download_bundle.py: match bwa/minibwa index by suffix

bin/download_bundle.py

@@ -10,8 +10,9 @@ Always downloaded:
 
 Optional:
   --index bwa|minibwa|all   aligner index (default: none)
-                            bwa     -> {genome}/*.fa.amb/.ann/.bwt/.pac/.sa
-                            minibwa -> everything under {genome}/minibwa/
+                            matched by file suffix under {genome}/:
+                            bwa     -> .amb .ann .bwt .pac .sa
+                            minibwa -> .l2b .mbw (incl. .meth.mbw)
   --extract-vep             extract the VEP cache into <outdir>/vep (default: no)
 
 Examples:
@@ -25,6 +26,7 @@ import argparse, fnmatch, os, sys, tarfile
 
 REPO = "pzweuj/SchemaBio_Bundle"
 BWA_EXT = (".amb", ".ann", ".bwt", ".pac", ".sa")
+MINIBWA_EXT = (".l2b", ".mbw")
 
 
 def select(files, genome, index):
@@ -32,14 +34,13 @@ def select(files, genome, index):
             f"{genome}/homo_sapiens_merged_vep_*.tar.gz",
             f"{genome}/bed/*", f"{genome}/schema_bundle/*"]
     out = [f for f in files if any(fnmatch.fnmatch(f, p) for p in pats)]
-    if index in ("bwa", "all"):
-        out += [f for f in files if f.startswith(f"{genome}/") and f.count("/") == 1
-                and f.endswith(tuple(".fa" + e for e in BWA_EXT))]
-    if index in ("minibwa", "all"):
-        mb = [f for f in files if f.startswith(f"{genome}/minibwa/")]
-        if not mb:
-            print(f"[warn] no minibwa index found under {genome}/minibwa/ yet, skipped", file=sys.stderr)
-        out += mb
+    gfiles = [f for f in files if f.startswith(f"{genome}/")]
+    for name, ext in (("bwa", BWA_EXT), ("minibwa", MINIBWA_EXT)):
+        if index in (name, "all"):
+            hit = [f for f in gfiles if f.endswith(ext)]
+            if not hit:
+                print(f"[warn] no {name} index ({' '.join(ext)}) found for {genome}, skipped", file=sys.stderr)
+            out += hit
     return sorted(set(out))