Update version number

SamuelNicaise · May 2, 2024 · 48a456c · 48a456c
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commit 48a456c
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Showing 27 changed files with 28 additions and 28 deletions.
diff --git a/src/variantconvert/__init__.py b/src/variantconvert/__init__.py
@@ -1,12 +1,12 @@
 # -*- coding: utf-8 -*-
 """
 @Author: Samuel Nicaise
-@Version: v2.0.0
+@Version: v2.0.1
 """
 import appdirs
 import os
 
-__version__ = "2.0.0"
+__version__ = "2.0.1"
 
 __default_config__ = os.path.join(os.path.dirname(__file__), "configs")
 

diff --git a/src/variantconvert/__main__.py b/src/variantconvert/__main__.py
@@ -3,7 +3,7 @@
 @Goal: Expand Celine Besnard's script with infinite conversion abilities between vcf and various other formats
 @Author: Samuel Nicaise
 @Date: 23/11/2021
-@Version: v2.0.0
+@Version: v2.0.1
 
 Prerequisites: pandas, pyfaidx (https://github.com/mdshw5/pyfaidx))
 

diff --git a/src/variantconvert/commons.py b/src/variantconvert/commons.py
@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 """
 @Author: Samuel Nicaise
-@Version: v2.0.0
+@Version: v2.0.1
 """
 
 import logging as log

diff --git a/src/variantconvert/converter_factory.py b/src/variantconvert/converter_factory.py
@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 """
 @Author: Samuel Nicaise
-@Version: v2.0.0
+@Version: v2.0.1
 """
 
 from variantconvert.converters.vcf_from_annotsv import VcfFromAnnotsv

diff --git a/src/variantconvert/converters/vcf_from_annotsv.py b/src/variantconvert/converters/vcf_from_annotsv.py
@@ -198,7 +198,7 @@ def _build_info_dic(self):
         annots_dic = {}
         supplemental_info_fields = []
 
-        # method of versions < 2.0.0: merge full and split annotations into one variant
+        # method of versions < 2.0.1: merge full and split annotations into one variant
         if self.config["GENERAL"]["mode"] == "combined":
             id_col = self.config["VCF_COLUMNS"]["INFO"]["AnnotSV_ID"]
             for variant_id, df_variant in self.input_annot_df.groupby(id_col):

diff --git a/src/variantconvert/helpers/helper_functions.py b/src/variantconvert/helpers/helper_functions.py
@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 """
 @Author: Samuel Nicaise
-@Version: v2.0.0
+@Version: v2.0.1
 """
 
 from commons import get_genome

diff --git a/src/variantconvert/varank_batch.py b/src/variantconvert/varank_batch.py
@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 """
 @Author: Samuel Nicaise
-@Version: v2.0.0
+@Version: v2.0.1
 
 #for testing:
 docker run --rm -ti --entrypoint=bash -v /home1:/home1 tsvconvert

diff --git a/src/variantconvert/variant.py b/src/variantconvert/variant.py
@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 """
 @Author: Samuel Nicaise
-@Version: v2.0.0
+@Version: v2.0.1
 """
 
 import hashlib

diff --git a/tests/controls/annotsv_combined/annotsv3_from_bed.vcf b/tests/controls/annotsv_combined/annotsv3_from_bed.vcf
@@ -2,7 +2,7 @@
 ##fileDate=18/04/2024
 ##inputFile=/home1/HUB/bin/variantconvert/current/tests/data/annotsv_from_bed.tsv
 ##source=variantconvert from AnnotSV
-##variantconvertVersion=2.0.0
+##variantconvertVersion=2.0.1
 ##variantconvertMode=combined
 ##FILTER=<ID=PASS,Description="Passed filter">
 ##ALT=<ID=DUP,Description="Duplication">

diff --git a/tests/controls/annotsv_combined/annotsv_wt_samples.vcf b/tests/controls/annotsv_combined/annotsv_wt_samples.vcf
@@ -2,7 +2,7 @@
 ##fileDate=18/04/2024
 ##inputFile=/home1/HUB/bin/variantconvert/current/tests/data/annotsv_wt_samples.tsv
 ##source=variantconvert from AnnotSV
-##variantconvertVersion=2.0.0
+##variantconvertVersion=2.0.1
 ##variantconvertMode=combined
 ##FILTER=<ID=PASS,Description="Passed filter">
 ##ALT=<ID=DUP,Description="Duplication">

diff --git a/tests/controls/annotsv_combined/decon_annotsv_test.vcf b/tests/controls/annotsv_combined/decon_annotsv_test.vcf
@@ -2,7 +2,7 @@
 ##fileDate=18/04/2024
 ##inputFile=/home1/HUB/bin/variantconvert/current/tests/data/DECON.results_all.AnnotSV.tsv
 ##source=variantconvert from AnnotSV
-##variantconvertVersion=2.0.0
+##variantconvertVersion=2.0.1
 ##variantconvertMode=combined
 ##FILTER=<ID=PASS,Description="Passed filter">
 ##ALT=<ID=DUP,Description="Duplication">

diff --git a/tests/controls/annotsv_combined/multisample_annotsv3_from_bed.vcf b/tests/controls/annotsv_combined/multisample_annotsv3_from_bed.vcf
@@ -2,7 +2,7 @@
 ##fileDate=18/04/2024
 ##inputFile=/home1/HUB/bin/variantconvert/current/tests/data/multisample_from_bed.annotated.tsv
 ##source=variantconvert from AnnotSV
-##variantconvertVersion=2.0.0
+##variantconvertVersion=2.0.1
 ##variantconvertMode=combined
 ##FILTER=<ID=PASS,Description="Passed filter">
 ##ALT=<ID=DUP,Description="Duplication">

diff --git a/tests/controls/annotsv_full/annotsv3_from_bed.vcf b/tests/controls/annotsv_full/annotsv3_from_bed.vcf
@@ -2,7 +2,7 @@
 ##fileDate=18/04/2024
 ##inputFile=/home1/HUB/bin/variantconvert/current/tests/data/annotsv_from_bed.tsv
 ##source=variantconvert from AnnotSV
-##variantconvertVersion=2.0.0
+##variantconvertVersion=2.0.1
 ##variantconvertMode=full
 ##FILTER=<ID=PASS,Description="Passed filter">
 ##ALT=<ID=DUP,Description="Duplication">

diff --git a/tests/controls/annotsv_full/annotsv_wt_samples.vcf b/tests/controls/annotsv_full/annotsv_wt_samples.vcf
@@ -2,7 +2,7 @@
 ##fileDate=18/04/2024
 ##inputFile=/home1/HUB/bin/variantconvert/current/tests/data/annotsv_wt_samples.tsv
 ##source=variantconvert from AnnotSV
-##variantconvertVersion=2.0.0
+##variantconvertVersion=2.0.1
 ##variantconvertMode=full
 ##FILTER=<ID=PASS,Description="Passed filter">
 ##ALT=<ID=DUP,Description="Duplication">

diff --git a/tests/controls/annotsv_full/decon_annotsv_test.vcf b/tests/controls/annotsv_full/decon_annotsv_test.vcf
@@ -2,7 +2,7 @@
 ##fileDate=18/04/2024
 ##inputFile=/home1/HUB/bin/variantconvert/current/tests/data/DECON.results_all.AnnotSV.tsv
 ##source=variantconvert from AnnotSV
-##variantconvertVersion=2.0.0
+##variantconvertVersion=2.0.1
 ##variantconvertMode=full
 ##FILTER=<ID=PASS,Description="Passed filter">
 ##ALT=<ID=DUP,Description="Duplication">

diff --git a/tests/controls/annotsv_full/multisample_annotsv3_from_bed.vcf b/tests/controls/annotsv_full/multisample_annotsv3_from_bed.vcf
@@ -2,7 +2,7 @@
 ##fileDate=18/04/2024
 ##inputFile=/home1/HUB/bin/variantconvert/current/tests/data/multisample_from_bed.annotated.tsv
 ##source=variantconvert from AnnotSV
-##variantconvertVersion=2.0.0
+##variantconvertVersion=2.0.1
 ##variantconvertMode=full
 ##FILTER=<ID=PASS,Description="Passed filter">
 ##ALT=<ID=DUP,Description="Duplication">

diff --git a/tests/controls/annotsv_fullandsplit/annotsv3_from_bed.vcf b/tests/controls/annotsv_fullandsplit/annotsv3_from_bed.vcf
@@ -2,7 +2,7 @@
 ##fileDate=18/04/2024
 ##inputFile=/home1/HUB/bin/variantconvert/current/tests/data/annotsv_from_bed.tsv
 ##source=variantconvert from AnnotSV
-##variantconvertVersion=2.0.0
+##variantconvertVersion=2.0.1
 ##variantconvertMode=full&split
 ##FILTER=<ID=PASS,Description="Passed filter">
 ##ALT=<ID=DUP,Description="Duplication">

diff --git a/tests/controls/annotsv_fullandsplit/annotsv_wt_samples.vcf b/tests/controls/annotsv_fullandsplit/annotsv_wt_samples.vcf
@@ -2,7 +2,7 @@
 ##fileDate=18/04/2024
 ##inputFile=/home1/HUB/bin/variantconvert/current/tests/data/annotsv_wt_samples.tsv
 ##source=variantconvert from AnnotSV
-##variantconvertVersion=2.0.0
+##variantconvertVersion=2.0.1
 ##variantconvertMode=full&split
 ##FILTER=<ID=PASS,Description="Passed filter">
 ##ALT=<ID=DUP,Description="Duplication">

diff --git a/tests/controls/annotsv_fullandsplit/decon_annotsv_test.vcf b/tests/controls/annotsv_fullandsplit/decon_annotsv_test.vcf
@@ -2,7 +2,7 @@
 ##fileDate=18/04/2024
 ##inputFile=/home1/HUB/bin/variantconvert/current/tests/data/DECON.results_all.AnnotSV.tsv
 ##source=variantconvert from AnnotSV
-##variantconvertVersion=2.0.0
+##variantconvertVersion=2.0.1
 ##variantconvertMode=full&split
 ##FILTER=<ID=PASS,Description="Passed filter">
 ##ALT=<ID=DUP,Description="Duplication">

diff --git a/tests/controls/annotsv_fullandsplit/multisample_annotsv3_from_bed.vcf b/tests/controls/annotsv_fullandsplit/multisample_annotsv3_from_bed.vcf
@@ -2,7 +2,7 @@
 ##fileDate=18/04/2024
 ##inputFile=/home1/HUB/bin/variantconvert/current/tests/data/multisample_from_bed.annotated.tsv
 ##source=variantconvert from AnnotSV
-##variantconvertVersion=2.0.0
+##variantconvertVersion=2.0.1
 ##variantconvertMode=full&split
 ##FILTER=<ID=PASS,Description="Passed filter">
 ##ALT=<ID=DUP,Description="Duplication">

diff --git a/tests/controls/arriba.vcf b/tests/controls/arriba.vcf
@@ -2,7 +2,7 @@
 ##fileDate=23/01/2023
 ##InputFile=/home1/HUB/bin/variantconvert/current/tests/data/arriba.fusions.tsv
 ##source=variantconvert from arriba
-##variantconvertVersion=2.0.0
+##variantconvertVersion=2.0.1
 ##FILTER=<ID=PASS,Description="Passed filter">
 ##INFO=<ID=Fusion_Gene1,Number=1,Type=String,Description="Fusion gene 1">
 ##INFO=<ID=Fusion_Gene2,Number=1,Type=String,Description="Fusion gene 2">

diff --git a/tests/controls/canoes_bed.vcf b/tests/controls/canoes_bed.vcf
@@ -2,7 +2,7 @@
 ##fileDate=23/01/2023
 ##InputFile=/home1/HUB/bin/variantconvert/current/tests/data/canoes.bed
 ##source=variantconvert from canoes_bed
-##variantconvertVersion=2.0.0
+##variantconvertVersion=2.0.1
 ##FILTER=<ID=PASS,Description="Passed filter">
 ##ALT=<ID=DUP,Description="Duplication">
 ##ALT=<ID=DEL,Description="Deletion">

diff --git a/tests/controls/chromothripsis.vcf b/tests/controls/chromothripsis.vcf
@@ -2,7 +2,7 @@
 ##fileDate=17/03/2023
 ##InputFile=/home1/HUB/bin/variantconvert/current/tests/data/chromothripsis.bedpe
 ##source=variantconvert from bedpe
-##variantconvertVersion=2.0.0
+##variantconvertVersion=2.0.1
 ##FILTER=<ID=PASS,Description="Passed filter">
 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
 ##INFO=<ID=MATEID,Number=1,Type=String,Description="ID of mate breakends">

diff --git a/tests/controls/decon_one_sample.vcf b/tests/controls/decon_one_sample.vcf
@@ -2,7 +2,7 @@
 ##fileDate=23/12/2023
 ##InputFile=/mnt/c/Users/Ichtyornis/Projects/variantconvert_project/variantconvert/tests/data/DECON.one_sample.all.tsv
 ##source=variantconvert from Decon
-##variantconvertVersion=2.0.0
+##variantconvertVersion=2.0.1
 ##FILTER=<ID=PASS,Description="Passed filter">
 ##ALT=<ID=DUP,Description="Duplication">
 ##ALT=<ID=DEL,Description="Deletion">

diff --git a/tests/controls/decon_test.vcf b/tests/controls/decon_test.vcf
@@ -2,7 +2,7 @@
 ##fileDate=23/01/2023
 ##InputFile=/home1/HUB/bin/variantconvert/current/tests/data/DECON.Design_results_all.txt
 ##source=variantconvert from Decon
-##variantconvertVersion=2.0.0
+##variantconvertVersion=2.0.1
 ##FILTER=<ID=PASS,Description="Passed filter">
 ##ALT=<ID=DUP,Description="Duplication">
 ##ALT=<ID=DEL,Description="Deletion">

diff --git a/tests/controls/snp_test.vcf b/tests/controls/snp_test.vcf
@@ -2,7 +2,7 @@
 ##fileDate=03/04/2023
 ##InputFile=/home1/BAS/hameaue/variant_convert/variantconvert/tests/data/snp_test.tsv
 ##source=variantconvert from SNP array
-##variantconvertVersion=2.0.0
+##variantconvertVersion=2.0.1
 ##FILTER=<ID=PASS,Description="Passed filter">
 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
 ##INFO=<ID=MATEID,Number=1,Type=String,Description="ID of mate breakends">

diff --git a/tests/controls/star-fusion.vcf b/tests/controls/star-fusion.vcf
@@ -2,7 +2,7 @@
 ##fileDate=23/01/2023
 ##InputFile=/home1/HUB/bin/variantconvert/current/tests/data/star-fusion.fusion_predictions.tsv
 ##source=variantconvert from star-fusion
-##variantconvertVersion=2.0.0
+##variantconvertVersion=2.0.1
 ##FILTER=<ID=PASS,Description="Passed filter">
 ##INFO=<ID=FusionName,Number=1,Type=String,Description="Fusion name">
 ##INFO=<ID=JunctionReadCount,Number=1,Type=Integer,Description="Number of RNA-Seq fragments containing a read that aligns as a split read at the site of the putative fusion junction">