From 626e24518768dfc97629cb8513b1335f5b38fb5c Mon Sep 17 00:00:00 2001 From: fcunial Date: Sun, 24 Mar 2024 17:49:37 -0400 Subject: [PATCH] fixes --- docker/truvari_intrasample/resolve.py | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/docker/truvari_intrasample/resolve.py b/docker/truvari_intrasample/resolve.py index 131a3b4..7bf9a83 100644 --- a/docker/truvari_intrasample/resolve.py +++ b/docker/truvari_intrasample/resolve.py @@ -29,6 +29,16 @@ def resolve(entry, ref): return None seq = ref.fetch(entry.chrom, entry.start, entry.stop) + + + # FC> Replacing non-standard DNA characters with an N + for i in range(len(seq)): + c = seq[i].upper() + if c!='A' and c!='C' and c!='G' and c!='T': + seq[i] = 'N' + + + if entry.alts[0] == '': entry.ref = seq entry.alts = [seq[0]]