Thomas Hickman

Abstract ref_to_m5 from cram_io

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This pull request extracts the function `m5_to_ref` from `cram_io` and adds tests. `m5_to_ref` and helper functions for it are added in a new file called `ref.c`. I've also added a...

Add mmap hfile backend

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The eventual use of this PR will be to replace the reference file wrapper in the reference fetching logic from an `mFILE` to an mmapped hFILE. This will eventually be...

Buffer overflow in hap.py’s `preprocess` program

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At https://github.com/Illumina/hap.py/blob/6c907ce3b02956bc239022db6edea7c48d6ddb8b/src/c++/lib/variant/VariantReader.cpp#L735, the size allocated for the array `ad` is `adcount`, whereas in the function https://github.com/Illumina/hap.py/blob/6c907ce3b02956bc239022db6edea7c48d6ddb8b/src/c++/lib/tools/BCFHelpers.cpp#L532  (which gets called at VarientReader:738 with `ad`) writes `values.size()` elements ( where `values` is...

itemSeparator with an array prints arguments twice

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### Inputs test.cwl: ``` cwlVersion: v1.0 class: CommandLineTool baseCommand: ['true'] inputs: - id: param type: type: array items: string inputBinding: prefix: --arr_prefix inputBinding: prefix: --before_prefix itemSeparator: " " outputs: []...

Add fastaref subcommand.

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This adds a fastaref subcommand, which creates a fasta file containing references for a given file, obtained by looking at SQ lines. Note: this depends on https://github.com/samtools/htslib/pull/589 getting merged, so...

ghc is broken https://ghc.haskell.org/trac/ghc/ticket/3397, so this means that breaking on an exception will freeze the debugger in some instances

In the docs, the prop `value` in the `AutoComplete` component says that this prop is: > value of the component in the controlled state However, from testing this out and...

## Expected Behavior No error should be thrown ## Actual Behavior An error is thrown ## Workflow Code `workflow.cwl` ``` cwlVersion: v1.2 class: Workflow inputs: file: type: File secondaryFiles: -...

If you define a `CommandLineTool` which has an input of type `[File, Directory]`, using this parameter in a wofkflow results in a spurious warning of: ``` Warning: invalid field `nameroot`,...