bump version

bump version

setup.py

@@ -2,7 +2,7 @@
 
 setup(
  name='sniffles',
- version='2.4',
+ version='2.4.1',
  packages=find_packages(),
  url='https:/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',
-)
+)

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: [email protected]
@@ -13,15 +13,14 @@
 import sys
 import datetime
 import argparse
-from collections import defaultdict
 
 from typing import Union, Optional
 
 from sniffles import util
 from sniffles.region import Region
 
 VERSION = "Sniffles2"
-BUILD = "2.4"
+BUILD = "2.4.1"
 SNF_VERSION = "S2_rc4"
 
 

src/sniffles/vcf.py

@@ -154,7 +154,7 @@ def write_header(self, contigs_lengths):
  self.write_header_line('INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Structural variation with imprecise breakpoints">')
  self.write_header_line('INFO=<ID=MOSAIC,Number=0,Type=Flag,Description="Structural variation classified as putative mosaic">')
  self.write_header_line('INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Length of structural variation">')
- self.write_header_line('INFO=<ID=SVLENGTHS,Number=.,Type=Integer,Description="Lengths of structural variation (all)">')
+ self.write_header_line('INFO=<ID=SVLENGTH,Number=.,Type=Integer,Description="Lengths of structural variation (all)">')
  self.write_header_line('INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variation">')
  self.write_header_line('INFO=<ID=CHR2,Number=1,Type=String,Description="Mate chromsome for BND SVs">')
  self.write_header_line('INFO=<ID=SUPPORT,Number=1,Type=Integer,Description="Number of reads supporting the structural variation">')
@@ -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"])