Generalize args to accept all and pass directly to samtools (#103) Remove dependency on CLI builder (#102)
Include xsamtools so that we can have a functioning release
Fix how version info is stored
Save version during release script (resolves #99) (#100)
Update README.md (#98) Add options for --force-samples and --print-header (#97) Spelling. Add curses lib. (#95) Add extra error parsing. (#75) Add decode container header function. (#91) Add int32 decode method. (#90) Add LFT8 decode/encode. (#89) Add decode itf8 array. (#83) Add functions to encode and decode itf8. (#82) Add cram file definition. (#81) Enable CI/CD (#85) Fix linting. (#87) Pin six (#84) Fix mypy. (#86) Switch to warning mixin in test_cram. (#80) Fix linting. (#79) Enable and test cram CLI. (#77) Add crai parsing. (#76) Bump TNU (#73) Add basic cram view with no slicing. (#74) Bump TNU (#72)
Pin CLI builder. (#71)
Workaround for firecloud installation issue (#70) Improve vcf merge tests (#69) Blob writer uses FIFO base class (#68) Blob reader uses FIFO base class (#67) Split tests into separate files (#66) Reorganize test warning suppression (#65) Introduce FIFO Pipe base class (#64) Perform access checks before opening FIFO pipes (#62) Introduce gs_utils access methods (#63)
Fix docker image tagging, rename env var (#61) Update makefile to clean before release (#59) Update docker login script (#58) Attach package version to dockerfile tag (#57) Add script to compute docker image tag (#56) XSAMTOOLS_IMAGE_NAME -> XSAMTOOLS_IMAGE_BASE_NAME (#55) Move docker recipes into common.mk (#54) Remove release undo recipe from Makefile (#53) Use XSAMTOOLS_HOME to verify env has been sourced (#52) Update with samtools docker dep. Fix makefile variables (#50) Add logging to pipes (#49) Share a process executor among all pipes (#48) Update type hint: use Sequence instead of Iterable (#47) Move access verification to utilities classes (#46) Verify bucket access before pipe subprocesses (#45) Check return codes of subprocesses (#44) Assert bcftools is available in VCF commands (#43) Add convenience methods for access verification (#42) Install samtools binary. Fix repo home env vars (#40) Improve type hints (#39) Add convenience stubbed object (#38) Readable/writable handles avoiding FIFO deadlock (#37) Correctly shutdown gscio.Reader (#36) Use ProcessPoolExecutor for process concurrency (#35) Use mpu queue for safer reader exit (#34) Enable requester pays for DRS objects (#33) Simplify environment (#31) Bump terra-notebook-utils (#32) Dockerfile installs xsamtools from local repo root (#28)
Add drs support (#25)