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RELEASES_NOTES.md

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Release 3.1.0 [2024-03-20]

Improvements

  • Add anacore.wig for reading/writing/processing wiggle files.
  • Manage illumina.run.[RunParameter|RTAComplete] from NovaSeq Control Software.
  • downstreamed, getMostDownstream, getMostUpstream and upstreamed are now available from anacore.vcf.VCFSymbAltRecord.
  • getMostDownstream and getMostUpstream form anacore.vcf.VCFRecord take sequence file reader instead of sequence string to improve speed.
  • Replace padding size to buffer size in up and down methods from anacore.vcf.VCFRecord. This change breaks padding limitations and keep performances.

Bug fixes

  • CNV are now always seen as DEL or DUP in anacore.vcf.VCFSymbAltRecord.
  • anacore.vcf.VCFSymbAltRecord.isInsAndDel now returns True for inversions.

Release 3.0.0 [2023-06-13]

Break changes

  • anacore.filters:
    • Default aggregator become None. Uniterable values must have aggregator set to None and iterable must have aggregator set to nb:X or ratio:X.X. Previous filters with explicit aggregator on uniterable value must be change to work.
    • Missing keys/attributes return None in getter function.
    • The operator contains works on strings instead of strings and lists previously.
    • Add EmptyIterFilter to select/exclude item with empty list returned by getter.
  • anacore.illumina:
    • SampleSheetV[1|2].samples return a list of Sample object instead of the previous list of dict.
    • DemultStat(demult_stats_path) replaced by demultiplex.DemultStatFactory.get(demult_folder_path).
    • SampleSheetIO(path) replaced by samplesheet.SampleSheetFactory.get(path).
    • Split illumina library in new sub-packages:
      • anacore.illumina.base
      • anacore.illumina.demultiplex
        • anacore.illumina.demultiplex.base
        • anacore.illumina.demultiplex.bcl2fastq
        • anacore.illumina.demultiplex.bclconvert
      • anacore.illumina.run
      • anacore.illumina.samplesheet

Improvements

  • Add anacore.vcf.VCFSymbAltRecord to handle structural variants with symbolic alternative like <DUP>, <DEL>, etc. anacore.vcf.VCFIO can now reads VCF containing standard variants and structural variants except BND. BND stay currently manage in anacore.fusion.
  • Add log and statistics reader for bcl-convert: anacore.illumina.demultiplex.bclconvert.DemultLog and anacore.illumina.demultiplex.bclconvert.DemultStat.

Bug fixes

  • Fix bug in anacore.vcf.VCFRecord.getPopRefAD and anacore.vcf.VCFRecord.getPopRefAF: Prevent exception when ref is not in INFO and it exists several samples.

Release 2.12.1 [2022-10-01]

Improvements

  • Add MiSeq invalid RFID markup management in anacore.illumina.RunParameters.

Bug fixes

  • Fix bug in anacore.msi.sample.setStatusByInstabilityRatio(): the value voting_loci was invalid.
  • Fix bug in anacore.msi.sample.setScore(): the value locus_weight_is_score was ignored.

Release 2.12.0 [2022-09-06]

Changes

  • anacore.vcf.VCFIO: Manage None value in a vcf INFO field as missing key. Example: for an INFO field equal to AF=0.5;DP=. the record.info is {"AF": 0.5}.
  • anacore.msi.msings:
    • Remove record.results["mSINGS"].data["peaks"] from returned records in parser anacore.msi.msings.MSINGSAnalysisIO: data can be retrieved from record.results["mSINGS"].data["lengths"].
    • Rename MSINGSAnalysis to MSINGSAnalysisIO.
    • Rename method name MSINGS to mSINGS.
  • Change parameter behaviour for min_voting_loci in anacore.msi.sample.MSISample.setStatusByInstabilityRatio(): from number of loci to rate of loci.
  • Move anacore.msi.MSIReport to anacore.msi.reportIO.ReportIO.
  • Refactor anacore.msi.LocusRes* to create anacore.msi.locus.LocusDataDistrib. This class store length distribution and is linked to anacore.msi.locus.LocusRes in data["lengths"]. The class anacore.msi.LocusResDistrib and children are removed.
  • Move MSI libraries in the new subpackage msi:
    • anacore.msi to anacore.msi.base
    • anacore.msiannot to anacore.msi.annot
    • anacore.msings to anacore.msi.msings

Improvements

  • Add anacore.illumina.DemultStat to read demultiplex statistics from bcl2fastq.
  • Add anacore.illumina.Run getters to known run information and status from the run folder.
  • Add anacore.msi.hubble to manage results from Hubble software.
  • Add anacore.msi.msisensorpro to manage results from MSIsensor-pro software.

Release 2.11.0 [2022-03-10]

Improvements

  • Update pysam from 0.15.3 to 0.18.0.
  • Update numpy from 1.6.0 (pypi) or 1.16.5 (conda) to 1.20.1.

Release 2.10.0 [2021-09-28]

Improvements

  • Add anacore.illumina.Bcl2fastqLog to read bcl2fastq log file.
  • Add alias "Description" for "Sample_Description" in samplesheet.samples (anacore.illumina.SampleSheetIO).
  • Add empty value for samplesheet.header["Description"] when "Description" is not present in SampleSheet (anacore.illumina.SampleSheetIO).
  • Add utilities to manage Homo sapiens genome accessions in anacore.db.homo_sapiens.accession.

Bug fixes

  • Fix bug in anacore.annotVcf.AnnotVCFIO when parsing ANN declaration from SnpEff.
  • Fix no casting itemRGB as list in anacore.bed.BEDIO.

Release 2.9.0 [2020-04-28]

Changes

  • anacore.genomicRegion.Protein.setTranscript and anacore.genomicRegion.Transcript.setProteins replaced by setter declaration.
  • Move anacore.sequenceIO.Sequence to anacore.sequence.Sequence.

Improvements

  • Implement getPosOnRegion() in anacore.genomicRegion.Transcript.
  • Add functions to get information about codon in anacore.genomicRegion.Protein: getCodonRefPos(), getCodonSeqFromProtPos() and getCodonInfo().
  • Add AA3LettersAlphabet, CodonAlphabet, DNAAlphabet and RNAAlphabet in anacore.sequence to validate sequences and provide translation and reverse complement utilities.
  • Add anacore.vcf.VCFRecord.fastDownstreamed to get quickly the most downstream version of the variant.
  • Add management of metadata in SV files (anacore.sv). Metadata must be present before title and/or data. They starts with a particular string: "##" by default.
  • Add anacore.hgvs.HGVSProtChange to manage change part of proteic HGVS (ex: "Val600Glu").
  • Add getSub and open mode "i" in anacore.vcf.VCFIO to return records overlapping the specified region in file with tabix index.
  • Add specific management for samples description rows in VCF header (anacore.vcf.VCFIO).
  • Add reader for picard tools outputs in anacore.picardIO.
  • Manage UMI in Illumina's sequence ID with anacore.illumina.getInfFromSeqID.

Release 2.8.0 [2020-10-09]

Improvements

  • Add management for None value in anacore.filters.Filter.
  • Increase speed to read the VCF in anacore.vcf.VCFIO.

Bug fixes

  • Fix bug in GTFIO from anacore.gtf when an attribute value contains semicolon.
  • Fix bug with empty list in an INFO field from VCF (anacore.vcf). Previously, the reader returned a list containing an empty string. For example, for the INFO field containing "AF=0.5;DB=;DP=100" where DB is a list, the reader returned: {..., "DB": [""], ...}. Now, the reader return: {..., "DB": [], ...}.

Release 2.7.0 [2020-05-13]

Changes

  • The value None is no longer supported for VCFRecord.filter in anacore.vcf. The field takes a list in three possible states:
  • If no filter was applied, the field contains an empty list ("." in VCF file)
  • If filters were applied but the record passes filters, the field should contain ["PASS"]
  • If filters were applied and the record does not pass filters, the field should contain ["filter_name", ...]

Improvements

  • Add a classes to manage fusions detected by Arriba and STAR-Fusion in anacore.fusion.
  • Add classes to manage VCF containing fusions in anacore.fusion.

Bug fixes

  • Fix bug in iterOverlappedByRegion from anacore.region when all chromosomes of queries are not in subjects.

Release 2.6.0 [2020-01-03]

Improvements

  • Add a Mutalyzer Batch manager in anacore.hgvs.
  • Add management for RTAComplete.txt V2 in anacore.illumina.RTAComplete.
  • Add a conda recipe.

Bug fixes

  • Add automatic management for multiple date formats in anacore.illumina.RunInfo.

Release 2.5.0 [2019-10-25]

First public release

Release 1.0.0 [2017‑10‑07]

First release