refactor: mark failed sites in merged VCF filter

Remove VCF header from params as well

Author: ahmig

workflow/rules/distances.smk

@@ -1,15 +1,15 @@
 rule compile_fail_sites_vcf:
     params:
-        header = ("#CHROM", "POS", "ID", "REF", "ALT", "QUAL", "FILTER", "INFO"),
-        filter_text = "mask",
+        filter_text = "fail_site",
         sub_text = "NA",
-        exc_text = "site_qual"
+        exc_text = "site_qual",
     input:
         sites = OUTDIR / f"{OUTPUT_NAME}.fail_sites.tsv",
     output:
         sites = temp(OUTDIR / f"{OUTPUT_NAME}.fail_sites.vcf"),
     run:
         import pandas as pd
+        HEADER = ["#CHROM", "POS", "ID", "REF", "ALT", "QUAL", "FILTER", "INFO"]
         sites = (
             pd.read_table(input.sites, sep="\t")
                 .drop_duplicates(subset=("CHROM", "POS", "REF"))
@@ -20,28 +20,27 @@ rule compile_fail_sites_vcf:
         sites["QUAL"] = "."
         sites["FILTER"] = params.filter_text
         sites["INFO"] = f"SUB={params.sub_text};EXC={params.exc_text}"
-        sites[list(params.header)].to_csv(output.sites, sep="\t", index=False)
+        sites[HEADER].to_csv(output.sites, sep="\t", index=False)
 
 
-rule merge_sites:
-    params:
-        header = ("#CHROM", "POS", "ID", "REF", "ALT", "QUAL", "FILTER", "INFO")
+rule merge_mask_sites_vcf:
     input:
         lambda wildcards: select_problematic_vcf(),
         OUTDIR / f"{OUTPUT_NAME}.fail_sites.vcf",
     output:
         sites = temp(OUTDIR / "all_mask_sites.vcf"),
     run:
         import pandas as pd
+        HEADER = ["#CHROM", "POS", "ID", "REF", "ALT", "QUAL", "FILTER", "INFO"]
         (
             pd.concat(
-                [pd.read_table(path, sep="\t", comment="#", names=params.header) for path in input],
+                [pd.read_table(path, sep="\t", comment="#", names=HEADER, dtype={"POS": "int64"}) for path in input],
                 axis="rows",
                 ignore_index=True
             )
-                .drop_duplicates(subset=("#CHROM", "POS", "FILTER"), keep="first")
-                .sort_values(list(params.header))
-                .to_csv(output.sites, sep="\t", index=False)
+            .drop_duplicates(subset=("#CHROM", "POS", "FILTER"), keep="first")
+            .sort_values(by=["#CHROM", "POS"])
+            .to_csv(output.sites, sep="\t", index=False)
         )
 
 
@@ -52,7 +51,7 @@ rule extract_afwdist_variants:
         position_col = "POS",
         sequence_col = "ALT",
         frequency_col = "ALT_FREQ",
-        mask_class = ["mask"],
+        mask_class = ["mask", "fail_site"],
     input:
         variants = OUTDIR/f"{OUTPUT_NAME}.variants.tsv",
         mask_vcf = OUTDIR / "all_mask_sites.vcf",