sstadick/perbase

Issues

• not all region return when using a bed file

  #71 opened 9 months ago by FunGeST
  1

• MacOS build on conda is incompatible with arm (but still gets installed)

  #72 opened 3 months ago by patbohn
  3

• Missing bam/cram file should return an error code

  #57 opened 2 years ago by patbohn
  2

• 'Chromosome not found in BAM/CRAM header'

  #50 opened 3 years ago by Surar
  2

• bgzipped and indexed reference fasta

  #70 opened 9 months ago by darked89
  0

• weird encoding for reference name

  #66 opened a year ago by twaddlac
  7

• Index out of bounds

  #68 opened a year ago by ChristopherRichie
  4

• Difference only-depth and base-depth

  #67 opened a year ago by Akazhiel
  3

• from_pileup_mate_aware very inefficient?

  #64 opened a year ago by brentp
  2

• parameters for sparse data

  #63 opened a year ago by brentp
  1

• New Tool for Per-Sequence Depths

  #62 opened a year ago by oschwengers
  1

• accessing qpos() ?

  #60 opened a year ago by brentp
  2

• base-depth become extremely slow when calculating highly covered site.

  #59 opened 2 years ago by y9c
  8

• ubuntu cant find perbase

  #56 opened 2 years ago by JMNGLS
  3

• Add Forward/Reverse mapping counts

  #54 opened 2 years ago by 25shmeckles
  2

• (optional?) Dependencies don't allow perbase to be used or compiled on Ubuntu 18.04.

  #55 opened 2 years ago by patbohn
  3

• Panic during base-depth, caused by secondary alignments?

  #53 opened 2 years ago by da-i
  2

• Can't use the base -depth function

  #49 opened 3 years ago by Surar
  5

• Support bedGraph output in only-depth

  #46 opened 3 years ago by ghuls
  1

• base-depth panicked with a 3-column BED file

  #41 opened 3 years ago by nh13
  0

• Better error message with an invalid bed file

  #42 opened 3 years ago by nh13
  0

• Allow for outputing positions with 0 depth in base-depth

  #44 opened 3 years ago by sstadick
  0

• read counter

  #37 opened 3 years ago by colindaven
  2

• Add bgzip output support

  #10 opened 3 years ago by sstadick
  4

• Add PGO pass

  #39 opened 3 years ago by sstadick
  0

• Possible to calculate only say INDEL column values?

  #35 opened 4 years ago by jelber2
  5

• Look into writing my own pileup engine

  #11 opened 4 years ago by sstadick
  2

• Resume OSX builds

  #28 opened 4 years ago by sstadick
  1

• How much faster than mosdepth?

  #30 opened 4 years ago by brainstorm
  3

• Create Benchmarking Suite

  #31 opened 4 years ago by sstadick
  0

• Add tests for > 8000 depth to `base-depth`

  #26 opened 4 years ago by sstadick
  0

• Clean up error messages

  #24 opened 4 years ago by sstadick
  0

• Include reference base in `simple-depth`

  #21 opened 4 years ago by sstadick
  1

• Add a strictly depth calculator

  #9 opened 4 years ago by sstadick
  1

• Investigate pre-processing the input bam to annoate mates

  #5 opened 4 years ago by sstadick
  1

• Add tests to `par_io`

  #4 opened 4 years ago by sstadick
  0

• Fix conda build recipe

  #13 opened 4 years ago by sstadick
  1

• Switch to using clap

  #7 opened 4 years ago by sstadick
  0

• Fix up all the doc comments

  #14 opened 4 years ago by sstadick
  0

• Migrate to updated version of rust_lapper

  #12 opened 4 years ago by sstadick
  0

• Move test bam to tempdir

  #16 opened 4 years ago by sstadick
  0

• Fix CI to regen / fix lockfile

  #17 opened 4 years ago by sstadick
  0

• Add an `indepth` tool that outputs more metrics

  #8 opened 4 years ago by sstadick
  0

• Add support of readgroup awareness and filtering

  #6 opened 4 years ago by sstadick
  0