stjude-rust-labs / ngs

Command line utility for working with next-generation sequencing files.

stjude-rust-labs/ngs Issues

feat: implement SAM viewing in `ngs view`
Updated 4 months ago
feat: implement BAM viewing in `ngs view`
Updated 4 months ago
feat: extend GFF to support query region for `ngs view`
Closed 4 months ago1
feat: extend GTF to support query region for `ngs view`
Closed 4 months ago1
feat: add indexing for SAM files
Closed 4 months ago1
feat: add SAM/BAM/CRAM sorting
Closed 4 months ago1
revise: remove custom header checks
Closed a year ago
revise: unify all contexts within `ngs`
Closed a year ago
feat: implement GTF for `ngs view`
Closed a year ago
revise: audit `ngs view` for better error messages with `with_context`
Closed a year ago
revise: audit `ngs convert` for better error messages with `with_context`
Closed a year ago
revise: use async readers/writers for `ngs view`
Closed a year ago
feat: implement SAM to CRAM conversion within `ngs convert`
Closed a year ago
feat: implement BAM to CRAM conversion within `ngs convert`
Closed a year ago
feat: implement GFF for `ngs view`
Closed 2 years ago
feat: implement SAM for `ngs view`
Closed 2 years ago
ngslib-lint: add basic linter with easiest checks to do.
Closed 2 years ago
ngslib-generate: given a reference genome and a SNV/Indel variant file, generate an example SAM/BAM/CRAM file
Closed 2 years ago