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Minor Improvements #2

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109 changes: 74 additions & 35 deletions src/merge.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ use datafusion::{
common::JoinType,
functions_aggregate::expr_fn::first_value,
prelude::{
DataFrame, cast, col, concat, concat_ws, encode, left, length, lit, nullif, sha256, to_hex,
cast, col, concat, concat_ws, encode, left, length, lit, nullif, sha256, to_hex, DataFrame, SessionContext
},
};
use noodles::{
Expand Down Expand Up @@ -47,6 +47,15 @@ mod flip;
mod report;
mod union;

enum MergeType {
Exact,
Locus,
ExactBreakend,
Approx,
Near,
Flip,
}

pub async fn merge_vcfs(
out: &str,
vcf: &Vec<String>,
Expand Down Expand Up @@ -85,46 +94,30 @@ pub async fn merge_vcfs(
acc = Some(df)
}
}
let orig = acc.unwrap();
let orig = orig
let results = acc.unwrap();
let mut results = results
.with_column("row_key", cast(col("row_id"), DataType::UInt32))?
.with_column("vix_count", lit(1))?
.with_column("vix_set", col("vix"))?
.with_column("flip", lit(false))?
.with_column("criteria", nullif(lit(""), lit("")))?;

let mut results = orig.clone();

if true {
log::info!("looking for exact matches on indel type variants");
let join = full_exact_indel_join(results.clone(), n)?;
results = merge_with(results, join, &ctx, "exact").await?;
}
if true {
log::info!("looking for almost exact matches on insertions");
let join = full_exact_locus_ins_join(results.clone(), n, &options)?;
results = merge_with(results, join, &ctx, "locus").await?;
}
if true {
log::info!("looking for exact matches on breakends");
let join = full_exact_bnd(results.clone(), n)?;
results = merge_with(results, join, &ctx, "exact").await?;
}
if true {
log::info!("looking for approximate matches on breakends");
let join = approx_bnd_join(results.clone(), n, &options)?;
results = merge_with(results, join, &ctx, "approx").await?;
}
if true {
log::info!("looking for nearby matches on indel type variants");
let join = approx_near_join(results.clone(), n, &options, &ctx).await?;
results = merge_with(results, join, &ctx, "near").await?;
}
if options.allow_breakend_flipping {
log::info!("looking for breakends we can flip");
let join = approx_flipped_bnd_join(results.clone(), n, &options)?;
results = merge_with(results, join, &ctx, "flip").await?;
}
let enabled_merges = vec![
MergeType::Exact,
MergeType::Locus,
MergeType::ExactBreakend,
MergeType::Approx,
MergeType::Near,
MergeType::Flip,
];

results = apply_enabled_merges(
results,
&enabled_merges,
n,
&options,
&ctx,
).await?;

let mut reference = None;
if let Some(reference_filename) = &options.reference {
Expand Down Expand Up @@ -382,6 +375,52 @@ pub async fn merge_vcfs(
Ok(())
}

async fn apply_enabled_merges(
mut results: DataFrame,
enabled_merges: &[MergeType],
n: usize,
options: &MergeOptions,
ctx: &SessionContext,
) -> std::io::Result<DataFrame> {
for m in enabled_merges {
match m {
MergeType::Exact => {
log::info!("looking for exact matches on indel type variants");
let join = full_exact_indel_join(results.clone(), n)?;
results = merge_with(results, join, &ctx, "exact").await?;
}
MergeType::Locus => {
log::info!("looking for almost exact matches on insertions");
let join = full_exact_locus_ins_join(results.clone(), n, &options)?;
results = merge_with(results, join, &ctx, "locus").await?;
}
MergeType::ExactBreakend => {
log::info!("looking for exact matches on breakends");
let join = full_exact_bnd(results.clone(), n)?;
results = merge_with(results, join, &ctx, "exact").await?;
}
MergeType::Approx =>{
log::info!("looking for approximate matches on breakends");
let join = approx_bnd_join(results.clone(), n, &options)?;
results = merge_with(results, join, &ctx, "approx").await?;
}
MergeType::Near => {
log::info!("looking for nearby matches on indel type variants");
let join = approx_near_join(results.clone(), n, &options, &ctx).await?;
results = merge_with(results, join, &ctx, "near").await?;
}
MergeType::Flip => {
if options.allow_breakend_flipping {
log::info!("looking for breakends we can flip");
let join = approx_flipped_bnd_join(results.clone(), n, &options)?;
results = merge_with(results, join, &ctx, "flip").await?;
}
}
}
}
Ok(results)
}

fn load_chroms(path: &str) -> std::io::Result<ChromSet> {
let reader = autocompress::autodetect_open(path)?;
let mut reader: vcf::io::Reader<Box<dyn BufRead>> =
Expand Down