Delete filter_hrun warning with beagle file (#225)

gymrek-lab · Aug 14, 2024 · be63e79 · be63e79
1 parent a1a3a39
commit be63e79
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Showing 2 changed files with 1 addition and 4 deletions.
diff --git a/trtools/dumpSTR/dumpSTR.py b/trtools/dumpSTR/dumpSTR.py
@@ -89,9 +89,6 @@ def CheckLocusFilters(args, vcftype, is_beagle: bool):
         common.WARNING("--use-length is only meaningful for HipSTR, which reports sequence level differences.")
     if args.filter_hrun and vcftype not in [trh.VcfTypes["hipstr"]]:
         common.WARNING("--filter-hrun only relevant to HipSTR files. This filter will have no effect.")
-    if args.filter_hrun and is_beagle:
-        common.WARNING("--filter-hrun cannot be applied to Beagle imputed files")
-        return False
     if args.filter_regions is not None:
         if args.filter_regions_names is not None:
             filter_region_files = args.filter_regions.split(",")

diff --git a/trtools/dumpSTR/tests/test_dumpSTR.py b/trtools/dumpSTR/tests/test_dumpSTR.py
@@ -514,7 +514,7 @@ def test_beagle_disallowed_locus_filters(tmpdir, vcfdir):
     args_obj = args(tmpdir)
     args_obj.vcf = os.path.join(vcfdir, 'beagle/hipstr_imputed.vcf.gz')
     args_obj.filter_hrun = True
-    assert main(args_obj) == 1
+    assert main(args_obj) == 0
 
 def test_beagle_disallowed_call_filters(tmpdir, vcfdir):
     args_obj = args(tmpdir)