Merge pull request #27 from bioinform/update_to_v0.1.3

updated version to 0.1.3

docker/Dockerfile

@@ -1,6 +1,6 @@
 FROM ubuntu:16.04
 
-ENV NEUSOMATIC_VERSION 0.1.2
+ENV NEUSOMATIC_VERSION 0.1.3
 ENV ZLIB_VERSION 1.2.11
 ENV NUMPY_VERSION 1.14.3
 ENV SCIPY_VERSION 1.1.0

neusomatic/python/_version.py

@@ -1 +1 @@
-__version__ = "0.1.2"
+__version__ = "0.1.3"

test/NeuSomatic_ensemble.vcf

@@ -1,5 +1,5 @@
 ##fileformat=VCFv4.2
-##NeuSomatic Version=0.1.2
+##NeuSomatic Version=0.1.3
 ##FORMAT=<ID=SCORE,Number=1,Type=Float,Description="Prediction probability score">
 ##FILTER=<ID=PASS,Description="Accept as a higher confidence somatic mutation calls with probability score value at least 0.7">
 ##FILTER=<ID=LowQual,Description="Less confident somatic mutation calls with probability score value at least 0.4">

test/NeuSomatic_standalone.vcf

@@ -1,5 +1,5 @@
 ##fileformat=VCFv4.2
-##NeuSomatic Version=0.1.2
+##NeuSomatic Version=0.1.3
 ##FORMAT=<ID=SCORE,Number=1,Type=Float,Description="Prediction probability score">
 ##FILTER=<ID=PASS,Description="Accept as a higher confidence somatic mutation calls with probability score value at least 0.7">
 ##FILTER=<ID=LowQual,Description="Less confident somatic mutation calls with probability score value at least 0.4">

test/docker_test.sh

@@ -10,24 +10,24 @@ if [ ! -f Homo_sapiens.GRCh37.75.dna.chromosome.22.fa ]
 then
 	if [ ! -f Homo_sapiens.GRCh37.75.dna.chromosome.22.fa.gz ]
 	then
-		docker run -v ${test_dir}:/mnt -u $UID --memory 30G  msahraeian/neusomatic:0.1.2 /bin/bash -c \
+		docker run -v ${test_dir}:/mnt -u $UID --memory 30G  msahraeian/neusomatic:0.1.3 /bin/bash -c \
 		"cd /mnt/example/ && wget ftp://ftp.ensembl.org/pub/release-75//fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.75.dna.chromosome.22.fa.gz"
 	fi
-	docker run -v ${test_dir}:/mnt -u $UID --memory 30G  msahraeian/neusomatic:0.1.2 /bin/bash -c \
+	docker run -v ${test_dir}:/mnt -u $UID --memory 30G  msahraeian/neusomatic:0.1.3 /bin/bash -c \
 	"cd /mnt/example/ && gunzip -f Homo_sapiens.GRCh37.75.dna.chromosome.22.fa.gz"
 
 fi
 if [ ! -f Homo_sapiens.GRCh37.75.dna.chromosome.22.fa.fai ]
 then
-	docker run -v ${test_dir}:/mnt -u $UID --memory 30G  msahraeian/neusomatic:0.1.2 /bin/bash -c \
+	docker run -v ${test_dir}:/mnt -u $UID --memory 30G  msahraeian/neusomatic:0.1.3 /bin/bash -c \
 	"samtools faidx /mnt/example/Homo_sapiens.GRCh37.75.dna.chromosome.22.fa"
 fi
 rm -rf work_standalone
 
 
 
 #Stand-alone NeuSomatic test 
-docker run -v ${test_dir}:/mnt -u $UID --memory 30G  msahraeian/neusomatic:0.1.2 /bin/bash -c \
+docker run -v ${test_dir}:/mnt -u $UID --memory 30G  msahraeian/neusomatic:0.1.3 /bin/bash -c \
 "python /opt/neusomatic/neusomatic/python/preprocess.py \
 	--mode call \
 	--reference /mnt/example/Homo_sapiens.GRCh37.75.dna.chromosome.22.fa \
@@ -45,7 +45,7 @@ docker run -v ${test_dir}:/mnt -u $UID --memory 30G  msahraeian/neusomatic:0.1.2
 	--num_threads 1 \
 	--scan_alignments_binary /opt/neusomatic/neusomatic/bin/scan_alignments"
 
-docker run -v ${test_dir}:/mnt -u $UID --memory 30G --shm-size 8G msahraeian/neusomatic:0.1.2 /bin/bash -c \
+docker run -v ${test_dir}:/mnt -u $UID --memory 30G --shm-size 8G msahraeian/neusomatic:0.1.3 /bin/bash -c \
 "CUDA_VISIBLE_DEVICES= python /opt/neusomatic/neusomatic/python/call.py \
 		--candidates_tsv /mnt/example/work_standalone/dataset/*/candidates*.tsv \
 		--reference /mnt/example/Homo_sapiens.GRCh37.75.dna.chromosome.22.fa \
@@ -54,7 +54,7 @@ docker run -v ${test_dir}:/mnt -u $UID --memory 30G --shm-size 8G msahraeian/neu
 		--num_threads 1 \
 		--batch_size 100"
 
-docker run -v ${test_dir}:/mnt -u $UID --memory 30G  msahraeian/neusomatic:0.1.2 /bin/bash -c \
+docker run -v ${test_dir}:/mnt -u $UID --memory 30G  msahraeian/neusomatic:0.1.3 /bin/bash -c \
 "python /opt/neusomatic/neusomatic/python/postprocess.py \
 		--reference /mnt/example/Homo_sapiens.GRCh37.75.dna.chromosome.22.fa \
 		--tumor_bam /mnt/tumor.bam \
@@ -66,7 +66,7 @@ docker run -v ${test_dir}:/mnt -u $UID --memory 30G  msahraeian/neusomatic:0.1.2
 
 rm -rf /mnt/example/work_ensemble
 #Ensemble NeuSomatic test 
-docker run -v ${test_dir}:/mnt -u $UID --memory 30G  msahraeian/neusomatic:0.1.2 /bin/bash -c \
+docker run -v ${test_dir}:/mnt -u $UID --memory 30G  msahraeian/neusomatic:0.1.3 /bin/bash -c \
 "python /opt/neusomatic/neusomatic/python/preprocess.py \
 	--mode call \
 	--reference /mnt/example/Homo_sapiens.GRCh37.75.dna.chromosome.22.fa \
@@ -85,7 +85,7 @@ docker run -v ${test_dir}:/mnt -u $UID --memory 30G  msahraeian/neusomatic:0.1.2
 	--ensemble_tsv /mnt/ensemble.tsv \
 	--scan_alignments_binary /opt/neusomatic/neusomatic/bin/scan_alignments"
 
-docker run -v ${test_dir}:/mnt -u $UID --memory 30G --shm-size 8G msahraeian/neusomatic:0.1.2 /bin/bash -c \
+docker run -v ${test_dir}:/mnt -u $UID --memory 30G --shm-size 8G msahraeian/neusomatic:0.1.3 /bin/bash -c \
 "CUDA_VISIBLE_DEVICES= python /opt/neusomatic/neusomatic/python/call.py \
 		--candidates_tsv /mnt/example/work_ensemble/dataset/*/candidates*.tsv \
 		--reference /mnt/example/Homo_sapiens.GRCh37.75.dna.chromosome.22.fa \
@@ -95,7 +95,7 @@ docker run -v ${test_dir}:/mnt -u $UID --memory 30G --shm-size 8G msahraeian/neu
 		--ensemble \
 		--batch_size 100"
 
-docker run -v ${test_dir}:/mnt -u $UID --memory 30G  msahraeian/neusomatic:0.1.2 /bin/bash -c \
+docker run -v ${test_dir}:/mnt -u $UID --memory 30G  msahraeian/neusomatic:0.1.3 /bin/bash -c \
 "python /opt/neusomatic/neusomatic/python/postprocess.py \
 		--reference /mnt/example/Homo_sapiens.GRCh37.75.dna.chromosome.22.fa \
 		--tumor_bam /mnt/tumor.bam \