diff --git a/setup.py b/setup.py index 0557cf6..34fb416 100644 --- a/setup.py +++ b/setup.py @@ -2,7 +2,7 @@ setup( name='sniffles', - version='2.4', + version='2.4.1', packages=find_packages(), url='https://github.com/fritzsedlazeck/Sniffles', license='MIT', @@ -11,4 +11,4 @@ description='A fast structural variation caller for long-read sequencing data', long_description=open('README.md').read(), long_description_content_type='text/markdown', -) \ No newline at end of file +) diff --git a/src/sniffles/config.py b/src/sniffles/config.py index c4ab71a..d0ed6e8 100644 --- a/src/sniffles/config.py +++ b/src/sniffles/config.py @@ -3,7 +3,7 @@ # Sniffles2 # A fast structural variant caller for long-read sequencing data # -# Created: 18.10.2021 +# Created: 18.10.2021 # Author: Moritz Smolka # Maintainer: Hermann Romanek # Contact: sniffles@romanek.at @@ -13,7 +13,6 @@ import sys import datetime import argparse -from collections import defaultdict from typing import Union, Optional @@ -21,7 +20,7 @@ from sniffles.region import Region VERSION = "Sniffles2" -BUILD = "2.4" +BUILD = "2.4.1" SNF_VERSION = "S2_rc4" diff --git a/src/sniffles/vcf.py b/src/sniffles/vcf.py index dda98cb..3b990af 100755 --- a/src/sniffles/vcf.py +++ b/src/sniffles/vcf.py @@ -154,7 +154,7 @@ def write_header(self, contigs_lengths): self.write_header_line('INFO=') self.write_header_line('INFO=') self.write_header_line('INFO=') - self.write_header_line('INFO=') + self.write_header_line('INFO=') self.write_header_line('INFO=') self.write_header_line('INFO=') self.write_header_line('INFO=') @@ -222,7 +222,7 @@ def write_call(self, call): infos = { "SVTYPE": call.svtype, "SVLEN": call.svlen, - "SVLENGTHS": ",".join(map(str, call.svlens)), + "SVLENGTHS": call.svlens, "END": end, "SUPPORT": call.support, "RNAMES": call.rnames if self.config.output_rnames else None, @@ -349,6 +349,9 @@ def read_svs_iter(self): if "SVLEN" in info_dict: call.svlen = int(info_dict["SVLEN"]) + if "SVLENGTHS`" in info_dict: + call.svlens = info_dict["SVLENGTHS"] + if "END" in info_dict: call.end = int(info_dict["END"])