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test-files.md

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Test Files

Test files are hosted on Netapp as zip files, and can be accessed via S3 commands.

To make repeated calls easier, you can place this alias in your ~/.bashrc or ~/.zshrc.

alias netapp="aws s3api --endpoint-url https://s3.ccia.org.au/ "

Finding test files

To get a list of available test files, run this command:

netapp list-objects --bucket mity --prefix tests/ --query "Contents[].Key"

Or without the alias:

aws s3api --endpoint-url https://s3.ccia.org.au/ list-objects --bucket mity --prefix tests/ --query "Contents[].Key"

The output will be a list of keys that look like this:

[
    "tests/ashkenazim-trio.zip",
    "tests/bad-header.zip",
    "tests/cram-support.zip"
]

Downloading test files

To download a test zip file, run this command:

netapp get-object --bucket mity --key <insert-key-here>

Or without the alias:

aws s3api --endpoint-url https://s3.ccia.org.au/ get-object --bucket mity --key <insert-key-here>

Zip file structure

Each test zip file will have an input and exp folder. For example:

ashkenazim-trio
├── exp
│   ├── ashkenazim.mity.vcf.gz
│   └── ashkenazim.mity.vcf.gz.tbi
└── input
    ├── HG002.hs37d5.2x250.small.MT.RG.bam
    ├── HG002.hs37d5.2x250.small.MT.RG.bam.bai
    ├── HG003.hs37d5.2x250.small.MT.RG.bam
    ├── HG003.hs37d5.2x250.small.MT.RG.bam.bai
    ├── HG004.hs37d5.2x250.small.MT.RG.bam
    └── HG004.hs37d5.2x250.small.MT.RG.bam.bai

Specific commands to run each test can be found in test-commands.md