Issues - bedtools - bedtools: a flexible suite of utilities for comparing genomic features.

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ID ▼	Type ▼	Status ▼	Priority ▼	Milestone ▼	Owner ▼	Summary + Labels ▼
3	Defect	Accepted	Low	----	----	anonymous svn checkout of 'trunk' returns no files
6	Enhancement	Accepted	Low	----	aaronqui...@gmail.com	Create Galaxy wrappers for all tools
14	Enhancement	Accepted	Low	----	aaronqui...@gmail.com	Add BAM support to closestBed
15	Enhancement	Accepted	Medium	----	aaronqui...@gmail.com	Add -wo and -wao options to windowBed.
20	Enhancement	Accepted	Medium	----	aaronqui...@gmail.com	New, single command interface.
28	Enhancement	Accepted	Low	----	aaronqui...@gmail.com	Add -xor option to pairToPair
30	Enhancement	Accepted	Medium	----	aaronqui...@gmail.com	Add option to intersectBed to require that overlapping features have the same name
32	Enhancement	Accepted	Medium	----	aaronqui...@gmail.com	Need MAD for groupBy
33	Enhancement	Accepted	Medium	----	aaronqui...@gmail.com	Support for remote annotation files
42	Enhancement	Accepted	Medium	----	aaronqui...@gmail.com	Add -split functionality to windowBed
44	Defect	Accepted	Medium	----	----	Feature request: coverageBed for PE inserts
47	Enhancement	Accepted	Medium	----	aaronqui...@gmail.com	mergeBed should have a function to merge scors, similar to -nms
49	Enhancement	Accepted	Low	----	aaronqui...@gmail.com	Force genomecoverageBed to report a chromosome with no coverage.
52	Defect	Accepted	Medium	----	----	Example in docs: windowBed defining assymetric windows (-l and -r) is wrong
58	Defect	Accepted	Medium	----	aaronqui...@gmail.com	-split should apply to the B file as well
65	Enhancement	Accepted	Medium	----	----	fastaFromBed should use 9th column for "-name" option if input is a GFF file
74	Defect	New	Medium	----	----	bamToBed cannot read from stdin on Solaris
75	Enhancement	New	Medium	----	----	intersectBed does not work correctly with -r option
78	Defect	Accepted	Medium	----	----	intersectBed -wo returning intersecting insertions with base-pair overlap of 0
82	Enhancement	Accepted	Medium	----	aaronqui...@gmail.com	Create a matrixBed tool
83	Defect	New	Medium	----	----	bedToIgv gives malformed scripts for windows
85	Enhancement	Accepted	Medium	----	aaronqui...@gmail.com	The -d option in coverageBed should optionally report positions based on strand
86	Defect	New	Medium	----	----	mergeBed problem with zero length bed features
89	Defect	Accepted	Medium	----	----	spelling error in BamStandardIndex_p.cpp and BamToolsIndex_p.cpp
94	Defect	Accepted	Medium	----	aaronqui...@gmail.com	chromsweep doesn't handle blank lines at EOF
95	Enhancement	Accepted	Medium	----	aaronqui...@gmail.com	For future templating, chromsweep should use GextNext() instead of !Empty()
97	Defect	Accepted	Medium	----	aaronqui...@gmail.com	unionBedGraphs should enfore sorted input
99	Defect	Accepted	Medium	----	aaronqui...@gmail.com	fastaFromBed fails on 32bit architectures.
106	Enhancement	Accepted	Medium	----	aaronqui...@gmail.com	Have built in chromSizes files for hg19, hg19-intm etc.
107	Enhancement	New	Medium	----	----	BamMapCount tool
110	Defect	New	Medium	----	----	closestBed runs slow when the second file (-b file) is small.
112	Defect	New	Medium	----	----	coverageBed: all exons with null read coverage
118	Defect	Accepted	Medium	----	----	Bedtools fails to recognise VCF file where ID field is purely numeric (valid)
119	Defect	New	Medium	----	----	add parameter to do range of reads in genomecoverage
120	Enhancement	Accepted	Medium	----	aaronqui...@gmail.com	genomecov needs to report coverage for all chroms in genome file
121	Defect	Accepted	Medium	----	aaronqui...@gmail.com	groupBy reports non-sensical output when input is empty.

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