Add HDL shared test fixtures

README.md

@@ -692,6 +692,14 @@ The earth sciences folder contain subfolders for different data formats encounte
     - 1000GP.chr*.chunks.txt: chunks of the chromosome obtain with GLIMPSE_chunk
     - AFR.gwas: Study locus file. From [SuShiE](https://github.com/mancusolab/sushie).
     - AFR.ld: LD matrix file. From [SuShiE](https://github.com/mancusolab/sushie).
+    - hdl/reference/chr1.1_toy.bim: toy HDL LD reference BIM sidecar for chunk 1.1
+    - hdl/reference/chr1.1_toy.rda: toy HDL LD reference payload for chunk 1.1
+    - hdl/reference/chr1.2_toy.bim: toy HDL LD reference BIM sidecar for chunk 1.2
+    - hdl/reference/chr1.2_toy.rda: toy HDL LD reference payload for chunk 1.2
+    - hdl/reference/toy_snp_counter.RData: toy HDL SNP count metadata
+    - hdl/reference/toy_snp_list.RData: toy HDL SNP list metadata
+    - hdl/sumstats/trait1_canonical.tsv: canonical HDL summary statistics for trait 1
+    - hdl/sumstats/trait2_canonical.tsv: canonical HDL summary statistics for trait 2
   - svsig:
 
     - NA03697B2_new.pbmm2.repeats.svsig.gz: structural variant file for NA03697B2_new.pbmm2.repeats.bam, created with PBSV discover version (2.9.0 default settings)

data/genomics/homo_sapiens/popgen/hdl/reference/chr1.1_toy.bim

@@ -0,0 +1,2 @@
+1 rs1 0 101 A G
+1 rs2 0 102 C T

data/genomics/homo_sapiens/popgen/hdl/reference/chr1.2_toy.bim

@@ -0,0 +1,2 @@
+1 rs3 0 201 A C
+1 rs4 0 202 G T

data/genomics/homo_sapiens/popgen/hdl/sumstats/trait1_canonical.tsv

@@ -0,0 +1,5 @@
+SNP	A1	A2	CHR	POS	RSID	EffectAllele	OtherAllele	N	Z
+rs1	A	G	1	101	rs1	A	G	10000	0.5
+rs2	C	T	1	202	rs2	C	T	10000	-0.2
+rs3	A	C	1	303	rs3	A	C	10000	0.4
+rs4	G	T	1	404	rs4	G	T	10000	-0.1

data/genomics/homo_sapiens/popgen/hdl/sumstats/trait2_canonical.tsv

@@ -0,0 +1,5 @@
+SNP	A1	A2	CHR	POS	RSID	EffectAllele	OtherAllele	N	Z
+rs1	A	G	1	101	rs1	A	G	12000	0.3
+rs2	C	T	1	202	rs2	C	T	12000	-0.4
+rs3	A	C	1	303	rs3	A	C	12000	0.2
+rs4	G	T	1	404	rs4	G	T	12000	-0.2