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Bioconductor
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Rsamtools
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
https://bioconductor.org/packages/Rsamtools
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Compilation problem on macOS Sonoma 14.2.1
#62
mohammedemamkhattabunipd
closed
5 months ago
3
FEATURE REQUEST: Improve seqinfo(<BamFile>) to return the genome assembly associated with each sequence
#61
hpages
opened
6 months ago
0
Fix gcc's "format-security" warning
#60
js2264
closed
7 months ago
1
Rsamtools pileup and Pysam pileup output discrepancy
#59
XqKang
closed
9 months ago
4
Support for CSI indexes
#58
diego-rt
opened
11 months ago
0
Add code of conduct
#57
bschilder
opened
1 year ago
1
CRAM support - why not?
#56
pd3
opened
1 year ago
5
Rsamtools with multiple threads?
#55
junjunlab
opened
1 year ago
2
Added documentation of behaviour when `param` is empty.
#54
Shians
closed
1 year ago
0
Convert Rsamtools-Overview.Rnw to Rsamtools-Overview.Rmd
#53
bellatrick
closed
1 year ago
6
Help with pileup
#52
joegeorgeson
closed
1 year ago
1
samtools markdup in Rsamtools
#51
Adnanhashim
closed
1 year ago
1
Installation issue related to linker files
#50
ShanSabri
closed
1 year ago
1
add nThreads and byTag options to sortBam
#49
kriemo
closed
1 year ago
1
Add rworkflows
#48
bschilder
closed
8 months ago
34
Installation Error
#47
cmfield
closed
1 year ago
8
using multiple threads for bam sorting, merging, and indexing
#46
kriemo
closed
1 year ago
1
Support for delimited tags
#45
joegeorgeson
closed
1 year ago
3
scanbam, with many reginos in which, is very slow
#44
gevro
closed
2 years ago
2
Update issue templates
#43
mtmorgan
opened
2 years ago
0
Loading bam file in chunks
#42
gevro
closed
2 years ago
2
Support for more recent HTSlib
#41
matthdsm
closed
2 years ago
6
Indexing a gzipped fasta file
#40
eggrandio
closed
2 years ago
2
scanBam 'which' returns the same record multiple times
#39
gevro
closed
2 years ago
1
Using both "yileldSize" and "which" parameters
#38
gacatag
closed
2 years ago
3
Resync with Rhtslib 1.99.1 (updated from htslib 1.7 to 1.15.1)
#37
hpages
closed
2 years ago
0
Rsamtools.so: undefined symbol: hts_open_format
#36
christophfink
closed
2 years ago
11
unable to load shared object '/build/r-rsamtools/src/00LOCK-Rsamtools/00new/Rsamtools/libs/Rsamtools.so'
#35
starsareintherose
closed
2 years ago
13
ScanBamParam: load all tags
#34
gevro
closed
2 years ago
4
`Error: scanTabix: '4' not present in tabix index`
#33
bschilder
closed
2 years ago
22
`Rsamtools::indexTabix`: Capture console output
#32
bschilder
closed
1 year ago
3
Is there a way to extract part of the sequence that maps to a specific area in the reference!
#31
loukesio
closed
2 years ago
9
installation error in Microsoft R Open (R4.0.2)
#30
reckonzzz
closed
2 years ago
2
installing error
#29
sunnyyakima
closed
2 years ago
7
countBam with empty GRanges object should return zero counts
#28
smped
closed
1 year ago
6
Bump version to avoid overwriting CRAM support
#27
ttriche
closed
2 years ago
1
example(applyPileups) ... code works
#26
vjcitn
closed
3 years ago
6
ScanBamParams documentation
#25
cmatKhan
closed
2 years ago
1
Symbol not found: _bcf_float_missing
#24
akhst7
closed
3 years ago
2
cram support
#23
matthdsm
closed
3 years ago
1
Error installing
#22
padpadpadpad
closed
3 years ago
9
Issue with CRAM support install
#21
lmckinno
closed
3 years ago
8
Issue with install on using conda
#20
metaGmetapop
closed
2 years ago
3
min_nucleotide_depth parameter of PileupParam doesn't take 0
#19
sarahwajid
opened
3 years ago
1
What pileup options to use for nanopore sequencing data?
#18
kac2053
closed
3 years ago
1
Rsamtools cannot handle csi index?
#17
Mailinnia
opened
3 years ago
0
scanBam() crashes when asMates=TRUE and RNEXT is *
#16
hpages
closed
4 years ago
4
request to add support for pacbio unaligned bam files?
#15
jayoung
closed
4 years ago
6
Bug in windows version of Rsamtools Fasta sequence retrieval
#14
dnieuw
opened
4 years ago
0
Rsamtools::pileup counts overlapping paired-end reads twice
#13
alkodsi
opened
4 years ago
5
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