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bedtools
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FastaFromBed error when a chr is not in the genome
#123
GoogleCodeExporter
closed
9 years ago
0
GFF features with length 1 cannot be intersected
#122
GoogleCodeExporter
closed
9 years ago
2
groupBy reports non-sensical output when input is empty.
#121
GoogleCodeExporter
closed
9 years ago
1
genomecov needs to report coverage for all chroms in genome file
#120
GoogleCodeExporter
opened
9 years ago
0
add parameter to do range of reads in genomecoverage
#119
GoogleCodeExporter
opened
9 years ago
0
Bedtools fails to recognise VCF file where ID field is purely numeric (valid)
#118
GoogleCodeExporter
closed
9 years ago
2
installing error
#117
GoogleCodeExporter
closed
9 years ago
1
Fix "2: bedtools: not found" error, when bedtools is not in $PATH
#116
GoogleCodeExporter
closed
9 years ago
2
make test fails
#115
GoogleCodeExporter
closed
9 years ago
3
intersectBed -wao/-wo has problems dealing with intervals of 1bp in gtf format
#114
GoogleCodeExporter
closed
9 years ago
1
bamToBed needs -h for help, other tools don't
#113
GoogleCodeExporter
closed
9 years ago
1
coverageBed: all exons with null read coverage
#112
GoogleCodeExporter
opened
9 years ago
4
failure with BED input for fastaFromBed (v2.15.0)
#111
GoogleCodeExporter
closed
9 years ago
2
closestBed runs slow when the second file (-b file) is small.
#110
GoogleCodeExporter
opened
9 years ago
2
intersectBed of VCF files with minimum overlap and reciprocal
#109
GoogleCodeExporter
closed
9 years ago
3
TSS from different strands overlapping in 1k window
#108
GoogleCodeExporter
closed
9 years ago
7
BamMapCount tool
#107
GoogleCodeExporter
opened
9 years ago
1
Have built in chromSizes files for hg19, hg19-intm etc.
#106
GoogleCodeExporter
opened
9 years ago
1
bamtobed hangs with large file
#105
GoogleCodeExporter
closed
9 years ago
2
subtractBed eror "Error: can't determine file type of 'X.bed': Value too large for defined data type"
#104
GoogleCodeExporter
closed
9 years ago
2
coverageBed gives all zero coverage
#103
GoogleCodeExporter
closed
9 years ago
3
Create a randomBed tool.
#102
GoogleCodeExporter
closed
9 years ago
2
shuffleBed should not first choose a chrom randomyl, then choose a coord.
#101
GoogleCodeExporter
closed
9 years ago
1
bamtools unnecessarily validates tags in header
#100
GoogleCodeExporter
closed
9 years ago
1
fastaFromBed fails on 32bit architectures.
#99
GoogleCodeExporter
opened
9 years ago
0
Split bam-file blocks incorrectly calculated in bamToBed and intersectBed
#98
GoogleCodeExporter
closed
9 years ago
3
unionBedGraphs should enfore sorted input
#97
GoogleCodeExporter
opened
9 years ago
0
closestBed -no option not recognized
#96
GoogleCodeExporter
closed
9 years ago
1
For future templating, chromsweep should use GextNext() instead of !Empty()
#95
GoogleCodeExporter
opened
9 years ago
0
chromsweep doesn't handle blank lines at EOF
#94
GoogleCodeExporter
opened
9 years ago
0
Makefile does not return proper status upon build failure
#93
GoogleCodeExporter
closed
9 years ago
1
New tool suggestions: range & reverse compliment
#92
GoogleCodeExporter
closed
9 years ago
2
intersectBed -wb option prints a & b instead of just b
#91
GoogleCodeExporter
closed
9 years ago
3
Debian packages available for bedtools.
#90
GoogleCodeExporter
closed
9 years ago
4
spelling error in BamStandardIndex_p.cpp and BamToolsIndex_p.cpp
#89
GoogleCodeExporter
opened
9 years ago
1
intersectBED only checks the validity of the first line of a file.
#88
GoogleCodeExporter
closed
9 years ago
1
genomes/mouse.mm9.genome broken by commit 9432b296f0fdeae39518275dcbb24de446eb003a
#87
GoogleCodeExporter
closed
9 years ago
1
mergeBed problem with zero length bed features
#86
GoogleCodeExporter
closed
9 years ago
2
The -d option in coverageBed should optionally report positions based on strand
#85
GoogleCodeExporter
opened
9 years ago
0
Add collapse unique and count unique to groupBy (Ira)
#84
GoogleCodeExporter
closed
9 years ago
2
bedToIgv gives malformed scripts for windows
#83
GoogleCodeExporter
opened
9 years ago
0
Create a matrixBed tool
#82
GoogleCodeExporter
opened
9 years ago
1
force fastaFromBED to print to screen
#81
GoogleCodeExporter
closed
9 years ago
2
Need to support "-" as well as "stdin"
#80
GoogleCodeExporter
closed
9 years ago
1
Need -S (opposite strands) feature.
#79
GoogleCodeExporter
closed
9 years ago
1
intersectBed -wo returning intersecting insertions with base-pair overlap of 0
#78
GoogleCodeExporter
opened
9 years ago
3
std::bad_alloc when using genomeCoverageBed
#77
GoogleCodeExporter
closed
9 years ago
4
coverageBed fails for BAM files generated by Novoalign
#76
GoogleCodeExporter
closed
9 years ago
2
intersectBed does not work correctly with -r option
#75
GoogleCodeExporter
closed
9 years ago
4
bamToBed cannot read from stdin on Solaris
#74
GoogleCodeExporter
opened
9 years ago
0
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