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Release 1.3.0
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@zhuchcn zhuchcn released this 11 Mar 17:09
· 66 commits to main since this release
v1.3.0
32cf179
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Learn about vigilant mode.

Fixed:

  • Adjacent variants were not merged as MNVs successfully. The function always exited with nothing.

  • Because of the updating to on-disk GTF, the coding transcripts were not generated and saved successfully. filterFasta is the only command affected.

  • Updated splitFasta and summarizeFasta to accept source combinations in --order-source.

  • Fixed parseCIRCexplorer so the exon/intron indices in variant IDs are sorted correctly.

  • Fixed parseVEP to handle insertions in start-inclusion. #840

  • Fixed callVariant of 'no reference out node found'. #842

  • Fixed mergeFasta to remove redundant FASTA header entries. #846

  • Fixed GenomicAnnotation to parse ENSEMBL style UTR correctly. #687

  • Switch to use python's logging package for logging.

  • Print basic summary to callVariant output. #412

Add

  • Added --timeout-seconds to callVariant.

  • Added metadata.json to the index directory for all essential parameters of how a moPepGen index directory is created, including cleavage parameters. #850

  • Added updateIndex #853

  • Output a peptide table for additional information. #833

Assets 2