Datasets:

marin-dna
/

evals_eqtl

	---
	license: apache-2.0
	tags:
	- biology
	- genomics
	- dna
	size_categories:
	- 1K<n<10K
	---

	# evals_eqtl

	Variant-effect-prediction benchmark of GTEx v8 fine-mapped eQTLs (49 tissues, pooled) vs tested-but-low-PIP variants, gene-matched 1:1 within consequence categories, MAF bins, and distance bins.

	## Description

	\| \| \|
	\|---\|---\|
	\| Positives \| GTEx v8 SuSiE fine-mapped variants with `max(PIP across tested tissues) > 0.9` \|
	\| Negatives \| `max(PIP) < 0.01` across all tested tissues; gene-matched 1:1 to positives \|
	\| Source \| [eQTL Catalogue r7](https://www.ebi.ac.uk/eqtl/), study `QTS000015` (GTEx v8), all 49 tissues × `ge` (gene-expression) quantification \|
	\| Genome build \| GRCh38 (Catalogue is hg38 native) \|
	\| Variant type \| SNVs only \|
	\| Coordinates \| 1-based (`pos` is 1-based; `ref` / `alt` are single bases) \|

	The negative pool is sourced from per-tissue full nominal sumstats (`*.all.tsv.gz`, ~3.5 GB per tissue), so it includes every variant tested in fine-mapping — including those that never reached a credible set. This is a structural improvement over earlier releases of this dataset (which sourced from a pre-filtered single-file release whose PIP floor at ~1e-4 capped the negative pool at ~1.3M variants); the current pool is ~10M tested variants.

	## Splits

	\| Split \| Variants (positives + matched negatives) \| Chromosomes \|
	\|---\|---:\|---\|
	\| `train` \| 4,612 (2,306 pos + 2,306 neg) \| odd: 1, 3, …, X \|
	\| `test` \| 3,854 (1,927 pos + 1,927 neg) \| even: 2, 4, …, Y \|
	\| total \| 8,466 (4,233 pairs) \| \|

	## Columns

	\| Column \| Type \| Description \|
	\|---\|---\|---\|
	\| `chrom`, `pos`, `ref`, `alt` \| str / int / str / str \| Variant coordinates (1-based, GRCh38) \|
	\| `label` \| bool \| `True` for high-PIP eQTL, `False` for tested-but-low-PIP matched negative \|
	\| `subset` \| str \| Consequence-group label for stratified eval (`distal`, `tss_proximal`, `non_coding_transcript_exon_variant`, `3_prime_UTR_variant`, `5_prime_UTR_variant`, `missense_variant`, `synonymous_variant`, `splicing`) \|
	\| `match_group` \| int \| Pos / neg pair ID (every group has 1 positive + 1 matched negative) \|
	\| `pip` \| float \| Maximum PIP across the 49 tissues in which the variant was tested. For negatives this is `< 0.01` (often `0` — see Source) \|
	\| `tissues` \| str \| Comma-separated list of tissues with PIP > 0.9 (empty for negatives) \|
	\| `genes` \| str \| Comma-separated list of eGene Ensembl IDs the variant regulates with PIP > 0.9 (empty for negatives) \|
	\| `biotype_classes` \| str \| Comma-separated `pc` / `nc` classes of the eGenes (e.g. `pc`, `nc`, `nc,pc`). Empty for negatives. Genes missing from Ensembl's biotype table default to `nc`. \|
	\| `MAF` \| float \| Cohort-matched GTEx donor MAF (mean across the 49 per-tissue donor cohorts; the cohorts overlap heavily so per-tissue MAFs are very close) \|
	\| `consequence`, `consequence_cre`, `consequence_final`, `consequence_group` \| str \| Ensembl VEP consequence + grouping used by the matcher \|
	\| `distance_tss_pc`, `distance_tss_nc`, `distance_tss` \| int \| Distance (0-based, half-open) to nearest protein-coding / non-protein-coding TSS, plus their min \|
	\| `tss_closest_pc_gene_id`, `tss_closest_nc_gene_id`, `tss_closest_gene_id` \| str \| Ensembl gene IDs at those distances \|
	\| `distance_exon_pc`, `distance_exon_nc`, `distance_exon` \| int \| Same shape, for nearest exon \|
	\| `exon_closest_pc_gene_id`, `exon_closest_nc_gene_id`, `exon_closest_gene_id` \| str \| Same shape \|
	\| `distance_tss_pc_bin`, `distance_tss_nc_bin`, `distance_exon_pc_bin`, `MAF_bin` \| str \| Categorical bins used as exact-match keys during gene-matching \|

	## Per-subset retention

	\| Subset \| n_pos in dataset_all \| matched (kept) \| retention \|
	\|---\|---:\|---:\|---:\|
	\| `distal` \| 5,333 \| 3,067 \| 57.5% \|
	\| `tss_proximal` \| 2,160 \| 437 \| 20.2% \|
	\| `non_coding_transcript_exon_variant` \| 1,290 \| 318 \| 24.7% \|
	\| `5_prime_UTR_variant` \| 544 \| 86 \| 15.8% \|
	\| `3_prime_UTR_variant` \| 535 \| 223 \| 41.7% \|
	\| `splicing` \| 333 \| 9 \| 2.7% \|
	\| `missense_variant` \| 269 \| 46 \| 17.1% \|
	\| `synonymous_variant` \| 230 \| 47 \| 20.4% \|
	\| total \| 10,694 \| 4,233 \| 39.6% \|

	(Two tiny subsets — `mature_miRNA_variant` n=1, `stop_retained_variant` n=1 — fail to match and are dropped.)

	Splicing has the worst retention (~3%) — splicing variants live next to a specific small set of exons, so the gene-id-based categorical match starves neg supply. The phenomenon is structural to the matching framework, not specific to eqtl.

	## Matching design

	Locked iter 33 from [issue #156](https://github.com/Open-Athena/bolinas-dna/issues/156), with one round-2 tweak for eqtl ([commit 1ad4fef7f7](https://github.com/Open-Athena/bolinas-dna/commit/1ad4fef7f7)) that closes a leak that only became detectable after switching to the richer Catalogue negative pool.

	Matching is exact on every categorical key, then Euclidean-nearest on the (RobustScaler-scaled) continuous features as a within-group tie-breaker. Without replacement, k=1.

	- Continuous features: `distance_tss_pc`, `distance_tss_nc`, `distance_exon_pc`, `distance_exon_nc`, `MAF`.
	- Categorical features:
	- `chrom`, `consequence_final`
	- `tss_closest_pc_gene_id`, `tss_closest_nc_gene_id`, `exon_closest_pc_gene_id`, `exon_closest_nc_gene_id`
	- `distance_tss_pc_bin` (`tss_proximal` only; edges `[0, 50, 100, 200, 500, 1000]`)
	- `distance_tss_nc_bin` — two-subset bin:
	- `tss_proximal`: edges `[0, 50, 100, 200, 500, 1000]` (iter 33)
	- `non_coding_transcript_exon_variant`: edges `[0, 200, 1000, 5000]` (round-2 widen-and-extend; ncRNA-exon variants span a much broader dist-to-nc-TSS range than tss_proximal, q=0.05 ≈ 9 bp, q=0.95 ≈ 8.7 kb)
	- `distance_exon_pc_bin` (`splicing` only; edges `[0, 5, 20, 30]`)
	- `MAF_bin` — per-subset tiered scheme with local-quantile bins for distal (`MAF_TIERED_LOG8_DISTAL_ONLY`):
	- `distal`: local equal-width log10(MAF) bins computed per categorical match group, 8 buckets, joint pos+neg reference. Closes the asymptotic distal MAF residual leak that fixed global edges leave.
	- `tss_proximal`, `non_coding_transcript_exon_variant`: 20-bin (`MAF_BIN_EDGES_20`)
	- `3_prime_UTR_variant`, `5_prime_UTR_variant`, `missense_variant`: 10-bin (`MAF_BIN_EDGES_10`)
	- `synonymous_variant`, `splicing`, …: 5-bin (`MAF_BIN_EDGES_5`)

	`tissues` / `genes` / `biotype_classes` are passthrough columns, not in the match key.

	Matched-feature diagnostic (round 2-1): one Bonferroni-significant leak closed vs. the round-2 kickoff (ncRNA × distance_tss_nc, PA 0.401 → 0.483). Two small-effect residual leaks in `distal` (PA=0.470 on `distance_tss_pc`, PA=0.536 on `MAF`) left as below the "don't bother" effect-size threshold.

	<details>
	<summary>Full per-(subset, feature) PA / p-value table (round 2-1)</summary>

	Format: PA / p. `*` = Bonferroni-significant at α = 0.05 / 40 = 1.25e-3 (8 subsets × 5 matched features). `` = p < 0.05. PA close to 0.5 = well-matched.

	\| subset \| n \| distance_tss_pc \| distance_tss_nc \| distance_exon_pc \| distance_exon_nc \| MAF \|
	\|---\|---:\|---\|---\|---\|---\|---\|
	\| `3_prime_UTR_variant` \| 223 \| 0.502 / 1.0 \| 0.457 / 0.23 \| 0.487 / 0.24 \| 0.439 / 0.03 \* \| 0.547 / 0.18 \|
	\| `5_prime_UTR_variant` \| 86 \| 0.360 / 0.013 \* \| 0.395 / 0.066 \| 0.494 / 1.0 \| 0.442 / 0.25 \| 0.535 / 0.59 \|
	\| `distal` \| 3,067 \| *0.470 / 7.8e-4 \\*** \| 0.494 / 0.49 \| 0.476 / 0.009 \* \| 0.494 / 0.49 \| *0.536 / 8.2e-5 \\*** \|
	\| `missense_variant` \| 46 \| 0.413 / 0.30 \| 0.435 / 0.46 \| 0.511 / 1.0 \| 0.489 / 1.0 \| 0.630 / 0.10 \|
	\| `non_coding_transcript_exon_variant` \| 318 \| 0.544 / 0.13 \| 0.483 / 0.57 \| 0.487 / 0.69 \| 0.502 / 1.0 \| 0.553 / 0.064 \|
	\| `splicing` \| 9 \| 0.556 / 1.0 \| 0.444 / 1.0 \| 0.667 / 0.51 \| 0.611 / 0.73 \| 0.333 / 0.51 \|
	\| `synonymous_variant` \| 47 \| 0.404 / 0.24 \| 0.340 / 0.040 \* \| n/a \| 0.489 / 1.0 \| 0.574 / 0.38 \|
	\| `tss_proximal` \| 437 \| 0.455 / 0.069 \| 0.460 / 0.10 \| 0.479 / 0.42 \| 0.481 / 0.44 \| 0.538 / 0.13 \|

	</details>

	## Source

	Per-tissue files from the [eQTL Catalogue r7 stable release](https://www.ebi.ac.uk/eqtl/) FTP at `ftp://ftp.ebi.ac.uk/pub/databases/spot/eQTL/`, study `QTS000015` (GTEx v8), all 49 GTEx tissue datasets × `ge` quantification. Two files per dataset:

	- `*.credible_sets.tsv.gz` — SuSiE credible-set members + PIP.
	- `*.all.tsv.gz` — full nominal sumstats (every tested variant × gene). Provides the "tested but never reached a credible set" negative pool.

	Per-variant `pip` is `max` across the (variant, tissue, gene) rows that mention it. Variants present in `all.tsv.gz` but absent from every credible set are 0-filled (sentinel: "tested, no signal"). Per-variant MAF is the mean across the rows.

	## Provenance

	Built by the [`bolinas-dna`](https://github.com/Open-Athena/bolinas-dna) eval pipeline at commit [`1ad4fef7f7`](https://github.com/Open-Athena/bolinas-dna/tree/1ad4fef7f7/snakemake/evals). PR thread: [#167](https://github.com/Open-Athena/bolinas-dna/pull/167).

	- Curation pipeline: [`snakemake/evals/`](https://github.com/Open-Athena/bolinas-dna/tree/1ad4fef7f7/snakemake/evals)
	- Catalogue parser: [`src/bolinas/evals/catalogue_parser.py`](https://github.com/Open-Athena/bolinas-dna/blob/1ad4fef7f7/src/bolinas/evals/catalogue_parser.py)
	- Labeling cascade: [`src/bolinas/evals/labeling.py`](https://github.com/Open-Athena/bolinas-dna/blob/1ad4fef7f7/src/bolinas/evals/labeling.py)
	- Matching algorithm: [`src/bolinas/evals/matching.py`](https://github.com/Open-Athena/bolinas-dna/blob/1ad4fef7f7/src/bolinas/evals/matching.py)
	- Design discussion: [issue #156](https://github.com/Open-Athena/bolinas-dna/issues/156) (iter 33 + round 2 ncRNA bin); eqtl-specific motivation: [issue #165](https://github.com/Open-Athena/bolinas-dna/issues/165)

	---
	license: apache-2.0
	tags:
	- biology
	- genomics
	- dna
	size_categories:
	- 1K<n<10K
	---

	# evals_eqtl

	Variant-effect-prediction benchmark of GTEx v8 fine-mapped eQTLs (49 tissues, pooled) vs tested-but-low-PIP variants, gene-matched 1:1 within consequence categories, MAF bins, and distance bins.

	## Description

	\| \| \|
	\|---\|---\|
	\| Positives \| GTEx v8 SuSiE fine-mapped variants with `max(PIP across tested tissues) > 0.9` \|
	\| Negatives \| `max(PIP) < 0.01` across all tested tissues; gene-matched 1:1 to positives \|
	\| Source \| [eQTL Catalogue r7](https://www.ebi.ac.uk/eqtl/), study `QTS000015` (GTEx v8), all 49 tissues × `ge` (gene-expression) quantification \|
	\| Genome build \| GRCh38 (Catalogue is hg38 native) \|
	\| Variant type \| SNVs only \|
	\| Coordinates \| 1-based (`pos` is 1-based; `ref` / `alt` are single bases) \|

	The negative pool is sourced from per-tissue full nominal sumstats (`*.all.tsv.gz`, ~3.5 GB per tissue), so it includes every variant tested in fine-mapping — including those that never reached a credible set. This is a structural improvement over earlier releases of this dataset (which sourced from a pre-filtered single-file release whose PIP floor at ~1e-4 capped the negative pool at ~1.3M variants); the current pool is ~10M tested variants.

	## Splits

	\| Split \| Variants (positives + matched negatives) \| Chromosomes \|
	\|---\|---:\|---\|
	\| `train` \| 4,612 (2,306 pos + 2,306 neg) \| odd: 1, 3, …, X \|
	\| `test` \| 3,854 (1,927 pos + 1,927 neg) \| even: 2, 4, …, Y \|
	\| total \| 8,466 (4,233 pairs) \| \|

	## Columns

	\| Column \| Type \| Description \|
	\|---\|---\|---\|
	\| `chrom`, `pos`, `ref`, `alt` \| str / int / str / str \| Variant coordinates (1-based, GRCh38) \|
	\| `label` \| bool \| `True` for high-PIP eQTL, `False` for tested-but-low-PIP matched negative \|
	\| `subset` \| str \| Consequence-group label for stratified eval (`distal`, `tss_proximal`, `non_coding_transcript_exon_variant`, `3_prime_UTR_variant`, `5_prime_UTR_variant`, `missense_variant`, `synonymous_variant`, `splicing`) \|
	\| `match_group` \| int \| Pos / neg pair ID (every group has 1 positive + 1 matched negative) \|
	\| `pip` \| float \| Maximum PIP across the 49 tissues in which the variant was tested. For negatives this is `< 0.01` (often `0` — see Source) \|
	\| `tissues` \| str \| Comma-separated list of tissues with PIP > 0.9 (empty for negatives) \|
	\| `genes` \| str \| Comma-separated list of eGene Ensembl IDs the variant regulates with PIP > 0.9 (empty for negatives) \|
	\| `biotype_classes` \| str \| Comma-separated `pc` / `nc` classes of the eGenes (e.g. `pc`, `nc`, `nc,pc`). Empty for negatives. Genes missing from Ensembl's biotype table default to `nc`. \|
	\| `MAF` \| float \| Cohort-matched GTEx donor MAF (mean across the 49 per-tissue donor cohorts; the cohorts overlap heavily so per-tissue MAFs are very close) \|
	\| `consequence`, `consequence_cre`, `consequence_final`, `consequence_group` \| str \| Ensembl VEP consequence + grouping used by the matcher \|
	\| `distance_tss_pc`, `distance_tss_nc`, `distance_tss` \| int \| Distance (0-based, half-open) to nearest protein-coding / non-protein-coding TSS, plus their min \|
	\| `tss_closest_pc_gene_id`, `tss_closest_nc_gene_id`, `tss_closest_gene_id` \| str \| Ensembl gene IDs at those distances \|
	\| `distance_exon_pc`, `distance_exon_nc`, `distance_exon` \| int \| Same shape, for nearest exon \|
	\| `exon_closest_pc_gene_id`, `exon_closest_nc_gene_id`, `exon_closest_gene_id` \| str \| Same shape \|
	\| `distance_tss_pc_bin`, `distance_tss_nc_bin`, `distance_exon_pc_bin`, `MAF_bin` \| str \| Categorical bins used as exact-match keys during gene-matching \|

	## Per-subset retention

	\| Subset \| n_pos in dataset_all \| matched (kept) \| retention \|
	\|---\|---:\|---:\|---:\|
	\| `distal` \| 5,333 \| 3,067 \| 57.5% \|
	\| `tss_proximal` \| 2,160 \| 437 \| 20.2% \|
	\| `non_coding_transcript_exon_variant` \| 1,290 \| 318 \| 24.7% \|
	\| `5_prime_UTR_variant` \| 544 \| 86 \| 15.8% \|
	\| `3_prime_UTR_variant` \| 535 \| 223 \| 41.7% \|
	\| `splicing` \| 333 \| 9 \| 2.7% \|
	\| `missense_variant` \| 269 \| 46 \| 17.1% \|
	\| `synonymous_variant` \| 230 \| 47 \| 20.4% \|
	\| total \| 10,694 \| 4,233 \| 39.6% \|

	(Two tiny subsets — `mature_miRNA_variant` n=1, `stop_retained_variant` n=1 — fail to match and are dropped.)

	Splicing has the worst retention (~3%) — splicing variants live next to a specific small set of exons, so the gene-id-based categorical match starves neg supply. The phenomenon is structural to the matching framework, not specific to eqtl.

	## Matching design

	Locked iter 33 from [issue #156](https://github.com/Open-Athena/bolinas-dna/issues/156), with one round-2 tweak for eqtl ([commit 1ad4fef7f7](https://github.com/Open-Athena/bolinas-dna/commit/1ad4fef7f7)) that closes a leak that only became detectable after switching to the richer Catalogue negative pool.

	Matching is exact on every categorical key, then Euclidean-nearest on the (RobustScaler-scaled) continuous features as a within-group tie-breaker. Without replacement, k=1.

	- Continuous features: `distance_tss_pc`, `distance_tss_nc`, `distance_exon_pc`, `distance_exon_nc`, `MAF`.
	- Categorical features:
	- `chrom`, `consequence_final`
	- `tss_closest_pc_gene_id`, `tss_closest_nc_gene_id`, `exon_closest_pc_gene_id`, `exon_closest_nc_gene_id`
	- `distance_tss_pc_bin` (`tss_proximal` only; edges `[0, 50, 100, 200, 500, 1000]`)
	- `distance_tss_nc_bin` — two-subset bin:
	- `tss_proximal`: edges `[0, 50, 100, 200, 500, 1000]` (iter 33)
	- `non_coding_transcript_exon_variant`: edges `[0, 200, 1000, 5000]` (round-2 widen-and-extend; ncRNA-exon variants span a much broader dist-to-nc-TSS range than tss_proximal, q=0.05 ≈ 9 bp, q=0.95 ≈ 8.7 kb)
	- `distance_exon_pc_bin` (`splicing` only; edges `[0, 5, 20, 30]`)
	- `MAF_bin` — per-subset tiered scheme with local-quantile bins for distal (`MAF_TIERED_LOG8_DISTAL_ONLY`):
	- `distal`: local equal-width log10(MAF) bins computed per categorical match group, 8 buckets, joint pos+neg reference. Closes the asymptotic distal MAF residual leak that fixed global edges leave.
	- `tss_proximal`, `non_coding_transcript_exon_variant`: 20-bin (`MAF_BIN_EDGES_20`)
	- `3_prime_UTR_variant`, `5_prime_UTR_variant`, `missense_variant`: 10-bin (`MAF_BIN_EDGES_10`)
	- `synonymous_variant`, `splicing`, …: 5-bin (`MAF_BIN_EDGES_5`)

	`tissues` / `genes` / `biotype_classes` are passthrough columns, not in the match key.

	Matched-feature diagnostic (round 2-1): one Bonferroni-significant leak closed vs. the round-2 kickoff (ncRNA × distance_tss_nc, PA 0.401 → 0.483). Two small-effect residual leaks in `distal` (PA=0.470 on `distance_tss_pc`, PA=0.536 on `MAF`) left as below the "don't bother" effect-size threshold.

	<details>
	<summary>Full per-(subset, feature) PA / p-value table (round 2-1)</summary>

	Format: PA / p. `*` = Bonferroni-significant at α = 0.05 / 40 = 1.25e-3 (8 subsets × 5 matched features). `` = p < 0.05. PA close to 0.5 = well-matched.

	\| subset \| n \| distance_tss_pc \| distance_tss_nc \| distance_exon_pc \| distance_exon_nc \| MAF \|
	\|---\|---:\|---\|---\|---\|---\|---\|
	\| `3_prime_UTR_variant` \| 223 \| 0.502 / 1.0 \| 0.457 / 0.23 \| 0.487 / 0.24 \| 0.439 / 0.03 \* \| 0.547 / 0.18 \|
	\| `5_prime_UTR_variant` \| 86 \| 0.360 / 0.013 \* \| 0.395 / 0.066 \| 0.494 / 1.0 \| 0.442 / 0.25 \| 0.535 / 0.59 \|
	\| `distal` \| 3,067 \| *0.470 / 7.8e-4 \\*** \| 0.494 / 0.49 \| 0.476 / 0.009 \* \| 0.494 / 0.49 \| *0.536 / 8.2e-5 \\*** \|
	\| `missense_variant` \| 46 \| 0.413 / 0.30 \| 0.435 / 0.46 \| 0.511 / 1.0 \| 0.489 / 1.0 \| 0.630 / 0.10 \|
	\| `non_coding_transcript_exon_variant` \| 318 \| 0.544 / 0.13 \| 0.483 / 0.57 \| 0.487 / 0.69 \| 0.502 / 1.0 \| 0.553 / 0.064 \|
	\| `splicing` \| 9 \| 0.556 / 1.0 \| 0.444 / 1.0 \| 0.667 / 0.51 \| 0.611 / 0.73 \| 0.333 / 0.51 \|
	\| `synonymous_variant` \| 47 \| 0.404 / 0.24 \| 0.340 / 0.040 \* \| n/a \| 0.489 / 1.0 \| 0.574 / 0.38 \|
	\| `tss_proximal` \| 437 \| 0.455 / 0.069 \| 0.460 / 0.10 \| 0.479 / 0.42 \| 0.481 / 0.44 \| 0.538 / 0.13 \|

	</details>

	## Source

	Per-tissue files from the [eQTL Catalogue r7 stable release](https://www.ebi.ac.uk/eqtl/) FTP at `ftp://ftp.ebi.ac.uk/pub/databases/spot/eQTL/`, study `QTS000015` (GTEx v8), all 49 GTEx tissue datasets × `ge` quantification. Two files per dataset:

	- `*.credible_sets.tsv.gz` — SuSiE credible-set members + PIP.
	- `*.all.tsv.gz` — full nominal sumstats (every tested variant × gene). Provides the "tested but never reached a credible set" negative pool.

	Per-variant `pip` is `max` across the (variant, tissue, gene) rows that mention it. Variants present in `all.tsv.gz` but absent from every credible set are 0-filled (sentinel: "tested, no signal"). Per-variant MAF is the mean across the rows.

	## Provenance

	Built by the [`bolinas-dna`](https://github.com/Open-Athena/bolinas-dna) eval pipeline at commit [`1ad4fef7f7`](https://github.com/Open-Athena/bolinas-dna/tree/1ad4fef7f7/snakemake/evals). PR thread: [#167](https://github.com/Open-Athena/bolinas-dna/pull/167).

	- Curation pipeline: [`snakemake/evals/`](https://github.com/Open-Athena/bolinas-dna/tree/1ad4fef7f7/snakemake/evals)
	- Catalogue parser: [`src/bolinas/evals/catalogue_parser.py`](https://github.com/Open-Athena/bolinas-dna/blob/1ad4fef7f7/src/bolinas/evals/catalogue_parser.py)
	- Labeling cascade: [`src/bolinas/evals/labeling.py`](https://github.com/Open-Athena/bolinas-dna/blob/1ad4fef7f7/src/bolinas/evals/labeling.py)
	- Matching algorithm: [`src/bolinas/evals/matching.py`](https://github.com/Open-Athena/bolinas-dna/blob/1ad4fef7f7/src/bolinas/evals/matching.py)
	- Design discussion: [issue #156](https://github.com/Open-Athena/bolinas-dna/issues/156) (iter 33 + round 2 ncRNA bin); eqtl-specific motivation: [issue #165](https://github.com/Open-Athena/bolinas-dna/issues/165)