Add real performance testing data

.gitignore

@@ -163,3 +163,4 @@ cython_debug/
 
 .vscode
 vcz_test_cache/
+**/.DS_Store

performance/compare.py

@@ -27,24 +27,22 @@ def run_vcztools(command: str, dataset_name: str):
 
 if __name__ == "__main__":
     commands = [
-        "view",
-        "view -s tsk_7068,tsk_8769,tsk_8820",
-        r"query -f '%CHROM %POS %REF %ALT{0}\n'",
-        r"query -f '%CHROM:%POS\n' -i 'POS=49887394 | POS=50816415'",
-        "view -s '' --force-samples",
+        ("view", "sim_10k"),
+        ("view -s tsk_7068,tsk_8769,tsk_8820", "sim_10k"),
+        (r"query -f '%CHROM %POS %REF %ALT{0}\n'", "sim_10k"),
+        (r"query -f '%CHROM:%POS\n' -i 'POS=49887394 | POS=50816415'", "sim_10k"),
+        ("view -s '' --force-samples", "sim_10k"),
+        ("view -i 'FMT/DP>10 & FMT/GQ>10'", "chr22"),
+        ("view -i 'QUAL>10 || FMT/GQ>10'", "chr22"),
+        (r"query -f 'GQ:[ %GQ] \t GT:[ %GT]\n'", "chr22"),
     ]
-    dataset = "sim_10k"
 
     if len(sys.argv) == 2 and sys.argv[1].isnumeric():
         index = int(sys.argv[1])
-        command = commands[index]
-        run_bcftools(command, dataset)
-        run_vcztools(command, dataset)
-    elif len(sys.argv) >= 2:
-        command = " ".join(sys.argv[1:])
+        command, dataset = commands[index]
         run_bcftools(command, dataset)
         run_vcztools(command, dataset)
     else:
-        for command in commands:
+        for command, dataset in commands:
             run_bcftools(command, dataset)
             run_vcztools(command, dataset)

performance/data/Makefile

@@ -9,21 +9,39 @@
 # The Python requirements are listed in requirements.txt:
 # pip install -r requirements.txt
 
-.PHONY: all clean
+# Flags / commandline arguments:
+CHROMOSOME ?= 22
+WGS ?= 1
 
-all: sim_10k.vcz
+ifeq ($(WGS), 1)
+        TGP_URL = "https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20190425_NYGC_GATK/CCDG_13607_B01_GRM_WGS_2019-02-19_chr$(CHROMOSOME).recalibrated_variants.vcf.gz"
+else
+        # Use URL for genotyping data:
+        TGP_URL = "http://hgdownload.cse.ucsc.edu/gbdb/hg19/1000Genomes/phase3/ALL.chr$(CHROMOSOME).phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz"
+endif
+
+.PHONY: all simulated real clean
+
+all: simulated real
+
+simulated: sim_10k.vcz
+
+real: chr22.vcz
 
 sim_10k.ts:
 	stdpopsim HomSap -c chr22 -o sim_10k.ts pop_0:10000
 
-sim_10k.vcf.gz: sim_10k.ts
-	tskit vcf sim_10k.ts | bgzip > sim_10k.vcf.gz
+chr22.vcf.gz:
+	bcftools view $(TGP_URL) | head -n 25000 | bcftools view -O z -o chr22.vcf.gz
+
+%.vcf.gz: %.ts
+	tskit vcf $< | bgzip > $@
 
-sim_10k.vcf.gz.csi: sim_10k.vcf.gz
-	bcftools index sim_10k.vcf.gz
+%.vcf.gz.csi: %.vcf.gz
+	bcftools index $<
 
-sim_10k.vcz: sim_10k.vcf.gz sim_10k.vcf.gz.csi
-	vcf2zarr convert sim_10k.vcf.gz sim_10k.vcz
+%.vcz: %.vcf.gz %.vcf.gz.csi
+	vcf2zarr convert $< $@
 
 clean:
 	rm -rf sim_10k.*