Search results

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

bugSomething isn't workingSomething isn't working

enhancementNew feature or requestNew feature or request

Status: Open.

#81 In sstadick/perbase;

· sstadick opened on Jun 19, 2025

Are Ns counted into DEPTH?

Status: Open.

#80 In sstadick/perbase;

· Y-Pei opened on Jun 16, 2025

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

Status: Open.

#75 In sstadick/perbase;

· rnaomics opened on Sep 10, 2024

bgzipped and indexed reference fasta

Status: Open.

#70 In sstadick/perbase;

· darked89 opened on Feb 5, 2024

weird encoding for reference name

bugSomething isn't workingSomething isn't working

Status: Open.

#66 In sstadick/perbase;

· twaddlac opened on Jun 26, 2023

from_pileup_mate_aware very inefficient?

enhancementNew feature or requestNew feature or request

Status: Open.

#64 In sstadick/perbase;

· brentp opened on May 30, 2023

parameters for sparse data

Status: Open.

#63 In sstadick/perbase;

· brentp opened on May 26, 2023

New Tool for Per-Sequence Depths

Status: Open.

#62 In sstadick/perbase;

· oschwengers opened on May 25, 2023

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

bugSomething isn't workingSomething isn't working

enhancementNew feature or requestNew feature or request

Status: Open.

#59 In sstadick/perbase;

· y9c opened on Nov 16, 2022

Missing bam/cram file should return an error code

bugSomething isn't workingSomething isn't working

Status: Open.

#57 In sstadick/perbase;

· patbohn opened on Sep 29, 2022

Add Forward/Reverse mapping counts

enhancementNew feature or requestNew feature or request

Status: Open.

#54 In sstadick/perbase;

· 25shmeckles opened on Jul 8, 2022

Support bedGraph output in only-depth

enhancementNew feature or requestNew feature or request

Status: Open.

#46 In sstadick/perbase;

· ghuls opened on Dec 1, 2021