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RELEASES_NOTES.md

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Release 3.6.0 [2022-10-01]

Improvements:

  • Add scripts to manage microsatellites classification:
    • bin/microsatCreateModel.py
    • bin/microsatLenDistrib.py
    • bin/microsatMergeResults.py
    • bin/microsatMsingsClassif.py
    • bin/microsatMSIsensorproProClassif.py
    • bin/microsatSklearnClassify.py
    • bin/microsatStatusToAnnot.py
  • Add storage for flag of main alternative annotation in bin/VCFToJSON.py. This flag is optional and is retrieved from PICK field in annotation (example: VCF coming from VEP with flag_pick option).

Bug fixes:

  • Fix bug with secondary mapping for aligners producing extra lines in the BAM (like STAR). These secondary mapping were taken into account and will no longer be taken into account.
  • Fix bug in annotating precise breakends with CIPOS > 0 on opposite strands and no overlap with an exon edge in bin/annotBND.py.

Release 3.5.1 [2022-03-19]

Improvements:

  • Update scipy from 1.2.1 to 1.7.3.

Bug fixes:

  • Fix bug with missing type of quality parameters in bin/inspectBND.py and bin/shallowsAnalysis.py.

Release 3.5.0 [2022-03-10]

Improvements:

  • Update pysam from 0.15.3 to 0.18.0.
  • Increase execution speed for bin/inspectBND.py.
  • Change JSON structure from bin/fusionsToJSON.py to improve usage in document databases: replacement of the dict feature_by_id by a list with _id in each feature.
  • Now bin/evalVariantControl.py takes into account false positives variants by default. The previous behavior can be recovered with the --only-expected option: exclude FP from the analysis.
  • Manage annotations out of transcript in bin/fixHGVSMutalyzer.py.
  • Add script to add UMI sequence in SAM RX tag from reads ID: bin/setUMITagFromID.py.

Bug fixes:

  • Fix bug with refskip for spliced alignment in bin/mergeCoOccurVar.py.
  • Fix bug with insertion and substitution of same nucleotid at same position in bin/evalVariantControl.py. Example: with 1:587874=A/T and 1:587874=./T only the last in VCF was taking into account.
  • Fix bug on depths in bin/depthsPanel.py, bin/inspectBND.py, bin/mergeVCF.py, bin/mergeVCFAmpli.py and bin/shallowsAnalysis.py. In overlapping read pairs, overlapping bases were only taken into account for one of the reads.

Release 3.4.0 [2021-10-13]

Improvements:

  • Add script to report depths on panel: bin/depthsPanel.py.
  • Add script to create known fusions partners database: bin/buildKnownBNDDb.py.
  • Add script to create data for saturation curve bin/saturationCurve.py.

Bug fixes:

  • Fix bug in bin/filterBND.py when a gene SYMBOL is None (in some lncRNA).

Release 3.3.0 [2020-04-28]

Improvements:

  • Replace non-allele specific COSMIC annotations produced by VEP to allelle-specific annotations in bin/fixVEPAnnot.py.

Release 3.2.0 [2020-11-11]

Improvements:

  • Manage new ID format from COSMIC in bin/VCFToJSON.py: COSM* -> COS*.
  • Add scripts to prepare data mining of fusions from breakends annotations: bin/ensemblInterProToGFF.py to generate the proteins domains annotations file and bin/inspectBND.py to produce a detailed annotation of each breakend.
  • Add management for included or near full overlapped amplicons in bin/addAmpliRG.py.
  • Add the shallow gene file as output from bin/shallowsAreas.py. It summarizes by gene the shallow areas and potentially missed variants.

Bug fixes:

  • Fix critical bug in bin/shallowsAnalysis.py: missing shallow area when there is no read on the area.
  • Fix bug in bin/fixVEPAnnot.py when alleles are in lower case.
  • Fix bug in writeJSON of bin/shallowsAnalysis.py when optional parameters input-annotations and inputs-variants are not provided.

Release 3.1.0 [2020-05-13]

Improvements:

  • Add count by target in --output-summary file from bin/addAmpliRG.py.
  • Add --single-mode for process single-end alignments in bin/addAmpliRG.py.
  • Replace bin/fusionCatcherToVCF.py by bin/fusionsToVCF.py to add management of Arriba and STAR-Fusion.

Bug fixes:

  • Fix bug in bin/splitBAMByRG.py with change in pysam.AlignmentHeader v1.5: reader.header.copy() to reader.header.to_dict().

Release 3.0.0 [2020-01-03]

Split AnaCore project in:

  • AnaCore (python libraries),
  • AnaCore-utils (scripts),
  • AnaCore-web (JS libraries and web components).

Replace section workflows managers utilities by the project AnaCore-snakemake (AnaCore-jflow is dropped).

Release 1.0.0 [2017‑10‑07]

First release