Madhava/wasm reporting

.gitmodules

@@ -1,6 +1,6 @@
 [submodule "monty"]
 	path = monty
-	url = git@github.com:pydantic/monty.git
+	url = git@github.com:madhavajay/monty.git
 [submodule "noodles"]
 	path = noodles
 	url = git@github.com:madhavajay/noodles.git

rust/bioscript-cli/src/cli_bootstrap.rs

@@ -369,6 +369,7 @@ fn run_cli_script(
         RuntimeConfig {
             limits: options.limits,
             loader: options.loader,
+            ..RuntimeConfig::default()
         },
     )
     .map_err(|err| err.to_string())?;

rust/bioscript-cli/src/report_execution.rs

@@ -205,6 +205,7 @@ fn run_bioscript_analysis_script(
         RuntimeConfig {
             limits,
             loader: loader.clone(),
+            ..RuntimeConfig::default()
         },
     )
     .map_err(|err| err.to_string())?;

rust/bioscript-ffi/src/run_file.rs

@@ -35,8 +35,15 @@ pub fn run_file_request(request: RunFileRequest) -> Result<RunFileResult, String
         run_auto_index(&request, &runtime_root, &mut loader, &mut ffi_timings)?;
     }
 
-    let runtime = BioscriptRuntime::with_config(runtime_root, RuntimeConfig { limits, loader })
-        .map_err(|err| err.to_string())?;
+    let runtime = BioscriptRuntime::with_config(
+        runtime_root,
+        RuntimeConfig {
+            limits,
+            loader,
+            ..RuntimeConfig::default()
+        },
+    )
+    .map_err(|err| err.to_string())?;
     let inputs = runtime_inputs(&request);
 
     runtime

rust/bioscript-formats/src/genotype.rs

@@ -1219,28 +1219,11 @@ mod tests {
                 ..GenotypeLoadOptions::default()
             },
         };
-        for variant in [
-            VariantSpec::default(),
-            VariantSpec {
-                grch38: Some(locus("1", 10, 10)),
-                alternate: Some("G".to_owned()),
-                kind: Some(VariantKind::Snp),
-                ..VariantSpec::default()
-            },
-            VariantSpec {
-                grch38: Some(locus("1", 10, 10)),
-                reference: Some("AT".to_owned()),
-                alternate: Some("G".to_owned()),
-                kind: Some(VariantKind::Snp),
-                ..VariantSpec::default()
-            },
-        ] {
-            assert!(
-                lookup_indexed_vcf_variants(&indexed, &[variant])
-                    .unwrap()
-                    .is_none()
-            );
-        }
+        assert!(
+            lookup_indexed_vcf_variants(&indexed, &[VariantSpec::default()])
+                .unwrap()
+                .is_none()
+        );
         let err = lookup_indexed_vcf_variants(
             &indexed,
             &[VariantSpec {

rust/bioscript-formats/src/genotype/vcf.rs

@@ -17,16 +17,14 @@ use super::{
     describe_query, genotype_from_vcf_gt, is_bgzf_path, types::VcfBackend, variant_sort_key,
 };
 
-mod indexed;
 mod matching;
 mod reader;
 
-use indexed::observe_indexed_vcf_variant;
+use matching::imputed_reference_observation;
 pub(crate) use matching::{
     choose_variant_locus_for_assembly, normalize_chromosome_name, vcf_row_matches_variant,
 };
-use matching::{first_single_base_allele, imputed_reference_observation};
-pub use reader::observe_vcf_snp_with_reader;
+pub use reader::{observe_vcf_snp_with_reader, observe_vcf_variant_with_reader};
 
 #[derive(Debug, Clone)]
 pub(crate) struct ParsedVcfRow {
@@ -208,12 +206,6 @@ pub(crate) fn lookup_indexed_vcf_variants(
         let Some(locus) = choose_variant_locus_for_assembly(variant, detected_assembly) else {
             return Ok(None);
         };
-        if matches!(variant.kind, None | Some(VariantKind::Snp))
-            && (first_single_base_allele(variant.reference.as_deref()).is_none()
-                || first_single_base_allele(variant.alternate.as_deref()).is_none())
-        {
-            return Ok(None);
-        }
         indexed_variants.push((idx, variant, locus));
     }
 
@@ -234,25 +226,15 @@ pub(crate) fn lookup_indexed_vcf_variants(
     );
 
     let mut results = vec![VariantObservation::default(); variants.len()];
-    let label = backend.path.display().to_string();
     for (idx, variant, locus) in indexed_variants {
-        let observation = if let (Some(reference), Some(alternate), true) = (
-            first_single_base_allele(variant.reference.as_deref()),
-            first_single_base_allele(variant.alternate.as_deref()),
-            matches!(variant.kind, None | Some(VariantKind::Snp)),
-        ) {
-            observe_vcf_snp_with_reader(
-                &mut indexed,
-                &label,
-                &locus,
-                reference,
-                alternate,
-                variant.rsids.first().cloned(),
-                detected_assembly,
-            )?
-        } else {
-            observe_indexed_vcf_variant(&mut indexed, &label, variant, &locus, detected_assembly)?
-        };
+        let observation = observe_vcf_variant_with_reader(
+            &mut indexed,
+            &backend.path.display().to_string(),
+            &locus,
+            variant,
+            variant.rsids.first().cloned(),
+            detected_assembly,
+        )?;
         results[idx] = if backend.options.impute_vcf_missing_as_reference
             && observation.genotype.is_none()
             && observation