From d2be5ec382b7007c528f34426755a3d69c5c7557 Mon Sep 17 00:00:00 2001
From: Floreal Cabanettes <floreal.cabanettes@inra.fr>
Date: Tue, 20 Jun 2017 16:39:23 +0200
Subject: [PATCH] Add missing short options
---
build_pop.py | 16 ++++++++--------
1 file changed, 8 insertions(+), 8 deletions(-)
diff --git a/build_pop.py b/build_pop.py
index eae3f35..8f30c20 100755
--- a/build_pop.py
+++ b/build_pop.py
@@ -21,16 +21,16 @@ def parse_args():
"""
parser = argparse.ArgumentParser(description='Generate simulated populations with SV',
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
- parser.add_argument("--nb-inds", help="Number of individuals to generate", required=True, type=int)
- parser.add_argument("--reference", help="Reference genome", required=True)
- parser.add_argument("--sv-list", help="File containing the SVs", required=False)
- parser.add_argument("--coverage", help="Coverage of reads", default=15, type=int)
- parser.add_argument("--output-directory", help="Output directory", default="res")
- parser.add_argument("--force-polymorphism", help="Force polymorphism for each SV", action='store_const', const=True,
+ parser.add_argument("-n", "--nb-inds", help="Number of individuals to generate", required=True, type=int)
+ parser.add_argument("-r", "--reference", help="Reference genome", required=True)
+ parser.add_argument("-s", "--sv-list", help="File containing the SVs", required=False)
+ parser.add_argument("-c", "--coverage", help="Coverage of reads", default=15, type=int)
+ parser.add_argument("-o", "--output-directory", help="Output directory", default="res")
+ parser.add_argument("-f", "--force-polymorphism", help="Force polymorphism for each SV", action='store_const', const=True,
default=False)
- parser.add_argument("--haploid", help="Make a haploid genome, instead of diploid one", action="store_const", const=True,
+ parser.add_argument("-a", "--haploid", help="Make a haploid genome, instead of diploid one", action="store_const", const=True,
default=False)
- parser.add_argument("--proba-del", help="Probabilty to have a deletion", type=float, default=0.000001)
+ parser.add_argument("-p", "--proba-del", help="Probabilty to have a deletion", type=float, default=0.000001)
parser.add_argument("-l", "--read-len", help="Generate reads having a length of LEN", type=int, default=100)
parser.add_argument("-m", "--insert-len-mean", help="Generate inserts (fragments) having an average length of LEN",
type=int, default=300)
--
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