Skip to content

Issues: arq5x/bedtools2

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

234 Open 605 Closed
234 Open 605 Closed
Author
Filter by author
Loading
Label
Filter by label
Loading
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Loading
Milestones
Filter by milestone
Loading
Assignee
Filter by who’s assigned
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Issues list

Bedtools runs infinitely with large memory usage under sorted option when there's unmapped reads
#1113 opened Jan 22, 2025 by kheber
bedtools intersect with -g option: chromosomes without regions cause intersections being missed
#1111 opened Jan 9, 2025 by ChrissiKalk97
static.binary missing for 2.31.1
#1110 opened Dec 16, 2024 by bartcharbon
Inconsistent naming convention warning
#1109 opened Nov 28, 2024 by fa8sanger
Bedtools Genomecov -pc Option: Name-Sorted BAM File Error in Version 2.31.0
#1108 opened Nov 14, 2024 by yeeun3712
Line limit of bedtools getfasta and other sub-commands?
#1107 opened Nov 11, 2024 by YuanfengZhang
2
CLI seg faults
#1106 opened Oct 29, 2024 by zeeev
Strand specific behavior is broken
#1103 opened Aug 21, 2024 by Thomas1664
terminate called after throwing an instance of 'std::out_of_range'
#1102 opened Aug 14, 2024 by hullv
Two Errors in Infographic for jaccard function
#1101 opened Aug 9, 2024 by keksundso
Latest conda version throws error for large chromStart values
#1099 opened Jul 25, 2024 by SohaibRais
2
Error: Invalid record in file
#1098 opened Jul 23, 2024 by r-poloni
need to include cstdint in ParseTools.h
#1096 opened Jun 19, 2024 by emyr666
Number can not keep consistant
#1092 opened May 30, 2024 by hsymoon
1
Are there any means to speedup intersect?
#1091 opened May 18, 2024 by lokapal
Option to skip first line
#1090 opened Apr 27, 2024 by bskubi
shuffle -incl: Fall out of -incl include.bed file
#1089 opened Apr 26, 2024 by chenludi
2
Undefined behavior in bedtools expand
#1088 opened Apr 25, 2024 by SoapGentoo
Command bedtools makewindows -w 200 -s 50 -g resources/hg19.autoX.chrom.sizes not working
#1086 opened Apr 19, 2024 by gurudatta-patil
The bedtools multiinter -header option outputs broken BED
#1085 opened Apr 5, 2024 by dbolser
2
getfasta -rna option does not work for plus strand line when setting -s option
#1084 opened Mar 27, 2024 by NaotoKubota
1
unable to install
#1082 opened Mar 13, 2024 by Heather1999
1
Stitching read pair R1 andf R2 sequences based on alignment from SAM/BAM
#1081 opened Feb 15, 2024 by mmokrejs
genomecov -d -pc -ibam showing no coverage for every position
#1080 opened Feb 15, 2024 by gcabebe
2
tutorial link broken
#1079 opened Jan 28, 2024 by notestaff
1
ProTip! Type g i on any issue or pull request to go back to the issue listing page.