Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / DataBiosphere/xsamtools issues and pull requests

#109 - Add samtools path.

Pull Request - State: closed - Opened by DailyDreaming over 2 years ago

#108 - Always use latest tnu.

Pull Request - State: closed - Opened by DailyDreaming over 2 years ago

#107 - Live install.

Pull Request - State: closed - Opened by DailyDreaming over 2 years ago

#106 - Remove unused import.

Pull Request - State: closed - Opened by DailyDreaming over 2 years ago

#105 - Upgrade samtools version.

Pull Request - State: closed - Opened by DailyDreaming over 2 years ago - 1 comment

#104 - Remove clean make target.

Pull Request - State: closed - Opened by DailyDreaming over 2 years ago

#103 - Generalize args to accept all and pass directly to samtools

Pull Request - State: closed - Opened by jessebrennan over 2 years ago - 2 comments

#102 - Remove dependency on CLI builder

Pull Request - State: closed - Opened by jessebrennan over 2 years ago

#101 - Update docker repo

Pull Request - State: closed - Opened by jessebrennan over 2 years ago

#100 - Save version during release script (resolves #99)

Pull Request - State: closed - Opened by jessebrennan over 2 years ago

#98 - Update README.md

Pull Request - State: closed - Opened by aofarrel over 2 years ago

#97 - Add options for --force-samples and --print-header

Pull Request - State: closed - Opened by jessebrennan over 2 years ago

#96 - Samtools cloud view

Pull Request - State: open - Opened by DailyDreaming almost 3 years ago

#95 - Add curses lib to readme.

Pull Request - State: closed - Opened by DailyDreaming almost 4 years ago

#94 - Add basic slicing.

Pull Request - State: open - Opened by DailyDreaming almost 4 years ago

#93 - Add basic slicing.

Pull Request - State: closed - Opened by DailyDreaming almost 4 years ago

#92 - Add cram view gs cloud streaming.

Pull Request - State: open - Opened by DailyDreaming almost 4 years ago - 2 comments

#91 - Add decode container header function.

Pull Request - State: closed - Opened by DailyDreaming almost 4 years ago

#90 - Add int32 decode method.

Pull Request - State: closed - Opened by DailyDreaming almost 4 years ago

#89 - Add LFT8 decode/encode.

Pull Request - State: closed - Opened by DailyDreaming almost 4 years ago

#88 - Enable CI/CD for entire test suite

Issue - State: open - Opened by xbrianh almost 4 years ago
Labels: xsamtools

#87 - Fix linting.

Pull Request - State: closed - Opened by DailyDreaming almost 4 years ago

#86 - Fix make mypy.

Pull Request - State: closed - Opened by DailyDreaming almost 4 years ago

#85 - Enable CI/CD

Pull Request - State: closed - Opened by xbrianh almost 4 years ago

#84 - Pin six

Pull Request - State: closed - Opened by xbrianh almost 4 years ago

#83 - Add decode itf8 array.

Pull Request - State: closed - Opened by DailyDreaming almost 4 years ago

#82 - Add functions to encode and decode itf8.

Pull Request - State: closed - Opened by DailyDreaming almost 4 years ago

#81 - Add cram file definition.

Pull Request - State: closed - Opened by DailyDreaming almost 4 years ago

#80 - Switch to warning mixin in test_cram.

Pull Request - State: closed - Opened by DailyDreaming almost 4 years ago

#79 - Fix linting.

Pull Request - State: closed - Opened by DailyDreaming almost 4 years ago

#78 - Add flake8 exception for E127.

Pull Request - State: closed - Opened by DailyDreaming almost 4 years ago - 1 comment

#77 - Enable and test cram CLI.

Pull Request - State: closed - Opened by DailyDreaming almost 4 years ago

#76 - Add crai parsing.

Pull Request - State: closed - Opened by DailyDreaming almost 4 years ago

#75 - Add extra error parsing.

Pull Request - State: closed - Opened by DailyDreaming almost 4 years ago - 8 comments

#74 - Add basic cram view with no slicing.

Pull Request - State: closed - Opened by DailyDreaming almost 4 years ago - 1 comment

#73 - Bump TNU

Pull Request - State: closed - Opened by xbrianh about 4 years ago

#72 - Bump terra-notebook-utils

Pull Request - State: closed - Opened by xbrianh about 4 years ago - 1 comment

#71 - [Easy] Pin CLI builder.

Pull Request - State: closed - Opened by xbrianh about 4 years ago

#70 - Workaround for firecloud installation issue

Pull Request - State: closed - Opened by xbrianh about 4 years ago

#69 - Improve VCF merge tests

Pull Request - State: closed - Opened by xbrianh about 4 years ago

#68 - Blob writer uses FIFO base class

Pull Request - State: closed - Opened by xbrianh about 4 years ago

#67 - Blob reader uses FIFO base class

Pull Request - State: closed - Opened by xbrianh about 4 years ago

#66 - Split tests into separate files

Pull Request - State: closed - Opened by xbrianh about 4 years ago

#65 - Reorganize test warning suppression

Pull Request - State: closed - Opened by xbrianh about 4 years ago

#64 - Introduce FIFO Pipe base class

Pull Request - State: closed - Opened by xbrianh about 4 years ago

#63 - Introduce gs_utils access methods

Pull Request - State: closed - Opened by xbrianh about 4 years ago

#62 - Perform access checks before opening FIFO pipes

Pull Request - State: closed - Opened by xbrianh about 4 years ago

#61 - Fix docker image tagging, rename env var

Pull Request - State: closed - Opened by xbrianh over 4 years ago

#60 - Move docker images to institutional account

Issue - State: open - Opened by xbrianh over 4 years ago
Labels: xsamtools

#59 - [Easy] Update makefile to clean before release

Pull Request - State: closed - Opened by xbrianh over 4 years ago

#58 - Update docker login script

Pull Request - State: closed - Opened by xbrianh over 4 years ago

#57 - Use version tag in Docker makefile recipes

Pull Request - State: closed - Opened by xbrianh over 4 years ago

#56 - Add script to compute docker image tag

Pull Request - State: closed - Opened by xbrianh over 4 years ago

#55 - XSAMTOOLS_IMAGE_NAME -> XSAMTOOLS_IMAGE_BASE_NAME

Pull Request - State: closed - Opened by xbrianh over 4 years ago

#54 - Move docker recipes into common.mk

Pull Request - State: closed - Opened by xbrianh over 4 years ago

#53 - Remove release undo recipe from Makefile

Pull Request - State: closed - Opened by xbrianh over 4 years ago

#52 - Use XSAMTOOLS_HOME to verify env has been sourced

Pull Request - State: closed - Opened by xbrianh over 4 years ago

#51 - Update with samtools docker dep.

Pull Request - State: closed - Opened by DailyDreaming over 4 years ago

#50 - Fix makefile variables

Pull Request - State: closed - Opened by xbrianh over 4 years ago

#49 - Add logging to pipes

Pull Request - State: closed - Opened by xbrianh over 4 years ago

#48 - Share a process executor among all pipes

Pull Request - State: closed - Opened by xbrianh over 4 years ago

#47 - Update type hint: use Sequence instead of Iterable

Pull Request - State: closed - Opened by xbrianh over 4 years ago

#46 - Move access verification to utilitie classes

Pull Request - State: closed - Opened by xbrianh over 4 years ago

#45 - Verify bucket access before pipe subprocesses

Pull Request - State: closed - Opened by xbrianh over 4 years ago

#44 - Check return codes of subprocesses

Pull Request - State: closed - Opened by xbrianh over 4 years ago

#43 - Assert bcftools is available in VCF commands

Pull Request - State: closed - Opened by xbrianh over 4 years ago

#42 - Add convenience methods for access verification

Pull Request - State: closed - Opened by xbrianh over 4 years ago

#41 - Clone canonical repos instead of using forks.

Pull Request - State: closed - Opened by DailyDreaming over 4 years ago - 1 comment

#40 - Fix repo home env vars

Pull Request - State: closed - Opened by xbrianh over 4 years ago

#39 - Improve type hints

Pull Request - State: closed - Opened by xbrianh over 4 years ago

#38 - Add convenience stubbed object

Pull Request - State: closed - Opened by xbrianh over 4 years ago

#37 - Readable/writable handles avoiding FIFO deadlock

Pull Request - State: closed - Opened by xbrianh over 4 years ago

#36 - Correctly shutdown gscio.Reader

Pull Request - State: closed - Opened by xbrianh over 4 years ago

#35 - Use ProcessPoolExecutor for process concurrency

Pull Request - State: closed - Opened by xbrianh over 4 years ago - 1 comment

#34 - Use mpu queue for safer reader exit

Pull Request - State: closed - Opened by xbrianh over 4 years ago - 1 comment

#33 - Enable requester pays for DRS objects

Pull Request - State: closed - Opened by xbrianh over 4 years ago

#32 - Bump terra-notebook-utils

Pull Request - State: closed - Opened by xbrianh over 4 years ago

#31 - Simplify environment

Pull Request - State: closed - Opened by xbrianh over 4 years ago

#30 - Add samtools.

Pull Request - State: closed - Opened by DailyDreaming over 4 years ago - 1 comment

#29 - Add cloud CRAM slicing functionality.

Pull Request - State: closed - Opened by DailyDreaming over 4 years ago - 3 comments

#28 - Dockerfile installs xsamtools from local repo root

Pull Request - State: closed - Opened by xbrianh over 4 years ago

#27 - fix versioning

Pull Request - State: closed - Opened by xbrianh over 4 years ago

#26 - Fix DRS resolution

Pull Request - State: closed - Opened by xbrianh over 4 years ago

#25 - Add drs support

Pull Request - State: closed - Opened by xbrianh over 4 years ago

#24 - Include repo build dir in samtools search paths

Pull Request - State: closed - Opened by xbrianh over 4 years ago

#23 - Update Makefile to improve test performance

Pull Request - State: closed - Opened by xbrianh over 4 years ago

#22 - Remove environment variable discovery

Pull Request - State: closed - Opened by xbrianh over 4 years ago - 1 comment

#21 - Add tooling to create Docker image

Pull Request - State: closed - Opened by xbrianh over 4 years ago

#20 - Consolidate vcf commands into single CLI

Pull Request - State: closed - Opened by xbrianh over 4 years ago

#19 - Add VCF test fixtures

Pull Request - State: closed - Opened by xbrianh over 4 years ago

#18 - Suppress warnings during tests

Pull Request - State: closed - Opened by xbrianh over 4 years ago

#17 - Add subsampling methods and scripts

Pull Request - State: closed - Opened by xbrianh over 4 years ago

#16 - Fix long description content type

Pull Request - State: closed - Opened by xbrianh over 4 years ago

#15 - Add subsampling to VCF streams

Pull Request - State: closed - Opened by xbrianh over 4 years ago

#14 - [Easy] Add timeout to writer FIFO pipe

Pull Request - State: closed - Opened by xbrianh over 4 years ago

#13 - Update readme

Pull Request - State: closed - Opened by xbrianh over 4 years ago

#12 - [Easy] Remove prints from scripts/merge_vcfs.py

Pull Request - State: closed - Opened by xbrianh over 4 years ago

#11 - Improve htslib/bcftools binary discovery

Pull Request - State: closed - Opened by xbrianh over 4 years ago

#10 - Perform ./configure during htslib build

Pull Request - State: closed - Opened by xbrianh over 4 years ago