From d169fc216f64736d5f3159c2bd9cf36c45328650 Mon Sep 17 00:00:00 2001
From: Raul Wijfjes <raul.wijfjes@wur.nl>
Date: Mon, 21 Mar 2022 09:59:51 +0100
Subject: [PATCH] Fixed tests
---
CHANGELOG.md | 7 +++++++
docker/Dockerfile | 2 +-
docker/docker_build.sh | 2 +-
nextflow/hecaton.nf | 2 +-
nextflow/hecaton_no_align.nf | 2 +-
scripts/filter/filter_ref_sites_vcf.py | 1 +
tests/functional_test.sh | 2 +-
tests/genotyping/expected_output.tsv | 8 +++----
tests/genotyping/expected_output.vcf | 29 +++++++++++++++-----------
9 files changed, 34 insertions(+), 21 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5472f8c..61e3dba 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,13 @@ All notable changes to this project will be documented in this file.
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+## Unreleased
+
+## [0.5.1] - 2022-03-21
+### Fixed
+- Updated the expected test output files
+- Changed the minimum number of samples in the filter_ref_sites_vcf.py test to 1
+
## [0.5.0] - 2021-01-08
### Changed
- merge_vcf_files.py now sets genotypes with a DHFFC of Inf, Nan, or higher than 4 to missing
diff --git a/docker/Dockerfile b/docker/Dockerfile
index d836bca..667c488 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -64,7 +64,7 @@ RUN source activate hecaton_py2 && \
# RUN git clone https://git.wur.nl/wijfj001/hecaton.git && cd hecaton && \
# git checkout e85bba0c && cd .. && \
RUN git clone https://git.wur.nl/bioinformatics/hecaton.git && \
- echo "aeb7ff36" && \
+ echo "5efce90c" && \
chmod +x hecaton/scripts/collapse/* && \
chmod +x hecaton/scripts/convert/* && \
chmod +x hecaton/scripts/filter/* && \
diff --git a/docker/docker_build.sh b/docker/docker_build.sh
index c29dc3f..e486265 100644
--- a/docker/docker_build.sh
+++ b/docker/docker_build.sh
@@ -2,4 +2,4 @@
set -euo pipefail
-docker build -t hecaton:v0.5.0 .
\ No newline at end of file
+docker build -t hecaton:v0.5.1 .
\ No newline at end of file
diff --git a/nextflow/hecaton.nf b/nextflow/hecaton.nf
index 47e2b2f..def890c 100755
--- a/nextflow/hecaton.nf
+++ b/nextflow/hecaton.nf
@@ -25,7 +25,7 @@ params.help = false
def helpMessage() {
log.info"""
=========================================
- Hecaton v0.5.0
+ Hecaton v0.5.1
=========================================
Usage:
nextflow run hecaton --genome_file reference.fa --reads "prefix_{1,2}.fastq" --manta_config configManta_weight_1.py.ini --model_file model_file.pkl --output_dir results
diff --git a/nextflow/hecaton_no_align.nf b/nextflow/hecaton_no_align.nf
index 76e4042..e4ca11e 100755
--- a/nextflow/hecaton_no_align.nf
+++ b/nextflow/hecaton_no_align.nf
@@ -25,7 +25,7 @@ params.help = false
def helpMessage() {
log.info"""
=========================================
- Hecaton v0.5.0
+ Hecaton v0.5.1
=========================================
Usage:
nextflow run hecaton --genome_file reference.fa --bwa_bams "*.bam" --manta_config configManta_weight_1.py.ini --model_file model_file.pkl --output_dir results
diff --git a/scripts/filter/filter_ref_sites_vcf.py b/scripts/filter/filter_ref_sites_vcf.py
index 916ef66..6522f37 100755
--- a/scripts/filter/filter_ref_sites_vcf.py
+++ b/scripts/filter/filter_ref_sites_vcf.py
@@ -53,6 +53,7 @@ def filter_ref_sites(input_fn, min_samples, output_fn):
else:
for sample in samples:
genotype = record.samples[sample]["GT"]
+ print(genotype)
non_variants = [(0, 0), (None, None), (None, 0)]
if genotype not in non_variants:
var_calls += 1
diff --git a/tests/functional_test.sh b/tests/functional_test.sh
index 3223b59..49af303 100644
--- a/tests/functional_test.sh
+++ b/tests/functional_test.sh
@@ -57,7 +57,7 @@ else
echo "Converting VCF to table test successful"
fi
-filter_ref_sites_vcf.py -v ../tests/genotyping/test_filter_ref_input.vcf -n 0 -o test_filter_ref_output.vcf
+filter_ref_sites_vcf.py -v ../tests/genotyping/test_filter_ref_input.vcf -n 1 -o test_filter_ref_output.vcf
cmp test_filter_ref_output.vcf ../tests/genotyping/test_filter_ref_expected_output.vcf
if [ $? -ne 0 ]
diff --git a/tests/genotyping/expected_output.tsv b/tests/genotyping/expected_output.tsv
index cc7e152..253ab58 100644
--- a/tests/genotyping/expected_output.tsv
+++ b/tests/genotyping/expected_output.tsv
@@ -1,11 +1,11 @@
CHROM POS REF ALT HOM-VAR VAR 1098.RQ 2098.RQ
1 43994 N <DEL> 1 1 0.0 0.9
1 44995 N <DEL> 1 1 0.86 0.0
-1 75823 N <DEL> 1 1 0.0 0.81
-1 76823 N <DEL> 1 1 0.81 0.0
-1 484431 N <DUP> 2 2 0.76 0.76
+1 75823 N <DEL> 0 1 0.0 0.81
+1 76823 N <DEL> 0 1 0.81 0.0
+1 484431 N <DUP> 0 1 0.76 0.76
1 4618775 N NCTTACAGTATAATCCAAGGCATGTATATATATCTTTCTTAGAGTTTTTTTTTTTTTTTGAACACACTCTTT 0 2 0.71 0.71
1 4618785 N NCTTACAGTATAATCCAAGGCATGTATATATATCTTTCTTAGAGTTTTTTTTTTTTTTTGAACACACTCT 0 1 0.0 0.72
-1 6134670 N <DUP> 2 2 0.8 0.8
+1 6134670 N <DUP> 0 2 0.8 0.8
1 6134670 N <DUP> 1 1 0.0 0.7
2 9057242 N <DEL> 1 1 0.83 0.83
diff --git a/tests/genotyping/expected_output.vcf b/tests/genotyping/expected_output.vcf
index 7f1747e..08f5e5e 100644
--- a/tests/genotyping/expected_output.vcf
+++ b/tests/genotyping/expected_output.vcf
@@ -1,10 +1,15 @@
-##fileformat=VCFv4.3
-##fileDate=20190207
+##fileformat=VCFv4.2
+##fileDate=20220320
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=END,Number=.,Type=Integer,Description="End position of the variant described in this region">
##INFO=<ID=INSCHROM,Number=.,Type=String,Description="Chromosome on which insertion site of the dispersed duplication is located">
##INFO=<ID=INSPOS,Number=.,Type=Integer,Description="Position of insertion site of the dispersed duplication">
+##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
+##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
+##INFO=<ID=CIPOS95,Number=2,Type=Integer,Description="Confidence interval (95%) around POS for imprecise variants">
+##INFO=<ID=CIEND95,Number=2,Type=Integer,Description="Confidence interval (95%) around END for imprecise variants">
##ALT=<ID=DEL,Description="Deletion">
+##ALT=<ID=DUP,Description="Duplication">
##ALT=<ID=DUP:DISPERSED,Description="Dispersed Duplication">
##ALT=<ID=DUP:TANDEM,Description="Tandem Duplication">
##ALT=<ID=INS,Description="Insertion of novel sequence">
@@ -20,13 +25,13 @@
##contig=<ID=1,length=30427671>
##contig=<ID=2,length=19698289>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 1098 2098
-1 43994 1 N <DEL> -1 PASS SVTYPE=DEL;END=45232 GT:SUP:RP:SR:TOOL:RQ:DHFC:DHBFC:DHFFC 0/0:0:0:0:.:0:-1:-1:-1 1/1:18.0:0.0:18.0:DELLY,LUMPY,MANTA,GRIDSS:0.9:0.0:0.0:0.0
-1 44995 2 N <DEL> -1 PASS SVTYPE=DEL;END=45231 GT:SUP:RP:SR:TOOL:RQ:DHFC:DHBFC:DHFFC 1/1:17.0:0.0:17.0:DELLY,LUMPY,MANTA,GRIDSS:0.86:0.0:0.0:0.0 0/0:0:0:0:.:0:-1:-1:-1
-1 75823 3 N <DEL> -1 PASS SVTYPE=DEL;END=77562 GT:SUP:RP:SR:TOOL:RQ:DHFC:DHBFC:DHFFC 0/0:0:0:0:.:0:-1:-1:-1 1/1:26.5:15.0:11.5:DELLY,LUMPY,MANTA,GRIDSS:0.81:0.5:0.5:0.5
-1 76823 4 N <DEL> -1 PASS SVTYPE=DEL;END=77560 GT:SUP:RP:SR:TOOL:RQ:DHFC:DHBFC:DHFFC 1/1:26.5:15.0:11.5:DELLY,LUMPY,MANTA,GRIDSS:0.81:0.25:0.25:0.25 0/0:0:0:0:.:0:-1:-1:-1
-1 484431 5 N <DUP> -1 PASS SVTYPE=DUP:TANDEM;END=586498 GT:SUP:RP:SR:TOOL:RQ:DHFC:DHBFC:DHFFC 1/1:14.0:0.0:14.0:GRIDSS:0.76:1.25:1.25:1.25 1/1:14.0:0.0:14.0:GRIDSS:0.76:1.5:1.5:1.5
-1 4618775 6 N NCTTACAGTATAATCCAAGGCATGTATATATATCTTTCTTAGAGTTTTTTTTTTTTTTTGAACACACTCTTT -1 PASS SVTYPE=INS GT:SUP:RP:SR:TOOL:RQ:DHFC:DHBFC:DHFFC ./1:10.0:0.0:10.0:DELLY:0.71:0.9090909957885742:0.9090909957885742:1.111109972000122 ./1:10.0:0.0:10.0:DELLY:0.71:0.9090909957885742:0.9090909957885742:1.111109972000122
-1 4618785 7 N NCTTACAGTATAATCCAAGGCATGTATATATATCTTTCTTAGAGTTTTTTTTTTTTTTTGAACACACTCT -1 PASS SVTYPE=INS GT:SUP:RP:SR:TOOL:RQ:DHFC:DHBFC:DHFFC 0/0:0:0:0:.:0:-1:-1:-1 ./1:11.0:0.0:11.0:DELLY:0.72:0.9090909957885742:0.9090909957885742:1.111109972000122
-1 6134670 8 N <DUP> -1 PASS SVTYPE=DUP:DISPERSED;END=6134722;INSCHROM=1;INSPOS=6134669 GT:SUP:RP:SR:TOOL:RQ:DHFC:DHBFC:DHFFC 1/1:0.0:0.0:0.0:GRIDSS:0.8:1.5:1.5:1.5 1/1:0.0:0.0:0.0:GRIDSS:0.8:1.5:1.5:1.5
-1 6134670 9 N <DUP> -1 PASS SVTYPE=DUP:DISPERSED;END=6134722;INSCHROM=2;INSPOS=6134669 GT:SUP:RP:SR:TOOL:RQ:DHFC:DHBFC:DHFFC 0/0:0:0:0:.:0:-1:-1:-1 1/1:0.0:0.0:0.0:GRIDSS:0.7:2.0:2.0:2.0
-2 9057242 10 N <DEL> -1 PASS SVTYPE=DEL;END=9059624 GT:SUP:RP:SR:TOOL:RQ:DHFC:DHBFC:DHFFC 0/0:23.0:12.0:11.0:DELLY,LUMPY,MANTA,GRIDSS:0.83:2.0:2.0:2.0 1/1:23.0:12.0:11.0:DELLY,LUMPY,MANTA,GRIDSS:0.83:0.0:0.0:0.0
+1 43994 1 N <DEL> -1 PASS SVTYPE=DEL;END=45232;CIPOS=-10,10;CIEND=-10,10;CIPOS95=-10,10;CIEND95=-10,10 GT:SUP:RP:SR:TOOL:RQ:DHFC:DHBFC:DHFFC 0/0:0:0:0:.:0:-1:-1:-1 1/1:18.0:0.0:18.0:DELLY,LUMPY,MANTA,GRIDSS:0.9:0.0:0.0:0.0
+1 44995 2 N <DEL> -1 PASS SVTYPE=DEL;END=45231;CIPOS=-10,10;CIEND=-10,10;CIPOS95=-10,10;CIEND95=-10,10 GT:SUP:RP:SR:TOOL:RQ:DHFC:DHBFC:DHFFC 1/1:17.0:0.0:17.0:DELLY,LUMPY,MANTA,GRIDSS:0.86:0.0:0.0:0.0 0/0:0:0:0:.:0:-1:-1:-1
+1 75823 3 N <DEL> -1 PASS SVTYPE=DEL;END=77562;CIPOS=-10,10;CIEND=-10,10;CIPOS95=-10,10;CIEND95=-10,10 GT:SUP:RP:SR:TOOL:RQ:DHFC:DHBFC:DHFFC 0/0:0:0:0:.:0:-1:-1:-1 0/1:26.5:15.0:11.5:DELLY,LUMPY,MANTA,GRIDSS:0.81:0.5:0.5:0.5
+1 76823 4 N <DEL> -1 PASS SVTYPE=DEL;END=77560;CIPOS=-10,10;CIEND=-10,10;CIPOS95=-10,10;CIEND95=-10,10 GT:SUP:RP:SR:TOOL:RQ:DHFC:DHBFC:DHFFC 0/1:26.5:15.0:11.5:DELLY,LUMPY,MANTA,GRIDSS:0.81:0.25:0.25:0.25 0/0:0:0:0:.:0:-1:-1:-1
+1 484431 5 N <DUP> -1 PASS SVTYPE=DUP:TANDEM;END=586498;CIPOS=-10,10;CIEND=-10,10;CIPOS95=-10,10;CIEND95=-10,10 GT:SUP:RP:SR:TOOL:RQ:DHFC:DHBFC:DHFFC 0/0:14.0:0.0:14.0:GRIDSS:0.76:1.25:1.25:1.25 0/1:14.0:0.0:14.0:GRIDSS:0.76:1.5:1.5:1.5
+1 4618775 6 N NCTTACAGTATAATCCAAGGCATGTATATATATCTTTCTTAGAGTTTTTTTTTTTTTTTGAACACACTCTTT -1 PASS SVTYPE=INS;CIPOS=-10,10;CIEND=-10,10;CIPOS95=-10,10;CIEND95=-10,10 GT:SUP:RP:SR:TOOL:RQ:DHFC:DHBFC:DHFFC ./1:10.0:0.0:10.0:DELLY:0.71:0.9090909957885742:0.9090909957885742:1.111109972000122 ./1:10.0:0.0:10.0:DELLY:0.71:0.9090909957885742:0.9090909957885742:1.111109972000122
+1 4618785 7 N NCTTACAGTATAATCCAAGGCATGTATATATATCTTTCTTAGAGTTTTTTTTTTTTTTTGAACACACTCT -1 PASS SVTYPE=INS;CIPOS=-10,10;CIEND=-10,10;CIPOS95=-10,10;CIEND95=-10,10 GT:SUP:RP:SR:TOOL:RQ:DHFC:DHBFC:DHFFC 0/0:0:0:0:.:0:-1:-1:-1 ./1:11.0:0.0:11.0:DELLY:0.72:0.9090909957885742:0.9090909957885742:1.111109972000122
+1 6134670 8 N <DUP> -1 PASS SVTYPE=DUP:DISPERSED;END=6134722;INSCHROM=1;INSPOS=6134669;CIPOS=-10,10;CIEND=-10,10;CIPOS95=-10,10;CIEND95=-10,10 GT:SUP:RP:SR:TOOL:RQ:DHFC:DHBFC:DHFFC 0/1:0.0:0.0:0.0:GRIDSS:0.8:1.5:1.5:1.5 0/1:0.0:0.0:0.0:GRIDSS:0.8:1.5:1.5:1.5
+1 6134670 9 N <DUP> -1 PASS SVTYPE=DUP:DISPERSED;END=6134722;INSCHROM=2;INSPOS=6134669;CIPOS=-10,10;CIEND=-10,10;CIPOS95=-10,10;CIEND95=-10,10 GT:SUP:RP:SR:TOOL:RQ:DHFC:DHBFC:DHFFC 0/0:0:0:0:.:0:-1:-1:-1 1/1:0.0:0.0:0.0:GRIDSS:0.7:2.0:2.0:2.0
+2 9057242 10 N <DEL> -1 PASS SVTYPE=DEL;END=9059624;CIPOS=-10,10;CIEND=-10,10;CIPOS95=-10,10;CIEND95=-10,10 GT:SUP:RP:SR:TOOL:RQ:DHFC:DHBFC:DHFFC 0/0:23.0:12.0:11.0:DELLY,LUMPY,MANTA,GRIDSS:0.83:2.0:2.0:2.0 1/1:23.0:12.0:11.0:DELLY,LUMPY,MANTA,GRIDSS:0.83:0.0:0.0:0.0
--
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