Bioconductor/Rsamtools

Issues

• Rsamtools pileup and Pysam pileup output discrepancy

  #59 opened a year ago by XqKang
  4

• Support for CSI indexes

  #58 opened a year ago by diego-rt
  0

• CRAM support - why not?

  #56 opened a year ago by pd3
  2

• Rsamtools with multiple threads?

  #55 opened 2 years ago by junjunlab
  2

• `Rsamtools::indexTabix`: Capture console output

  #32 opened 2 years ago by bschilder
  3

• countBam with empty GRanges object should return zero counts

  #28 opened 2 years ago by smped
  6

• Help with pileup

  #52 opened 2 years ago by joegeorgeson
  1

• Support for delimited tags

  #45 opened 2 years ago by joegeorgeson
  3

• samtools markdup in Rsamtools

  #51 opened 2 years ago by Adnanhashim
  1

• Installation issue related to linker files

  #50 opened 2 years ago by ShanSabri
  1

• Installation Error

  #47 opened 2 years ago by cmfield
  8

• using multiple threads for bam sorting, merging, and indexing

  #46 opened 2 years ago by kriemo
  1

• Issue with CRAM support install

  #21 opened 4 years ago by lmckinno
  8

• scanbam, with many reginos in which, is very slow

  #44 opened 2 years ago by gevro
  2

• Support for more recent HTSlib

  #41 opened 2 years ago by matthdsm
  6

• Issue with install on using conda

  #20 opened 2 years ago by metaGmetapop
  3

• installing error

  #29 opened 2 years ago by sunnyyakima
  7

• ScanBamParams documentation

  #25 opened 2 years ago by cmatKhan
  1

• Loading bam file in chunks

  #42 opened 2 years ago by gevro
  2

• Indexing a gzipped fasta file

  #40 opened 2 years ago by eggrandio
  2

• Using both "yileldSize" and "which" parameters

  #38 opened 2 years ago by gacatag
  3

• scanBam 'which' returns the same record multiple times

  #39 opened 2 years ago by gevro
  1

• `Error: scanTabix: '4' not present in tabix index`

  #33 opened 3 years ago by bschilder
  22

• Rsamtools.so: undefined symbol: hts_open_format

  #36 opened 3 years ago by christophfink
  11

• unable to load shared object '/build/r-rsamtools/src/00LOCK-Rsamtools/00new/Rsamtools/libs/Rsamtools.so'

  #35 opened 3 years ago by starsareintherose
  13

• Bug in scanTabix

  #8 opened 5 years ago by timoast
  4

• ScanBamParam: load all tags

  #34 opened 3 years ago by gevro
  4

• Is there a way to extract part of the sequence that maps to a specific area in the reference!

  #31 opened 3 years ago by loukesio
  9

• installation error in Microsoft R Open (R4.0.2)

  #30 opened 3 years ago by reckonzzz
  2

• Rsamtools::pileup counts overlapping paired-end reads twice

  #13 opened 5 years ago by alkodsi
  5

• example(applyPileups) ... code works

  #26 opened 3 years ago by vjcitn
  6

• Error with getSeq from opened fasta file (Rsamtools 2.0.2)

  #12 opened 5 years ago by farshadf
  7

• min_nucleotide_depth parameter of PileupParam doesn't take 0

  #19 opened 4 years ago by sarahwajid
  1

• Symbol not found: _bcf_float_missing

  #24 opened 4 years ago by akhst7
  2

• Error installing

  #22 opened 4 years ago by padpadpadpad
  9

• cram support

  #23 opened 4 years ago by matthdsm
  1

• What pileup options to use for nanopore sequencing data?

  #18 opened 4 years ago by kac2053
  1

• Rsamtools cannot handle csi index?

  #17 opened 4 years ago by Mailinnia
  0

• scanBam() crashes when asMates=TRUE and RNEXT is *

  #16 opened 5 years ago by hpages
  4

• request to add support for pacbio unaligned bam files?

  #15 opened 5 years ago by jayoung
  6

• Bug in windows version of Rsamtools Fasta sequence retrieval

  #14 opened 5 years ago by dnieuw
  0

• CVE_2012_1461-1 FOUND

  #11 opened 5 years ago by mmahmoudian
  5

• ERROR in scanBcfHeader [Reported to maintainer@bioconductor.org]

  #10 opened 5 years ago by lshep
  5

• How to use Rsamtools to extracting reads map into single chromosome from BAM file

  #9 opened 5 years ago by Timothy-WANG
  2

• scanTabix should return a stream

  #7 opened 5 years ago by romanzenka
  7

• handle multiple calls to scanBam() on an open BamFile

  #6 opened 6 years ago by mtmorgan
  2

• indexFa breaks FaFile object when using getSeq

  #5 opened 6 years ago by FelixErnst
  0

• .bai files are not found when "bam" is part of the file path

  #4 opened 6 years ago by ericfournier2
  0

• Rsamtools::seqinfo() with corrupt BamFile messes up R session

  #3 opened 6 years ago by kjohnsen
  11

• Overhaul with new Samtools source code

  #2 opened 7 years ago by kjohnsen
  2