-pod2usage(-msg => "Seed length should be at least 25!\n", -exitval => 2, -verbose => 2) if ($L < 25);
-pod2usage(-msg => "--sampling-for-bam cannot be specified if --out-bam is not specified!\n", -exitval => 2, -verbose => 2) if ($sampling && !$genBamF);
+pod2usage(-msg => "Seed length should be at least 5!\n", -exitval => 2, -verbose => 2) if ($L < 5);
+pod2usage(-msg => "--sampling-for-bam cannot be specified if --no-bam-output is specified!\n", -exitval => 2, -verbose => 2) if ($sampling && !$genBamF);
+pod2usage(-msg => "--output-genome-bam cannot be specified if --no-bam-output is specified!\n", -exitval => 2, -verbose => 2) if ($genGenomeBamF && !$genBamF);
+
+if ($L < 25) { print "Warning: the seed length set is less than 25! This is only allowed if the references are not added poly(A) tails.\n"; }