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completed a first draft of the changelog
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nevrome committed Jul 11, 2024
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Expand Up @@ -25,6 +25,8 @@ It specifically preserves the following `POSEIDON.yml` fields:

Note that this does not include the package `title`, but this can be easily set to be identical to the source with `-n` or `-o` if it is desired. The `poseidonVersion` field is also not copied, because `trident` can only ever produce output packages with the latest Poseidon schema version. `--preservePyml` also copies the `README` and the `CHANGELOG` files to the output package.

While implementing this we clearly separated the different `forge` output modes (`--onlyGeno`, `--minimal`, `--preservePyml` and the default) and made them mutually exclusive. We did so to avoid an increasingly complex set of interactions for the future.

One particular application of `--preservePyml` is the reordering of samples in an existing Poseidon package `MyPac` with the new `--ordered` flag. We suggest the following workflow for this application:

1. Generate a `--forgeFile` with the desired order of the samples in `MyPac`. This can be done manually or with any tool. Here is an example, where we employ `qjanno` to generate a `forge` selection so that the samples are ordered alphabetically and descendingly by their `Poseidon_ID`:
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#### Better error messages

In previous `trident` versions some common error messages were not well rendered on the command line. This concerned particularly errors when parsing command line input, the `POSEIDON.yml` file or genotype data. We applied multiple changes here to improve the cli output.



The behaviour of the global `trident` option `--errLength` was also changed. It now only truncates genotype data-related messages, but does so as well if these are raised on the `[Warning]` log level. This change should make the `trident` output upon broken genotype data much more readable.

### V 1.5.0.1

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