derive_masks: keep pysam's downloaded tabix indexes in data/pgx/cache, not the working directory

scripts/pgx/derive_masks.py

@@ -38,6 +38,7 @@ def main() -> int:
     ap.add_argument("--manifest", required=True)
     ap.add_argument("--min-concordance", type=float, default=0.95)
     ap.add_argument("--out", required=True, type=Path)
+    ap.add_argument("--cache", type=Path, default=Path("data/pgx/cache"), help="where pysam keeps remote .tbi files")
     a = ap.parse_args()
     ident = {}
     with a.identity.open() as fh:
@@ -86,6 +87,11 @@ def main() -> int:
     for c, p, r, al, g in keys:
         by_gene[(g, c)].append((p, r, al))
     inds = sorted(set(use.values()))
+    import os
+
+    a.out = a.out.resolve()
+    a.cache.mkdir(parents=True, exist_ok=True)
+    os.chdir(a.cache)  # pysam downloads the remote tabix indexes into the working directory
     for (g, c), vs in sorted(by_gene.items()):
         core = c.removeprefix("chr")
         chrom = "chrM" if core in ("MT", "M") else f"chr{core}"