From 2a18541f72f2f25f73149e9e3702674056c9714a Mon Sep 17 00:00:00 2001
From: Astra Bertelli <133636879+AstraBert@users.noreply.github.com>
Date: Fri, 29 Dec 2023 01:04:14 +0100
Subject: [PATCH] Update simON_reads.py

---
 scripts/simON_reads.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/simON_reads.py b/scripts/simON_reads.py
index c32217c..fc8457c 100644
--- a/scripts/simON_reads.py
+++ b/scripts/simON_reads.py
@@ -20,7 +20,7 @@
 argparse = ArgumentParser()
 argparse.add_argument("-v", "--version", help="Print the version of the code", required=False, default=False, action='store_true')
 argparse.add_argument("-i", "--infile", help="Path to the input fasta file that contains the reference sequence(s)", required=False)
-argparse.add_argument("-snp", "--single_nucleotide_polymorphism", help="Insert a single nucleotide variant; the syntax of this option should be SAMPLE:POS:REF>ALT,SAMPLE:POS:REF>ALT,...,SAMPLE:POS:REF>ALT (it should be separated by commas without blank spaces) where SAMPLE is the header of the sequence (withouth \">\") in the original fasta file, POS is an integer that indicates the position (0-based) of the polymorphic site, REF is the reference allele, ALT is the alternative allele you want to be put. This will generate a diploid-like distribution of variants", required=False, default="NO_SNP")
+argparse.add_argument("-snp", "--single_nucleotide_polymorphism", help="Insert a single nucleotide variant; Insert a single nucleotide variant; the syntax of this option should be SAMPLE:POS:REF>ALT,SAMPLE:POS:REF>ALT:1/0,...,SAMPLE:POS:REF>ALT:1/0 (it should be separated by commas without blank spaces) where SAMPLE is the header of the sequence (withouth \">\") in the original fasta file, POS is an integer that indicates the position (0-based) of the polymorphic site, REF is the reference allele, ALT is the alternative allele you want to be put and 1/0 (where you should report either 1 or 0, not both of them) is the haplotype phasing information: all the SNPs referred to 1 will end up on the same sequences, separate from the ones attributed to 0: this will generate a diploid-like distribution of variants. (Default is \"NO_SNP\")", required=False, default="NO_SNP")
 argparse.add_argument("-n", "--nreads", help="Insert the number of reads you want to generate for each provided reference sequence: deafult is 2000", required=False, default=2000, type=int)
 argparse.add_argument("-ehp", "--enable_homopolymer_error", help="This will set a 30%% chance of getting an extra nucleotide around homopolymeric regions", required=False, default=False, action='store_true')
 argparse.add_argument("-ese", "--enable_sequencing_error", help="This will set a 5%% chance of getting a random single nucleotide variant or insertion, while it retains also a 5%% chance of skipping a base (single delition)", required=False, default=False, action='store_true')