Dev (#57)

* fix changlog

* Check mira version

* update changelog

* Add prepmirareports (#40)

* creating the prepare-mira-reports subprocess

* fix argument passing

* fix error handling

* using polars to read in samplesheet and convert to df

* add code for creating cov df

* adding utils..

* Add lib.rs

* add read df creation

* df filtering and converting for vtype df

* Use a maintained version of YAML or switch to something else later

* Binary only crate

* De-lint some more, but please check

* Continue to prune unwanted features

* working sample name back into df

* going back to rust data processing in structures. Removing polars. polars df code saved in dataframes_polars.rs but not imported into app

* clean up the process_txt_with_sample function and added allele table processing

* add in indel processing

* renaming dataframe.rs to data_ingest.rs. Settting up structure for writing file out

* added prelim logic to write to json

* getting the stage of reads data

* tweaking header and columns situation

* add csv writing out logic

* adding in parquet writing logic - dicey rightnow -working to improve

* full parq fix

* cleaning up

* read in amened_consensus

* added dais structs

* read in dais-ribosome data to structs

* tweak DaisSeqData struct

* working in dais ref struct reading

* read out coverage info. Added platform and runid handling

* update structs

* writing more csv and josn files. Adding more specific types were I can.

* scoop up ref lengths

* striping down the cargo.toml a bit

* write out ref_data.json with it's unique pattern

* clean up

* clean up paths with @sammysheep

* aavar computing for flu. make dais_vars.json and aavars.csv. started data_processing.rs.

* organizing. kind of,

* hold qc_statement progress

* tweaking container (#34)

* qc_statement processing

* Var of int format tweak (#36)

* tweaking container (#33)

* coloumns of output tweaked

* tweaked to specifc positions not covered

* create positions_of_interest subprocess

* add variant of int logic for tweaking

* tweaked to print all positions whether codon difference or not

* converting read df for irma summary merge and starting the coverage calcs for irma summary

* worked in sc2-spike protein handling

* fixing the ref names for sc2 situations

* tweak dais file reading to ignore the gen files

* add in sc2 and rsv handling dais data processing

* set up preliminary irma_summary

* tweaking so that we are picking up failed samples

* minor allele and indel count bug squash

* add subtype logic for flu

* adding subtype into irma_summary

* sc2 subtype handling

* bug squash

* adding metadata into irma_sumarry

* Vec references to slices

* lints

* tweaks

* tweak

* optimizing

* starting the rebuild of summary with qc values

* updating summary pass fail logic

* trash

* fix append_with_comma and unused variables

* alignment utils and lints

* so many things

* bug squash, clean up and pass_fail_handling

* calc tweaks

* clear warning

* starting the nt seq processing for fastas

* nt seq df creation for flu

* add in sc2 and rsv handling of the nt_seq_df

* start pass/fail division process

* added in sc2 ilumina handling for pass/fail dividing

* finsh al platofrm and virus pass/fail processing

* working on AA fasta handling. This code is broken, but need to store

* amino acid pass/fail processing for fasta

* little restructure. get all csv files in order.

* structure update and gh action tweak

* oops

* clearing errors and warnings

* tweak ingest - took way longer than it should have

* restructure. setup parq write out.

* coverage parq setup

* alleles, indels, nt_seq and aa_seq parq handling and tweak aa_seq csv output

* final parq file editting. plus typo fix.

* update docs. squashed some bugs.

* indel parq bug squash

* squash irma summary parq bug. convert med to i32 to cdp compatibility

* alleles json bug fix

* Maybe I fixed everything this time? who knows. all allele vs filtered allele fix for vairants. rounding decimals. irma summary tweak fo sc2-wgs.

* added in samplesheet.parq

* remove prints

* typo fix

* write out for coverage plot jsons (per sample)

* fix sc2 and rsv orf boxes in plots

* tweak for rsv and restruct

* starting the sankey plot. It's black though and I gotta make it pretty. fix reads.json for dashboard

* fix sankey color. Starting coverage_to_heatmap.rs

* finished coverage heatmap. Need to fix sc2-spike though

* fixed sc2-spike with coverage plots. Squashed much larger underlying bug where hmm_position was not being used

* pass fail heatmap. need to tweak to handle missing data better

* Add error handling for reading in files. Adding emtpy value handling for coverage_to_heatmap.rs

* clear warnings

* handling missing data in pass_fail_heatmap

* remove unnecessary function

* add barcode distribution json creation step

* fix coloring on coverage plots

* fix filtering for sankey plot

* no longer generating ref_data.json. No longer need for coverage plot.

* Add statichtmls (#52)

* preliminary writing of the statichtml. logo and tables in, but gray

* Got the barcode_distribution, pass/fail heatmap and coverage heatmap in there

* getting closers to coverage htmls per sample

* coverage and sankey plot htmlss per sample created but link broken in main html

* fix the coverage.html links in the main html

* tweak main html apperance

* fix fasta links in html

* fixed minor variant columns and create aavars csv for download

* format

* Fix indel table in html and correct nulls in runid and instrument

* formatting

* more formating

* make tables within scrolling window and sankey color update

* update coverage fig so that specific colors assigned to flu segments

* sankey block colors for flu segments match the coverage plot line colors now

* fixed centering of everything

* Update Coverage and Sankey html to not sit on each other

* all colors in compliance with CDC color palette

* pretty print statements

* pretty prints

* clear warnings

* clean up

* update changelog

* fix docker build file

* fix Undetermine subtype handling

* make outdir if doesn't exist

* clean up

* tweak

* tweak 2

* update documentation

* changlog update

---------

Co-authored-by: William Chettleburgh <zcs0@cdc.gov>
Co-authored-by: Samuel Shepard <vfn4@cdc.gov>
Co-authored-by: Sam Wiley <dzw2@cdc.gov>

* fix date and version

* updating action to trigger on tagging

* fix trigger

* update chagelog

* Mira nf compatibility fix (#55)

* compatibility tweaks and names fixes

* fixing DAIS_ribosome.seq ingest to work with MIRA-NF and fixing null values for spike protein coverages in sc2 wgs data

* update changlog

* samplesheet schema fix

* update changelog

---------

Co-authored-by: Sam Wiley <dzw2@cdc.gov>
Co-authored-by: William Chettleburgh <zcs0@cdc.gov>
Co-authored-by: Samuel Shepard <vfn4@cdc.gov>

Author: 4 people

CHANGELOG.md

@@ -3,6 +3,14 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [1.2.2] - 2025-12-23
+
+- [Amanda Sullivan](https://github.com/mandysulli)
+- [Kristine Lacek](https://github.com/kristinelacek)
+
+### `Fixed`
+- [PR #57](https://github.com/CDCgov/mira-oxide/pull/57) - Fix samplesheet.parq schema fix for handling Illumina.
+
 ## [1.2.1] - 2025-12-18
 
 - [Amanda Sullivan](https://github.com/mandysulli)

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "mira-oxide"
-version = "1.2.0"
+version = "1.2.2"
 edition = "2024"
 description = "A set of rusty tools for use in MIRA"
 

src/io/write_parquet_files.rs

@@ -738,7 +738,6 @@ pub fn write_samplesheet_to_parquet(
     match samplesheet {
         Samplesheet::Illumina(data) => {
             // Extract fields from SamplesheetI
-            let barcode_vec: Vec<Option<String>> = vec![None; data.len()];
             let sample_id_vec: Vec<String> = extract_field(&data, |item| item.sample_id.clone());
             let sample_type_vec: Vec<Option<String>> =
                 extract_field(&data, |item| item.sample_type.clone());
@@ -748,15 +747,13 @@ pub fn write_samplesheet_to_parquet(
             let instrument_vec: Vec<String> = vec![instrument.to_string(); data.len()];
 
             // Convert the vectors into Arrow columns
-            let barcode_array: ArrayRef = Arc::new(StringArray::from(barcode_vec));
             let sample_id_array: ArrayRef = Arc::new(StringArray::from(sample_id_vec));
             let sample_type_array: ArrayRef = Arc::new(StringArray::from(sample_type_vec));
             let runid_array: ArrayRef = Arc::new(StringArray::from(runid_vec));
             let instrument_array: ArrayRef = Arc::new(StringArray::from(instrument_vec));
 
             // Define the schema for the Arrow IPC file
             let fields = vec![
-                Field::new("Barcode #", DataType::Utf8, true),
                 Field::new("Sample ID", DataType::Utf8, false),
                 Field::new("Sample Type", DataType::Utf8, true),
                 Field::new("Run ID", DataType::Utf8, false),
@@ -768,7 +765,6 @@ pub fn write_samplesheet_to_parquet(
             let record_batch = RecordBatch::try_new(
                 schema.clone(),
                 vec![
-                    barcode_array,
                     sample_id_array,
                     sample_type_array,
                     runid_array,