Bycon

Latest version: v2.0.5

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1.1.1

* services: new frequency plot type `histoheatplot`:
- also some new related parameters, e.g. `plotHeatIntensity`
- [/services/intervalFrequencies/?datasetIds=progenetix&filters=NCIT:C,!NCIT:C3247,!NCIT:C3510&filterPrecision=start&collationTypes=NCIT&output=histoheatplot&plotAreaHeight=20&plotRegionGapWidth=&plotChros=3,17&plotHeatIntensity=1.5&plotGeneSymbols=TP53,BCL6&plotDendrogramStroke=2](http://progenetix.org/services/intervalFrequencies/?datasetIds=progenetix&filters=NCIT:C,!NCIT:C3247,!NCIT:C3510&filterPrecision=start&collationTypes=NCIT&output=histoheatplot&plotAreaHeight=20&plotRegionGapWidth=&plotChros=3,17&plotHeatIntensity=1.5&plotGeneSymbols=TP53,BCL6&plotDendrogramStroke=2)
* `intervalFrequencies` now supports start-anchored greedy term matches as well
as exclusion of individual terms through `!` prefix (as for normal filter searches)

1.1.0

* fixed gene position queries (had hardcoded `progenetix` database ...)
* general overhaul of query generation
- `class ByconQuery`
- called directly in `query_execution`
- removed some variant query types (e.g. "type only")
- better handling of `id` type queries (including the retrieval of the associated
variants)
- move to collection of query objects per entity instead of collection (is
mostly a logical change for general use of entities instead of the database
impolementation as target - that is resolved at the query execution)
- TODO: probably will move from the dynamic variant query type detection
to a stacked "test one after the other with hard-coded parameter checks"
just for sanity reasons - but right now see above
- TODO: variant requests and request type detection still not part of class
- TODO: geo queries into class ...
* there is now a `force_empty_plot` (forceEmptyPlot) parameter so that sample
queries w/o any CNV (e.g. from cancercelllines.org samples) generate an empty
strip, to add non-CNV as labels
* fixed error in `interval_utils` (renamed config key...)
* fixed associated `byconaut` errors

1.0.72

* cleaning of handovers
- no "all variants from matched biosamples" ... anymore due to performance
problems
- now variant storage and handovers only for matched variants - _i.e._ if
there was a variant query - _or_ if a sample, individual ... had been requested
by path id
* CNV VCF fix
* some general handover creation cosmetics
* VRS schema components moved

1.0.71

* finished the `ByconVariant` `vrsVariant` method and implemented this as the format
for the Beacon variant response
* added sorting to `.pgxseg` files
* added compact `VRSallele` and `VRScopyNumberChange` schemas & using them in
`ByconVariant().vrsVariant(v)`

`byconaut`

* moved `geoloc_utils` to `byconaut/services/lib`
* improved index generation for `2dsphere` indexes
* moved `geolocs` to `_byconServicesDB` and adjusted code accordingly
* fixed `frequencyMapsGenerator` for the new database

1.0.70

* refactored the VCF export into `exportfile_generation`
* minor pagination code cleanup

1.0.69

* fixed datatable & pgxseg download error (introduced w. 1.0.68)
- thanks to ClmtHua in [20](https://github.com/progenetix/bycon/issues/20)
* internal change of more consistant use of `genomicVariant` for variant entity,
schema

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