From 3028cc610830c13e0db1a1bce464e0feeb382fdf Mon Sep 17 00:00:00 2001 From: Richard de Borja Date: Tue, 13 Feb 2024 18:26:46 -0500 Subject: [PATCH] added N as a possible base in pileup --- workflow/scripts/format_pileup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflow/scripts/format_pileup.py b/workflow/scripts/format_pileup.py index 94c3f19..c84cde4 100644 --- a/workflow/scripts/format_pileup.py +++ b/workflow/scripts/format_pileup.py @@ -12,7 +12,7 @@ print("\t".join(["contig", "position", "depth", "ref_base", "count_A", "count_C", "count_G", "count_T", "count_del", "alt_frequency"])) for pc in samfile.pileup(ignore_orphans=False): - freqs = {'A': 0, 'T': 0, 'G': 0, 'C': 0, '-': 0, 'R': 0 } + freqs = {'A': 0, 'T': 0, 'G': 0, 'C': 0, '-': 0, 'R': 0, 'N': 0 } for pr in pc.pileups: if pr.is_del: freqs['-'] += 1