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arq5x
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bedtools
A powerful toolset for genome arithmetic.
http://code.google.com/p/bedtools/
GNU General Public License v2.0
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BED/GFF headers
#70
fgvieira
opened
11 years ago
5
Add -split option to tag sub command
#69
arq5x
opened
11 years ago
0
Bug in slop if chrom not present in genome file?
#68
arq5x
opened
11 years ago
0
BigWig and BigBed support
#67
arq5x
opened
11 years ago
2
multiple bam support
#66
xubeisi
opened
11 years ago
1
add multiple file support for genomecov
#65
xubeisi
closed
11 years ago
1
Update advanced-usage.rst
#64
alexpenson
closed
11 years ago
1
error of running genomecov
#63
ymwur
opened
11 years ago
0
Update coverage.rst
#62
xubeisi
closed
11 years ago
1
coverageBed coverage/number of features discrepancy
#61
ghost
opened
11 years ago
1
Update sort.rst
#60
lbthrice
closed
11 years ago
1
Update coverage.rst
#59
cdelzinga
closed
11 years ago
1
removed duplicate description of -s option
#58
dvanic
closed
11 years ago
1
Incompatibility of clusterBed with BED-converted BAMs?
#57
yarden
closed
11 years ago
3
shuffle -bedpe ignores the -chrom option.
#56
arq5x
opened
11 years ago
0
coverageBed output incorrect with -abam option, correct with -abam stdin
#55
nkrumm
closed
11 years ago
1
add n_intersections to jaccard output
#54
brentp
closed
11 years ago
1
Finding closest intervals on _both_ sides of a query interval
#53
arq5x
opened
11 years ago
0
Minor build infrastructure patches
#52
jmarshall
closed
11 years ago
1
Controlling delimiter in -nms option of mergeBed
#51
yarden
opened
11 years ago
4
bedtools slop "until end of chr" option
#50
avilella
closed
11 years ago
2
Handle \r\n and \n line endings.
#49
arq5x
closed
10 years ago
0
filename length dependent segfault in tagBam
#48
yarden
closed
11 years ago
4
warning/error in jaccard when attempting "stdin" as input
#47
brentp
closed
11 years ago
1
freeze with shuffle -excl
#46
brentp
closed
11 years ago
8
Fix for tagBam -names segfault
#45
pryvkin
closed
11 years ago
1
Support for remote files.
#44
arq5x
opened
12 years ago
1
allow specifying multiple columns and multiple ops to bedtools map (a la groupby)
#43
brentp
closed
8 years ago
2
Have chrom_sizes built into the tool
#42
arq5x
opened
12 years ago
0
Add a 'flip' tool.
#41
arq5x
opened
12 years ago
6
Add a 'shift' tool.
#40
arq5x
opened
12 years ago
14
support both -incl and -excl in shuffle
#39
arq5x
closed
11 years ago
0
-f and -r options for merge?
#38
arq5x
opened
12 years ago
0
WIP: let subtract bed calculate -f based on all overlapping intervals.
#37
brentp
closed
12 years ago
5
output values from a given column in multiinter
#36
brentp
closed
12 years ago
8
Specify and ignore missing values in groupby
#35
arq5x
opened
12 years ago
0
Improve the description of -wb
#34
arq5x
closed
12 years ago
0
Report ERROR, then print HELP
#33
arq5x
opened
12 years ago
0
Fix help for all tools using -abam
#32
arq5x
closed
12 years ago
0
Bug in enforcing sorted files
#31
arq5x
opened
12 years ago
0
empty bed files
#30
jpaulLD
closed
11 years ago
8
Allow overriding BT to test bedtools from other paths.
#29
charles-plessy
closed
12 years ago
1
WIP: improvements to getfasta / fastaFromBed
#28
brentp
closed
12 years ago
1
3 one-line changes to allow regression tests to run on OS X / BSD, and compilation on FreeBSD
#27
nathanweeks
closed
12 years ago
1
let groupby handle a header line (starting with "#") as do other
#26
brentp
closed
12 years ago
5
Groupby columns specified like cut (but retaining order)
#25
brentp
closed
12 years ago
3
Support "cut"-like column selection in groupby
#24
arq5x
closed
12 years ago
4
multicov needs to handle split alignments and BED12
#23
arq5x
closed
12 years ago
0
BamToBed: properly fail on non-existing input files.
#22
agordon
closed
12 years ago
1
Checked-in .o files in src/utils/gzstream
#21
jmarshall
closed
12 years ago
2
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