Issues

• base-depth aborts with "CSV error: found record with N fields" when --keep-zeros and --ref-fasta are combined

  sstadick/perbase#109 · Filter by author CristEin opened on Sep 21, 2026

• channel-size-modifier units confusing

  enhancement
  sstadick/perbase#102 · Filter by author chrisamiller opened on Feb 2, 2026
  1

• Short usage doesn't match full help

  sstadick/perbase#101 · Filter by author chrisamiller opened on Feb 2, 2026
  2

• Update base-depth docs to reflect that N's are counted toward depth.

  bugenhancement
  sstadick/perbase#81 · Filter by author sstadick opened on Jun 19, 2025
  1

  

• Are Ns counted into DEPTH?

  sstadick/perbase#80 · Filter by author Y-Pei opened on Jun 16, 2025
  2

  

• For bam files aligned to transcriptome, I am getting the error 'Unknown sequence name'?

  sstadick/perbase#75 · Filter by author rnaomics opened on Sep 10, 2024
  4

• bgzipped and indexed reference fasta

  sstadick/perbase#70 · Filter by author darked89 opened on Feb 5, 2024
  1

• weird encoding for reference name

  bug
  sstadick/perbase#66 · Filter by author twaddlac opened on Jun 26, 2023
  8

• from_pileup_mate_aware very inefficient?

  enhancement
  sstadick/perbase#64 · Filter by author brentp opened on May 30, 2023
  2

• parameters for sparse data

  sstadick/perbase#63 · Filter by author brentp opened on May 26, 2023
  1

• New Tool for Per-Sequence Depths

  sstadick/perbase#62 · Filter by author oschwengers opened on May 25, 2023
  1

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

  bugenhancement
  sstadick/perbase#59 · Filter by author y9c opened on Nov 16, 2022
  8

• Missing bam/cram file should return an error code

  bug
  sstadick/perbase#57 · Filter by author patbohn opened on Sep 29, 2022
  2

• Add Forward/Reverse mapping counts

  enhancement
  sstadick/perbase#54 · Filter by author 25shmeckles opened on Jul 8, 2022
  2

• Support bedGraph output in only-depth

  enhancement
  sstadick/perbase#46 · Filter by author ghuls opened on Dec 1, 2021
  1

• Add PGO pass

  sstadick/perbase#39 · Filter by author sstadick opened on Jul 12, 2021

• Create Benchmarking Suite

  investigation
  sstadick/perbase#31 · Filter by author sstadick opened on Nov 16, 2020
  

• Clean up error messages

  enhancement
  sstadick/perbase#24 · Filter by author sstadick opened on Oct 29, 2020
  

• Look into writing my own pileup engine

  investigation
  sstadick/perbase#11 · Filter by author sstadick opened on Sep 27, 2020
  2

• Add an indepth tool that outputs more metrics

  enhancement
  sstadick/perbase#8 · Filter by author sstadick opened on Sep 27, 2020

• Add support of readgroup awareness and filtering

  enhancement
  sstadick/perbase#6 · Filter by author sstadick opened on Sep 27, 2020
  1