arq5x/bedtools2 issues and pull requests

#1008 - bamtofastq outputs empty reads at beginning of fastqs for specific bam file

Issue - State: open - Opened by mebbert over 2 years ago

#1007 - bamtobed -bedpe bug results in additional entry in BED

Issue - State: open - Opened by k1sauce over 2 years ago

#1006 - Unexpected behavior of generating a interleaved fastq by bamToFastq

Issue - State: open - Opened by chtsai0105 over 2 years ago

#1005 - segmentation fault for multiinter

Issue - State: closed - Opened by tom21100227 over 2 years ago - 1 comment

#1004 - The resource of bedtools 2.14.3

Issue - State: closed - Opened by Gummy89 over 2 years ago - 1 comment

#1003 - bedtools groupby could not generate correct results.

Issue - State: closed - Opened by ccmeth over 2 years ago - 3 comments

#1002 - Truncated output when using bedtools

Issue - State: closed - Opened by mrvollger over 2 years ago - 3 comments

#1001 - multicov count junction reads

Issue - State: open - Opened by yuanjianwen-gif over 2 years ago

#1000 - bedtools merge error when handling reciporally overlap region

Issue - State: closed - Opened by wildist-github over 2 years ago - 1 comment

#999 - Ignore Windows-style line termination in genome files

Pull Request - State: closed - Opened by jmarshall over 2 years ago - 1 comment

#998 - bedtools complement ". Exiting...illegal number "

Issue - State: closed - Opened by marija-kra over 2 years ago - 12 comments

#997 - filtering BED files by region length

Issue - State: closed - Opened by peterjc over 2 years ago - 1 comment

#996 - Document making a "genome file" from FASTA

Issue - State: closed - Opened by peterjc over 2 years ago - 6 comments

#995 - -n in makewindows sometimes makes the last bin to an extremely unequal size

Issue - State: open - Opened by ifantasy over 2 years ago - 4 comments

#994 - bedtools fisher

Issue - State: open - Opened by juicybrain over 2 years ago - 4 comments

#993 - Cherry-pick htslib#1258

Pull Request - State: closed - Opened by iii-i over 2 years ago

#992 - "moving average" to coverage signal with bedtools

Issue - State: closed - Opened by Shicheng-Guo over 2 years ago - 1 comment

#991 - Why does the sixth column of the non-chain-specific bed file show +&- ?

Issue - State: closed - Opened by 5Tony over 2 years ago - 5 comments

#990 - pairToBed and bamToBed possible small bug

Issue - State: open - Opened by goranvinterhalter over 2 years ago

#989 - Compiling and Installation

Issue - State: open - Opened by SaumyaSarkar over 2 years ago - 2 comments

#988 - How to output merged fasta?

Issue - State: open - Opened by Saveli01 over 2 years ago - 1 comment

#987 - Non numeric value warning with bedtools map

Issue - State: closed - Opened by dgoekbuget over 2 years ago

#986 - Support for IBM Integrated Accelerator for Z Sort

Issue - State: open - Opened by michaelmhoffman over 2 years ago - 3 comments

#985 - error with bedtools maskfasta

Issue - State: closed - Opened by raungar over 2 years ago - 2 comments

#984 - bedtools merge can't handle properly overlapped regions

Issue - State: closed - Opened by dlopez-bioinfo over 2 years ago - 1 comment

#983 - Bedtools intersect truncates name column to 1000 chars?

Issue - State: closed - Opened by mebbert over 2 years ago - 2 comments

#982 - slopBed: usage grammar/whitespace fixes

Pull Request - State: closed - Opened by cbrueffer over 2 years ago - 1 comment

#981 - bedtools map: **** ERROR: illegal number "1.00000". Exiting...

Issue - State: open - Opened by tjakobi over 2 years ago - 6 comments

#979 - `bedtools complement` working differently when passing a BED file or a subset of it

Issue - State: closed - Opened by MatteoSchiavinato almost 3 years ago - 1 comment

#978 - Error: Sorted input specified, but the file stdin has the following record with a different sort order than the genomeFile

Issue - State: closed - Opened by drowsygoat almost 3 years ago - 1 comment

#977 - Description of columns in the bedtools documentation is missing/not actual.

Issue - State: closed - Opened by JaZwy almost 3 years ago - 1 comment

#973 - intersectBed has a limitation on the output of character length

Issue - State: closed - Opened by ifantasy almost 3 years ago - 9 comments

#956 - Bamtofastq generate duplicated reads - latest version - 2.30.0

Issue - State: open - Opened by andreirozanski about 3 years ago - 2 comments

#953 - weighted averages for bedtools map?

Issue - State: open - Opened by vsbuffalo about 3 years ago - 9 comments

#952 - the -is option for pairToPair documentation might not be up to date

Issue - State: open - Opened by ralsallaq about 3 years ago - 2 comments

#951 - bedtools bamtofastq difference in version 2.29.1 and 2.30

Issue - State: closed - Opened by FenggChengg about 3 years ago - 2 comments

#919 - Bedtools intersect truncates bed12 intervals

Issue - State: closed - Opened by ddubocan over 3 years ago - 7 comments

#917 - terminate called after throwing an instance of 'std::invalid_argument'

Issue - State: closed - Opened by Shicheng-Guo over 3 years ago - 7 comments

#906 - Building on Windows using MSYS2

Pull Request - State: open - Opened by mkviatkovskii over 3 years ago - 4 comments

#902 - Spurious strand indication in fasta header with option -nameOnly of getfasta

Issue - State: open - Opened by blaiseli almost 4 years ago - 3 comments

#887 - "pybedtools coverage -f" don't work properly

Issue - State: open - Opened by CrazyHsu almost 4 years ago - 1 comment

#885 - Error: Type checker found wrong number of fields while tokenizing data line.

Issue - State: open - Opened by mmokrejs almost 4 years ago - 6 comments

#882 - circular genomes and getfasta

Issue - State: open - Opened by mmp3 almost 4 years ago - 2 comments

#879 - bedtools nuc throws a segmentation fault, when the reference genome is compressed using bgzip

Issue - State: closed - Opened by dvav almost 4 years ago - 3 comments

#869 - bedtools intersect: ERROR: Received illegal bin number -1 from getBin call.

Issue - State: open - Opened by phil-grayson about 4 years ago - 3 comments

#867 - cDNA sequences / genomecov: ignore local deletions, split on large deletions / exon skips

Issue - State: closed - Opened by gringer about 4 years ago - 3 comments

#852 - Broken makefile on systems without python2

Issue - State: open - Opened by frankdekievit over 4 years ago - 2 comments

#842 - refGene.txt hq19 - file turncated

Issue - State: open - Opened by joni73 over 4 years ago - 5 comments

#805 - something wrong in bedtools getfasta -name

Issue - State: open - Opened by StayHungryStayFool almost 5 years ago - 4 comments

#743 - Empty links in documentation

Issue - State: closed - Opened by cmdcolin over 5 years ago - 3 comments
Labels: enhancement, next-major-release, documentation

#698 - fix binOffsets and test more big stuff

Pull Request - State: closed - Opened by brentp over 5 years ago

#696 - Bin fix

Pull Request - State: closed - Opened by brentp over 5 years ago

#693 - dont make htslib tests

Pull Request - State: closed - Opened by brentp over 5 years ago

#689 - Jaccard fix

Pull Request - State: closed - Opened by brentp over 5 years ago

#685 - added 2 options -tn5 and -ext

Pull Request - State: open - Opened by lldelisle almost 6 years ago - 1 comment

#673 - "bedtools coverage -split -f 1.0 -counts" is not working properly

Issue - State: open - Opened by sterding about 6 years ago - 1 comment
Labels: bug, next-major-release

#628 - Inconsistent naming convention for record results in no output

Issue - State: closed - Opened by mjgage over 6 years ago - 4 comments

#616 - bedtools jaccard complains because chromosome is not represented in both query and database files

Issue - State: closed - Opened by nw11 almost 7 years ago - 6 comments
Labels: next-major-release

#606 - intersect reports wrong number of fields in .gz file

Issue - State: closed - Opened by jaime11 almost 7 years ago - 6 comments

#585 - Support CIGARs with >65535 ops, via full clipping

Pull Request - State: closed - Opened by lh3 about 7 years ago - 4 comments

#497 - Switching order of -a and -b paramter in bedtools intersect when -b file is BAM file, outputs BAM header.

Issue - State: closed - Opened by ghuls over 7 years ago - 5 comments

#391 - bedtools annotate header line disappears

Issue - State: open - Opened by igordot over 8 years ago - 3 comments

#379 - add long stuff found by @ryanlayer's compiler settings.

Pull Request - State: closed - Opened by brentp over 8 years ago

#371 - scientific notation for large numbers of reads

Issue - State: closed - Opened by map2085 almost 9 years ago - 20 comments

#359 - zero length intervals are not handled properly.

Issue - State: open - Opened by arq5x almost 9 years ago - 3 comments
Labels: bug

#336 - Error if missing values in last column

Issue - State: closed - Opened by dwaggott almost 9 years ago - 9 comments

#315 - Create header with command used.

Issue - State: open - Opened by arq5x about 9 years ago - 1 comment

#235 - bedtools intersect fails when GFF file contains a ##FASTA section

Issue - State: open - Opened by sjackman over 9 years ago - 12 comments

#229 - Non-writable IO device error when intersecting BAM and BED files

Issue - State: closed - Opened by jma1991 over 9 years ago - 24 comments

#182 - Feature request: getfasta extract name or ID from GFF3 attributes field

Issue - State: open - Opened by colindaven almost 10 years ago - 4 comments

#56 - could bedtools getfasta work with gzipped fasta?

Issue - State: open - Opened by pamag over 10 years ago - 17 comments

#23 - Speed up genomecov

Issue - State: open - Opened by arq5x almost 11 years ago - 2 comments
Labels: enhancement

GitHub / arq5x/bedtools2 issues and pull requests