From 3fb68ce878049a1121d6b259a1d5ee6a0dd04675 Mon Sep 17 00:00:00 2001
From: Floreal Cabanettes <floreal.cabanettes@inra.fr>
Date: Wed, 8 Aug 2018 13:29:10 +0200
Subject: [PATCH] Change pindel window size to 10M with a overlap change from
100K to 50K
---
snakecnv/detection.snk | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/snakecnv/detection.snk b/snakecnv/detection.snk
index 785c50a..d113526 100644
--- a/snakecnv/detection.snk
+++ b/snakecnv/detection.snk
@@ -54,13 +54,13 @@ def get_chr_batches(ref_file, chr):
# Make ranges:
groups = []
start = 1
- end = min(start + 19999999, len_chr)
- while (len_chr - end + 1 >= 19900000) or (len_chr + 1 == end):
+ end = min(start + 9999999, len_chr)
+ while (len_chr - end + 1 >= 9950000) or (len_chr + 1 == end):
groups.append((start, end))
if len_chr + 1 == end:
break
- start = end - 99999
- end = min(start + 19999999, len_chr + 1)
+ start = end - 9999
+ end = min(start + 9999999, len_chr + 1)
last_group = (start, len_chr + 1)
if last_group not in groups:
groups.append(last_group)
--
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