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

GitHub / arq5x/bedtools issues and pull requests