From c0561753409f50e839f56f69db81d2751c0fbab8 Mon Sep 17 00:00:00 2001
From: farhangkl <fjaryani@yahoo.com>
Date: Mon, 25 Mar 2024 12:16:19 -0500
Subject: [PATCH] update contigs

---
 .../Tyke/TykeVarSimulator/TykeVarSimulator.py | 29 +++++++++++++++++--
 1 file changed, 27 insertions(+), 2 deletions(-)

diff --git a/scripts/Tyke/TykeVarSimulator/TykeVarSimulator.py b/scripts/Tyke/TykeVarSimulator/TykeVarSimulator.py
index e101f04..03b1a2a 100644
--- a/scripts/Tyke/TykeVarSimulator/TykeVarSimulator.py
+++ b/scripts/Tyke/TykeVarSimulator/TykeVarSimulator.py
@@ -19,8 +19,8 @@
 minAFsnp=0.05   # minimum allele frequency SNV   
 maxAFsnp=0.25   # maximum allele frequency SNV
 file=sys.argv[1]   # source bam to simulate SVs from
-nosv=50 # no of SVs to simulate
-nosnv=200 # no of SNVs to simulate
+nosv=5 # no of SVs to simulate
+nosnv=1 # no of SNVs to simulate
 minsvl=50 # minimum SV length
 maxsvl=10000 # maximum SV length
 maxsnp=10 # maximum size of indel SNV
@@ -171,6 +171,31 @@ def main():
         '##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Length of structural variation">',
         '##INFO=<ID=END,Number=1,Type=Integer,Description="End position of structural variation">',
         '##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">',
+        '##contig=<ID=chr1,length=248956422>',
+        '##contig=<ID=chr2,length=242193529>',
+        '##contig=<ID=chr3,length=198295559>',
+        '##contig=<ID=chr4,length=190214555>',
+        '##contig=<ID=chr5,length=181538259>',
+        '##contig=<ID=chr6,length=170805979>',
+        '##contig=<ID=chr7,length=159345973>',
+        '##contig=<ID=chr8,length=145138636>',
+        '##contig=<ID=chr9,length=138394717>',
+        '##contig=<ID=chr10,length=133797422>',
+        '##contig=<ID=chr11,length=135086622>',
+        '##contig=<ID=chr12,length=133275309>',
+        '##contig=<ID=chr13,length=114364328>',
+        '##contig=<ID=chr14,length=107043718>',
+        '##contig=<ID=chr15,length=101991189>',
+        '##contig=<ID=chr16,length=90338345>',
+        '##contig=<ID=chr17,length=83257441>',
+        '##contig=<ID=chr18,length=80373285>',
+        '##contig=<ID=chr19,length=58617616>',
+        '##contig=<ID=chr20,length=64444167>',
+        '##contig=<ID=chr21,length=46709983>',
+        '##contig=<ID=chr22,length=50818468>',
+        '##contig=<ID=chrX,length=156040895>',
+        '##contig=<ID=chrY,length=57227415>',
+        '##contig=<ID=chrM,length=16569>',
         '\t'.join(['#CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER', 'INFO', 'FORMAT', 'SAMPLE'])
     ]
     insertno=1