cancerit/alleleCount

Issues

• Choosing SNPs

  #78 opened 5 months ago by bounlu
  3

• Null Iterator Error

  #69 opened 3 years ago by nitishnih
  6

• Unpaired data - No alleleCount when reads available

  #72 opened 8 months ago by ShixiangWang
  9

• Is LWP::UserAgent required?

  #77 opened a year ago by ItIsI-Orient
  1

• .exe file

  #76 opened a year ago by vlachosg37
  1

• Scipt convertAlleleCounts.r deleted?

  #75 opened 2 years ago by justalilibit
  1

• how to install in R

  #74 opened 2 years ago by esraajamal
  1

• Can I use this tools on RNAseq BAM file ?

  #73 opened 2 years ago by panxiaoguang
  2

• Confusing error when input is unmapped

  #71 opened 3 years ago by keiranmraine
  0

• Is htslib 1.10.2 supported?

  #63 opened 3 years ago by roryk
  1

• htslib for dockerfile is not updated

  #67 opened 3 years ago by keiranmraine
  2

• base image update to Ubuntu 20.04

  #68 opened 3 years ago by keiranmraine
  0

• Error in cli help

  #66 opened 4 years ago by keiranmraine
  0

• 10X test data doesn't work

  #65 opened 4 years ago by keiranmraine
  0

• AlleleCounter bahavior with soft-clipped reads

  #64 opened 4 years ago by DominikGlodzik
  1

• C alleleCounter - filter by long form

  #37 opened 7 years ago by keiranmraine
  3

• "-b|--hts-file" isn't obvious means BAM/CRAM

  #62 opened 5 years ago by keiranmraine
  0

• 10x data

  #47 opened 5 years ago by thelingxichen
  1

• Running aC on scRNA BAMs (10X or otherwise)

  #61 opened 5 years ago by nansari-pour
  4

• Clipping reads and reference bias

  #59 opened 5 years ago by danchubb
  3

• sorting of loci file for dense-snps

  #58 opened 5 years ago by nurmians
  1

• Memory use vs. size of SNP list

  #54 opened 5 years ago by ilykos
  0

• AlleleCounter for unpaired data

  #53 opened 5 years ago by m4merg
  1

• Running alleleCounter with or without reference file

  #52 opened 5 years ago by ilykos
  1

• Description

  #48 opened 6 years ago by nurmians
  3

• Indel support

  #50 opened 6 years ago by ibwoo
  1

• RNA STAR aligned files may have different flags

  #46 opened 7 years ago
  0

• allelecount runs endlessly or gets killed on CentOS 7

  #41 opened 7 years ago by mheskett
  3

• test failed: t/01bam.t .... Failed 235/235 subtests

  #42 opened 7 years ago by weiliuyuan
  3

• Prototype overlapping read count corrections in alleleCounter.pl

  #32 opened 7 years ago by keiranmraine
  0

• migrate perl alleleCounter.pl to wrap the C version

  #30 opened 7 years ago by keiranmraine
  0

• Pre-release tag for fragment analysis

  #40 opened 7 years ago by keiranmraine
  0

• int(block_str) error

  #44 opened 7 years ago by girdhar3
  2

• installation error

  #36 opened 7 years ago by mheskett
  8

• Installation error

  #34 opened 7 years ago by keyuan
  2

• installation error on linux

  #35 opened 7 years ago by mheskett
  0

• Add sam flag filter option

  #28 opened 7 years ago
  0

• Option to run through file rather than use pileup/fetch

  #29 opened 7 years ago
  0

• Add travis status to README

  #26 opened 8 years ago by keiranmraine
  0

• Readme - not clear that all dependancies are installed by setup.sh

  #17 opened 9 years ago by keiranmraine
  1

• Clarification of dependencies

  #18 opened 9 years ago by verdurin
  7

• Throw informative error when BAM index missing

  #14 opened 9 years ago by sdentro
  1

• Not possible to emit version on cmd

  #19 opened 9 years ago by keiranmraine
  1

• patch not required

  #20 opened 9 years ago by keiranmraine
  1

• Update to htslib / add CRAM support

  #9 opened 10 years ago by keiranmraine
  2