ( 10 ) ,
40224040 } ,
@@ -4064,7 +4082,7 @@ mod test {
40644082 src: Some ( 143 ) ,
40654083 srv: Some ( 43 ) ,
40664084 amq: Some ( 99 ) ,
4067- cn: Some ( 1 ) ,
4085+ cn: Some ( 1. ) ,
40684086 anc: Some ( 0.5 ) ,
40694087 pc: Some ( 10 ) ,
40704088 } ,
@@ -4078,7 +4096,7 @@ mod test {
40784096 src: Some ( 143 ) ,
40794097 srv: Some ( 43 ) ,
40804098 amq: Some ( 99 ) ,
4081- cn: Some ( 1 ) ,
4099+ cn: Some ( 1. ) ,
40824100 anc: Some ( 0.5 ) ,
40834101 pc: Some ( 10 ) ,
40844102 } ,
@@ -4092,7 +4110,7 @@ mod test {
40924110 src: Some ( 143 ) ,
40934111 srv: Some ( 43 ) ,
40944112 amq: Some ( 99 ) ,
4095- cn: Some ( 1 ) ,
4113+ cn: Some ( 1. ) ,
40964114 anc: Some ( 0.5 ) ,
40974115 pc: Some ( 10 ) ,
40984116 } ,
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