From 07f39030a24dca2d50448541e572598e59f79e7c Mon Sep 17 00:00:00 2001
From: rlyu <rlyu@svi.edu.au>
Date: Mon, 1 Aug 2022 15:10:04 +1000
Subject: [PATCH] improve countAllele
---
src/sgcocaller/utils.nim | 7 +++++--
1 file changed, 5 insertions(+), 2 deletions(-)
diff --git a/src/sgcocaller/utils.nim b/src/sgcocaller/utils.nim
index 9935127..86d13bf 100755
--- a/src/sgcocaller/utils.nim
+++ b/src/sgcocaller/utils.nim
@@ -67,8 +67,9 @@ proc get_base_offset*(position:int, align: Record): int =
if off <= position:
continue
over = off - position
- # get the base
- base_offset = qoff - over-1
+ base_offset = qoff - over - 1
+ if($event.op == 'N') or ($event.op == 'D') or ($event.op == 'H'):
+ base_offset = -1
break
return base_offset
@@ -147,6 +148,8 @@ proc countAllele*(ibam:Bam, maxTotalReads:int,
if not barcodeTable.hasKey(currentCB): continue
base_off = get_base_offset(position = stopPos, align = aln)
base = aln.base_at(base_off)
+ if base_off < 0:
+ continue
if aln.base_quality_at(base_off).cint < minbsq:
continue
total_reads+=1
--
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