From 8b60619484158bbbbf8c51f52b6ec91620704acf Mon Sep 17 00:00:00 2001
From: rlyu <rlyu@svi.edu.au>
Date: Wed, 12 May 2021 10:46:30 +1000
Subject: [PATCH] fix splitN read count bug
---
.gitlab-ci.yml | 2 ++
src/sscocaller.nim | 11 +++++------
tests/bcAA.tsv | 2 +-
3 files changed, 8 insertions(+), 7 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index f6f0c99..9addc7f 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -28,6 +28,7 @@ testUbuntu:
stage: testStatic
script:
- ./src/sscocaller -h
+
testDebian:
tags:
- docker
@@ -35,6 +36,7 @@ testDebian:
stage: testStatic
script:
- ./src/sscocaller -h
+
## shell executer
testFunction:
stage: testStatic
diff --git a/src/sscocaller.nim b/src/sscocaller.nim
index 51c77c9..5002669 100755
--- a/src/sscocaller.nim
+++ b/src/sscocaller.nim
@@ -33,8 +33,7 @@ proc sscocaller(argv: var seq[string]): int =
-minDP --minDP <minDP> the minimum DP for a SNP to be included in the output file [default: 1]
-maxDP --maxDP <maxDP> the maximum DP for a SNP to be included in the output file [default: 5]
-maxTotalDP --maxTotalDP <maxTotalDP> the maximum DP across all barcodes for a SNP to be included in the output file [default: 25]
- -minTotalDP --minTotalDP <minTotalDP> the minimum DP across all barcodes for a SNP to be included in the output file [default: 10]
-
+ -minTotalDP --minTotalDP <minTotalDP> the minimum DP across all barcodes for a SNP to be included in the output file [default: 10]
-chrName --chrName <chrName> the chr names with chr prefix or not, if not supplied then no prefix
-thetaREF --thetaREF <thetaREF> the theta for the binomial distribution conditioning on hidden state being REF [default: 0.1]
-thetaALT --thetaALT <thetaALT> the theta for the binomial distribution conditioning on hidden state being ALT [default: 0.9]
@@ -243,12 +242,12 @@ proc sscocaller(argv: var seq[string]): int =
qoff+=event.len ## the offs to the query sequences
if cons.reference:
off += event.len ## the offs to the reference sequences
- if not cons.query:
- roff_only += event.len
+ # if not cons.query:
+ # roff_only += event.len
if off <= position: continue
- over = off - position - roff_only
+ over = off - position
# get the base
- base = aln.base_at(qoff - over)
+ #base = aln.base_at(qoff - over-1)
break
if aln.base_quality_at(qoff - over-1).cint < minbsq: continue
total_reads+=1
diff --git a/tests/bcAA.tsv b/tests/bcAA.tsv
index 5d5963d..858dd56 100644
--- a/tests/bcAA.tsv
+++ b/tests/bcAA.tsv
@@ -1,2 +1,2 @@
AAAGTAGCACGTCTCT-1
-AAAGTAGCACGTCTCT-1
+TAAGTAGCACGTCTCT-1
--
GitLab