Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / arq5x/bedtools issues and pull requests
#102 - Update intersect.rst
Pull Request -
State: closed - Opened by ghost over 10 years ago
#100 - Fixed small error in example output of mergeBed -d
Pull Request -
State: closed - Opened by bergeycm almost 11 years ago
- 1 comment
#99 - Title correction on -counts part
Pull Request -
State: closed - Opened by Guitss almost 11 years ago
#98 - Update cluster.rst
Pull Request -
State: closed - Opened by rchikhi almost 11 years ago
- 3 comments
#97 - Update installation.rst
Pull Request -
State: closed - Opened by arjanvandervelde almost 11 years ago
- 1 comment
#96 - Potential bug causing segfault dump in makewindows
Issue -
State: open - Opened by yarden almost 11 years ago
- 2 comments
#95 - Update window.rst
Pull Request -
State: closed - Opened by cbirger almost 11 years ago
- 1 comment
#94 - Update subtract.rst
Pull Request -
State: closed - Opened by cbirger almost 11 years ago
- 1 comment
#93 - fix description of option -Sm
Pull Request -
State: closed - Opened by dangenet almost 11 years ago
- 1 comment
#92 - Enhancement: subtractBed: Add switch to allow -a file to be read in memory and -b from disk
Issue -
State: open - Opened by ghuls almost 11 years ago
- 1 comment
#91 - Update merge.rst
Pull Request -
State: closed - Opened by ecwooten about 11 years ago
- 1 comment
#90 - VCF output truncated, if blank line follows header
Issue -
State: open - Opened by daler about 11 years ago
- 2 comments
#89 - Fix output format of optional BED fields
Pull Request -
State: closed - Opened by kcha about 11 years ago
- 1 comment
#88 - Blank BED files throw an error
Issue -
State: open - Opened by jsilter about 11 years ago
- 1 comment
#87 - Update intersect.rst
Pull Request -
State: closed - Opened by bergeycm about 11 years ago
- 1 comment
#86 - Update window.rst
Pull Request -
State: closed - Opened by jsilter about 11 years ago
- 1 comment
#85 - Invalid -f Argument in windowBed
Issue -
State: open - Opened by duartemolha about 11 years ago
- 4 comments
#84 - Update merge.rst
Pull Request -
State: open - Opened by kzarns about 11 years ago
- 2 comments
#83 - added mouse.mm10.genome
Pull Request -
State: closed - Opened by theoryno3 about 11 years ago
- 1 comment
#82 - Update slop.rst
Pull Request -
State: closed - Opened by wac over 11 years ago
#81 - Update quick-start.rst
Pull Request -
State: closed - Opened by daler over 11 years ago
- 1 comment
#80 - Update quick-start.rst
Pull Request -
State: closed - Opened by daler over 11 years ago
#79 - Change the actual default delim for merge (it's ";" not ",")
Pull Request -
State: closed - Opened by nachocab over 11 years ago
- 1 comment
#78 - Does bedtools handle the ##FASTA tag in gff files?
Issue -
State: closed - Opened by ctSkennerton over 11 years ago
- 3 comments
#77 - bedtools coverage should have a -sorted option
Issue -
State: open - Opened by brentp over 11 years ago
- 3 comments
#76 - ENH: shuffle intervals to non-overlapping locations.
Pull Request -
State: closed - Opened by brentp over 11 years ago
- 2 comments
#75 - Update merge.rst
Pull Request -
State: closed - Opened by lbthrice over 11 years ago
- 1 comment
#74 - ENH: shuffle within a window or distance
Issue -
State: open - Opened by brentp over 11 years ago
#73 - ENH: implement new tool bedtools sample
Issue -
State: open - Opened by brentp over 11 years ago
#72 - Intersect library fragments and not alignment in multibamcov
Pull Request -
State: open - Opened by dawe over 11 years ago
- 1 comment
#71 - Add -f option to window
Issue -
State: open - Opened by arq5x over 11 years ago
#70 - BED/GFF headers
Issue -
State: open - Opened by fgvieira over 11 years ago
- 5 comments
#69 - Add -split option to tag sub command
Issue -
State: open - Opened by arq5x over 11 years ago
#68 - Bug in slop if chrom not present in genome file?
Issue -
State: open - Opened by arq5x over 11 years ago
#67 - BigWig and BigBed support
Issue -
State: open - Opened by arq5x over 11 years ago
- 2 comments
#66 - multiple bam support
Pull Request -
State: open - Opened by xubeisi over 11 years ago
- 1 comment
#65 - add multiple file support for genomecov
Pull Request -
State: closed - Opened by xubeisi over 11 years ago
- 1 comment
#64 - Update advanced-usage.rst
Pull Request -
State: closed - Opened by alexpenson over 11 years ago
- 1 comment
#63 - error of running genomecov
Issue -
State: open - Opened by ymwur over 11 years ago
#62 - Update coverage.rst
Pull Request -
State: closed - Opened by xubeisi over 11 years ago
- 1 comment
#61 - coverageBed coverage/number of features discrepancy
Issue -
State: open - Opened by ghost over 11 years ago
- 1 comment
#60 - Update sort.rst
Pull Request -
State: closed - Opened by lbthrice over 11 years ago
- 1 comment
#59 - Update coverage.rst
Pull Request -
State: closed - Opened by cdelzinga over 11 years ago
- 1 comment
#58 - removed duplicate description of -s option
Pull Request -
State: closed - Opened by dvanic over 11 years ago
- 1 comment
#57 - Incompatibility of clusterBed with BED-converted BAMs?
Issue -
State: closed - Opened by yarden over 11 years ago
- 3 comments
#56 - shuffle -bedpe ignores the -chrom option.
Issue -
State: open - Opened by arq5x almost 12 years ago
#55 - coverageBed output incorrect with -abam option, correct with -abam stdin
Issue -
State: closed - Opened by nkrumm almost 12 years ago
- 1 comment
#54 - add n_intersections to jaccard output
Pull Request -
State: closed - Opened by brentp almost 12 years ago
- 1 comment
#53 - Finding closest intervals on _both_ sides of a query interval
Issue -
State: open - Opened by arq5x almost 12 years ago
#52 - Minor build infrastructure patches
Pull Request -
State: closed - Opened by jmarshall almost 12 years ago
- 1 comment
#51 - Controlling delimiter in -nms option of mergeBed
Issue -
State: open - Opened by yarden almost 12 years ago
- 4 comments
#50 - bedtools slop "until end of chr" option
Issue -
State: closed - Opened by avilella almost 12 years ago
- 2 comments
#49 - Handle \r\n and \n line endings.
Issue -
State: closed - Opened by arq5x almost 12 years ago
#48 - filename length dependent segfault in tagBam
Issue -
State: closed - Opened by yarden almost 12 years ago
- 4 comments
#47 - warning/error in jaccard when attempting "stdin" as input
Issue -
State: closed - Opened by brentp almost 12 years ago
- 1 comment
#46 - freeze with shuffle -excl
Issue -
State: closed - Opened by brentp almost 12 years ago
- 8 comments
#45 - Fix for tagBam -names segfault
Pull Request -
State: closed - Opened by pryvkin almost 12 years ago
- 1 comment
#44 - Support for remote files.
Issue -
State: open - Opened by arq5x almost 12 years ago
- 1 comment
#43 - allow specifying multiple columns and multiple ops to bedtools map (a la groupby)
Issue -
State: closed - Opened by brentp almost 12 years ago
- 2 comments
#42 - Have chrom_sizes built into the tool
Issue -
State: open - Opened by arq5x about 12 years ago
#41 - Add a 'flip' tool.
Issue -
State: open - Opened by arq5x about 12 years ago
- 6 comments
#40 - Add a 'shift' tool.
Issue -
State: open - Opened by arq5x about 12 years ago
- 14 comments
#39 - support both -incl and -excl in shuffle
Issue -
State: closed - Opened by arq5x about 12 years ago
#38 - -f and -r options for merge?
Issue -
State: open - Opened by arq5x about 12 years ago
#37 - WIP: let subtract bed calculate -f based on all overlapping intervals.
Pull Request -
State: closed - Opened by brentp about 12 years ago
- 5 comments
#36 - output values from a given column in multiinter
Issue -
State: closed - Opened by brentp about 12 years ago
- 8 comments
#35 - Specify and ignore missing values in groupby
Issue -
State: open - Opened by arq5x about 12 years ago
#34 - Improve the description of -wb
Issue -
State: closed - Opened by arq5x about 12 years ago
#33 - Report ERROR, then print HELP
Issue -
State: open - Opened by arq5x about 12 years ago
#32 - Fix help for all tools using -abam
Issue -
State: closed - Opened by arq5x about 12 years ago
#31 - Bug in enforcing sorted files
Issue -
State: open - Opened by arq5x about 12 years ago
#30 - empty bed files
Issue -
State: closed - Opened by jpaulLD about 12 years ago
- 8 comments
#29 - Allow overriding BT to test bedtools from other paths.
Pull Request -
State: closed - Opened by charles-plessy about 12 years ago
- 1 comment
#28 - WIP: improvements to getfasta / fastaFromBed
Pull Request -
State: closed - Opened by brentp about 12 years ago
- 1 comment
#27 - 3 one-line changes to allow regression tests to run on OS X / BSD, and compilation on FreeBSD
Pull Request -
State: closed - Opened by nathanweeks about 12 years ago
- 1 comment
#26 - let groupby handle a header line (starting with "#") as do other
Pull Request -
State: closed - Opened by brentp about 12 years ago
- 5 comments
#25 - Groupby columns specified like cut (but retaining order)
Pull Request -
State: closed - Opened by brentp over 12 years ago
- 3 comments
#24 - Support "cut"-like column selection in groupby
Issue -
State: closed - Opened by arq5x over 12 years ago
- 4 comments
#23 - multicov needs to handle split alignments and BED12
Issue -
State: closed - Opened by arq5x over 12 years ago
#22 - BamToBed: properly fail on non-existing input files.
Pull Request -
State: closed - Opened by agordon over 12 years ago
- 1 comment
#21 - Checked-in .o files in src/utils/gzstream
Issue -
State: closed - Opened by jmarshall over 12 years ago
- 2 comments
#20 - WindowMaker: bugfix with using "srcwinnum" + genome
Pull Request -
State: closed - Opened by agordon over 12 years ago
- 1 comment
#19 - Second attempt at auto-versioning
Pull Request -
State: closed - Opened by agordon over 12 years ago
- 1 comment
#18 - Makefile: add DEBUG compiler option.
Pull Request -
State: closed - Opened by agordon almost 13 years ago
- 2 comments
#17 - Restructure auto-git-version
Pull Request -
State: closed - Opened by agordon almost 13 years ago
- 1 comment
#16 - Makefile: Auto-generate version string from Git version
Pull Request -
State: closed - Opened by agordon almost 13 years ago
#15 - Feature/makewindows with i ds1
Pull Request -
State: closed - Opened by agordon almost 13 years ago
- 1 comment
#14 - Regression on -wao?
Pull Request -
State: closed - Opened by jakebiesinger almost 13 years ago
- 2 comments
#13 - Add ignore options for features up- and downstream of A
Pull Request -
State: closed - Opened by jakebiesinger almost 13 years ago
- 4 comments
#12 - Build fails on VectorOps, groupBy
Issue -
State: closed - Opened by aksarkar almost 13 years ago
- 4 comments
#11 - include <algorithm> for gcc 4.4.3
Pull Request -
State: closed - Opened by daler almost 13 years ago
#10 - bedtools git archive is very large due to old binaries and data files
Issue -
State: closed - Opened by bpow almost 13 years ago
- 3 comments
#9 - Signed distance for closestBed
Pull Request -
State: closed - Opened by jakebiesinger about 13 years ago
- 3 comments
#8 - -sm -> -Sm
Pull Request -
State: closed - Opened by daler about 13 years ago
#7 - include <cstdlib> in lineFileUtilities.h for gcc 4.4.3
Pull Request -
State: closed - Opened by daler over 13 years ago
#6 - fjoin fails with empty files
Issue -
State: closed - Opened by jakebiesinger over 13 years ago
- 3 comments
#5 - commit 455c52e54a025279df28 causes regression in fFB range checking
Issue -
State: closed - Opened by kortschak over 13 years ago
- 1 comment
#4 - enhancement: allow flag to report multiple overlaps on same line in closestBed
Issue -
State: closed - Opened by brentp over 13 years ago
- 2 comments
#3 - Zero Length features for coverageBed get enlarged
Issue -
State: closed - Opened by idot almost 14 years ago
- 1 comment
#2 - coverageBed output positions wrong for bed input files (regression)
Issue -
State: closed - Opened by idot almost 14 years ago
- 1 comment