arq5x/bedtools2 issues and pull requests

#1108 - Bedtools Genomecov -pc Option: Name-Sorted BAM File Error in Version 2.31.0

Issue - State: open - Opened by yeeun3712 11 days ago

#1107 - Line limit of bedtools getfasta and other sub-commands?

Issue - State: open - Opened by YuanfengZhang 14 days ago

#1106 - CLI seg faults

Issue - State: open - Opened by zeeev 26 days ago

#1105 - Pre-compiled binary for bedtools 2.31.1

Issue - State: closed - Opened by madelonst about 2 months ago - 1 comment

#1104 - Support native builds on Windows with MinGW/UCRT

Pull Request - State: open - Opened by theAeon 3 months ago

#1103 - Strand specific behavior is broken

Issue - State: open - Opened by Thomas1664 3 months ago

#1102 - terminate called after throwing an instance of 'std::out_of_range'

Issue - State: open - Opened by hullv 3 months ago

#1101 - Two Errors in Infographic for jaccard function

Issue - State: open - Opened by keksundso 4 months ago

#1100 - bedtools not merging identical segments

Issue - State: closed - Opened by mirahan 4 months ago - 1 comment

#1099 - Latest conda version throws error for large chromStart values

Issue - State: open - Opened by SohaibRais 4 months ago - 2 comments

#1098 - Error: Invalid record in file

Issue - State: open - Opened by r-poloni 4 months ago

#1097 - Update ParseTools.h

Pull Request - State: open - Opened by emyr666 4 months ago

#1096 - need to include cstdint in ParseTools.h

Issue - State: open - Opened by emyr666 5 months ago

#1095 - adding a revcomp tool

Pull Request - State: open - Opened by kloetzl 5 months ago

#1094 - fix memory leak in shiftBed

Pull Request - State: open - Opened by kloetzl 5 months ago

#1093 - Correct link to Bedtools tutorial in the docs

Pull Request - State: open - Opened by dtdoering 6 months ago

#1092 - Number can not keep consistant

Issue - State: open - Opened by hsymoon 6 months ago - 1 comment

#1091 - Are there any means to speedup intersect?

Issue - State: open - Opened by lokapal 6 months ago

#1090 - Option to skip first line

Issue - State: open - Opened by bskubi 7 months ago

#1089 - shuffle -incl: Fall out of -incl include.bed file

Issue - State: open - Opened by chenludi 7 months ago - 2 comments

#1088 - Undefined behavior in `bedtools expand`

Issue - State: open - Opened by SoapGentoo 7 months ago

#1087 - allow python from environment and missing includes on musl

Pull Request - State: open - Opened by SoapGentoo 7 months ago - 2 comments

#1086 - Command bedtools makewindows -w 200 -s 50 -g resources/hg19.autoX.chrom.sizes not working

Issue - State: open - Opened by gurudatta-patil 7 months ago

#1085 - The `bedtools multiinter -header` option outputs broken BED

Issue - State: open - Opened by dbolser 8 months ago - 2 comments

#1084 - getfasta -rna option does not work for plus strand line when setting -s option

Issue - State: open - Opened by NaotoKubota 8 months ago - 1 comment

#1083 - typo fix: chromomsome

Pull Request - State: closed - Opened by chrisamiller 8 months ago - 2 comments

#1082 - unable to install

Issue - State: open - Opened by Heather1999 9 months ago - 1 comment

#1081 - Stitching read pair R1 andf R2 sequences based on alignment from SAM/BAM

Issue - State: open - Opened by mmokrejs 9 months ago

#1080 - genomecov -d -pc -ibam showing no coverage for every position

Issue - State: open - Opened by gcabebe 9 months ago - 2 comments

#1079 - tutorial link broken

Issue - State: open - Opened by notestaff 10 months ago - 1 comment

#1078 - Example BED file(s) referenced throughout the docs are not tab delimited

Issue - State: open - Opened by skchronicles 10 months ago

#1077 - Bedtools install on Mac

Issue - State: open - Opened by luigallucci 10 months ago - 3 comments

#1076 - remote file support

Issue - State: open - Opened by geertvandeweyer 11 months ago

#1075 - Feature request: add -min option to genomecov

Issue - State: open - Opened by ammaraziz 11 months ago

#1074 - Fix minor `shuffleBed` option typo

Pull Request - State: open - Opened by ryancey1 11 months ago - 1 comment

#1073 - Length calculation in `summary` is incorrect if intervals in the input file overlap

Issue - State: open - Opened by tdanhorn 11 months ago

#1072 - "intersect" tool test failure on i386

Issue - State: closed - Opened by emollier about 1 year ago - 2 comments

#1071 - the distance maximal by default of bedtools closest -D

Issue - State: open - Opened by fafaris39 about 1 year ago - 1 comment

#1070 - describe bed coordinates as zero-based half-open intervals

Pull Request - State: open - Opened by kloetzl about 1 year ago - 1 comment

#1069 - Does bedtools intersect still work when meets a line out of order?

Issue - State: open - Opened by Cher-HAN about 1 year ago

#1068 - Does not compile in gcc 13.2.1

Issue - State: closed - Opened by balwierz about 1 year ago - 3 comments

#1067 - Fix various GCC 13 warnings and errors

Pull Request - State: closed - Opened by jmarshall about 1 year ago - 3 comments

#1066 - add cstdint imports to ParseTools

Pull Request - State: closed - Opened by tomp about 1 year ago - 1 comment

#1065 - Difference of depth/mean coverage calculation among sambamba, bedtools, and mosdepth in high coverage panel data

Issue - State: open - Opened by ipstone about 1 year ago

#1064 - Minor typo fix in help

Pull Request - State: open - Opened by nikhil about 1 year ago

#1063 - bamtobed WARNING

Issue - State: open - Opened by songxh1996 over 1 year ago

#1062 - install bedtools on mac M2 chip

Issue - State: closed - Opened by yijiesung over 1 year ago - 1 comment

#1061 - bedtools genomecov and non-primary alignments

Issue - State: open - Opened by awgymer over 1 year ago - 2 comments

#1060 - Potential 32 bit overflow on parse of data with 2.2B lines

Issue - State: open - Opened by wasade over 1 year ago

#1059 - Incorrect examples for intersect "-c/-C" (counting overlaps) with multiple query DBs

Issue - State: open - Opened by cljacobs over 1 year ago

#1058 - bamToFastq v2.31.0 records repeated

Issue - State: open - Opened by brianjohnhaas over 1 year ago - 3 comments

#1057 - [resolved] Strandedness `-s` not working in flankBed, producing no output

Issue - State: closed - Opened by mobilegenome over 1 year ago - 1 comment

#1056 - missing include statements

Issue - State: closed - Opened by vpbrendel over 1 year ago - 3 comments

#1055 - gene overlap

Issue - State: open - Opened by BeatrizFaustino over 1 year ago

#1054 - Memory issue while using coverage

Issue - State: open - Opened by Sameerpython over 1 year ago - 1 comment

#1053 - bedtools merge input too long

Issue - State: open - Opened by yongze-yin over 1 year ago - 2 comments

#1052 - workaround for issue arq5x#1049

Pull Request - State: open - Opened by hkawaji over 1 year ago

#1051 - Received illegal bin number

Issue - State: open - Opened by bijendrabio over 1 year ago

#1050 - -sorted support for getfasta (willing to collaborate)

Issue - State: open - Opened by bmorledge-hampton19 over 1 year ago

#1049 - Broken output for a long BED record by intersectBed

Issue - State: open - Opened by hkawaji over 1 year ago

#1048 - bedtools unionbedg with header won't work

Issue - State: open - Opened by ekushele over 1 year ago

#1047 - misleading tutorial figure of reldist

Issue - State: open - Opened by xzhuo over 1 year ago

#1046 - non-deterministic error, VCF file line contains an unexpected number of fields

Issue - State: closed - Opened by williambrandler over 1 year ago - 1 comment

#1045 - Add missing <cstdint> include

Pull Request - State: closed - Opened by SoapGentoo over 1 year ago - 3 comments

#1044 - Getting gene name with getfasta

Issue - State: closed - Opened by davidaknowles over 1 year ago - 3 comments

#1043 - Avoid dangling reference to temporary string object

Pull Request - State: closed - Opened by jmarshall over 1 year ago - 1 comment

#1042 - ***** WARNING: file GRCm38.p6.genome.size.bed has inconsistent naming convention for record

Issue - State: open - Opened by li1311139481 over 1 year ago - 1 comment

#1041 - bedtools 2.30.0 intersect with 0-length intervals

Issue - State: open - Opened by ddrichel over 1 year ago

#1040 - documentation for pairtopair not uptodate

Issue - State: open - Opened by yfarjoun over 1 year ago - 1 comment

#1039 - bedtools genomecov for a specific set of chromosomes

Issue - State: open - Opened by vkkodali over 1 year ago

#1038 - 'shuffle' runs for a long time

Issue - State: open - Opened by HengkuanLi over 1 year ago

#1037 - Cannot exclude empty rows in unionbedg

Issue - State: closed - Opened by Fujisawa0328 over 1 year ago

#1036 - What is the Expected Output of bedtools flank when input is VCF?

Issue - State: open - Opened by felixm3 almost 2 years ago

#1035 - A installation error

Issue - State: open - Opened by dianzhiyong almost 2 years ago

#1034 - add test for (fixed) #919

Pull Request - State: closed - Opened by brentp almost 2 years ago

#1033 - requested chromosome chr does not exist in the genome file

Issue - State: closed - Opened by ylevmirom almost 2 years ago - 2 comments

#1032 - Error: malformed GFF entry at line 15. Coordinate detected that is < 1.

Issue - State: closed - Opened by simone-says almost 2 years ago - 1 comment

#1031 - fix coverage formatting when scale == 1

Pull Request - State: closed - Opened by brentp almost 2 years ago - 1 comment

#1030 - genomecov: use integer when scale == 1.0

Pull Request - State: closed - Opened by brentp almost 2 years ago - 1 comment

#1029 - use htslib/faidx.h to get fasta sequences

Pull Request - State: closed - Opened by brentp almost 2 years ago - 4 comments

#1028 - Query intersect with directory of multiple .bed files not working - code or command?

Issue - State: closed - Opened by cas-lemaster about 2 years ago - 1 comment

#1027 - bedtools strategies for circular chromosomes?

Issue - State: open - Opened by ryandward about 2 years ago

#1026 - Fix for Issue #1023

Pull Request - State: open - Opened by JoeVieira about 2 years ago - 1 comment

#1025 - Normalizing the length of a set of variable length intervals

Issue - State: open - Opened by amatria about 2 years ago - 2 comments

#1024 - Minor typo

Issue - State: open - Opened by Proginski about 2 years ago

#1023 - pairToBed writes 1 BedPE line per match in either mode

Issue - State: open - Opened by JoeVieira about 2 years ago - 1 comment

#1022 - Query to correctly overlap structural variants

Issue - State: open - Opened by prasundutta87 about 2 years ago

#1021 - BED file made from R is not being recognized by bedtools (BED file will eventually be used in fastQTL)

Issue - State: closed - Opened by harrsha4 about 2 years ago - 1 comment

#1020 - Migration to Rust?

Issue - State: open - Opened by vivekkiran about 2 years ago

#1019 - Strand information for coverage

Issue - State: open - Opened by erajshafiq about 2 years ago

GitHub / arq5x/bedtools2 issues and pull requests