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Merged
mandysulli merged 2 commits into from
Jul 9, 2025
Merged

Dev #25

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848b446
update docs
mandysulli Jul 8, 2025
f0025b4
tweaking package to include subtype as a filter when filtering varian…
mandysulli Jul 9, 2025
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1 change: 1 addition & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -8,3 +8,4 @@
*test*
*lock
**/*lock
*.crt
3 changes: 1 addition & 2 deletions Cargo.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -19,5 +19,4 @@ zoe = { version = "0.0.19", default-features = false, features = [
] }

[profile.release]
strip = true
csv = "1.3.1"
strip = true
11 changes: 10 additions & 1 deletion variants_of_interest_table/src/main.rs
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Expand Up @@ -96,6 +96,7 @@ pub struct RefInput {

#[derive(Deserialize, Debug)]
pub struct MutsOfInterestInput {
subtype: String,
protein: String,
aa_position: String,
aa: String,
Expand All @@ -121,6 +122,7 @@ pub struct Entry<'a> {
impl Entry<'_> {
fn update_entry_from_alignment(
&mut self,
subtype: &str,
aa_1: u8,
aa_2: u8,
muts_columns: &Vec<MutsOfInterestInput>,
Expand All @@ -130,7 +132,10 @@ impl Entry<'_> {
let hold_aa_mut = self.aa_mut.to_string();
//aa differences that are also in our "mutations of interest" list are written to file
for muts_entry in muts_columns {
if self.protein == muts_entry.protein
//println!("ref {}", subtype);
//println!("mut {}", muts_entry.subtype);
if subtype == muts_entry.subtype
&& self.protein == muts_entry.protein
&& self.aa_position.to_string() == muts_entry.aa_position
{
if hold_aa_mut == muts_entry.aa {
Expand Down Expand Up @@ -296,6 +301,7 @@ fn main() -> Result<(), Box<dyn Error>> {

//aa difference moved forward in process;
if entry.update_entry_from_alignment(
&ref_entry.subtype,
ref_aa,
query_aa,
&muts_interest,
Expand Down Expand Up @@ -346,6 +352,7 @@ fn main() -> Result<(), Box<dyn Error>> {

//aa difference moved forward in process;
if entry.update_entry_from_alignment(
&ref_entry.subtype,
partial_codon,
partial_codon,
&muts_interest,
Expand Down Expand Up @@ -435,6 +442,7 @@ fn main() -> Result<(), Box<dyn Error>> {

//aa difference moved forward in process;
if entry.update_entry_from_alignment(
&ref_entry.subtype,
ref_aa,
query_aa,
&muts_interest,
Expand Down Expand Up @@ -485,6 +493,7 @@ fn main() -> Result<(), Box<dyn Error>> {

//aa difference moved forward in process;
if entry.update_entry_from_alignment(
&ref_entry.subtype,
partial_codon,
partial_codon,
&muts_interest,
Expand Down