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@zhuchcn zhuchcn released this 25 Feb 17:45
· 1298 commits to main since this release
v0.3.0
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Learn about vigilant mode.

Added

  • Enable filterFasta to filter by number of miscleavages per peptide. #382

  • Added CLI command mergeFasta to merge multiple variant peptide database Fasta files into one. This could be useful when working with multiplexed proteomic experiments such as TMT. #380

  • Added CLI command decoyFasta to generate decoy database by shuffling or reversing each sequence. #386

  • Added parameter --min-coverage-rna to parseREDItools to filter by total RNA reads at a given position. #392

  • Added CLI command encodeFasta to replace the variant peptide headers with UUIDs. The original FASTA headers are stored in a text file together with the UUIDs. This is to make the FASTA header short enough for library search engines. #389

Changed

  • Donor and accepter transcript IDs are now explicitly included in the variant IDs of fusion in both GVFs and variaint peptide FASTA headers. Closed #376 via #377

  • For fusion, callVariant now looks at the entire accepter sequence for potential variant peptides, rather than only the peptides that contains the breakpoint. #377

  • filterFasta updated to support filter by number of miscleavages. #383

  • In parseVEP, chromosome seqname for each record is now read directly from the gene annotation, to avoid the 'chr' prefix issue. #391

  • The --transcript-id-column parameter of parseREDItools is changed to take 1-based index. #392

  • Changed splitDatabase to splitFasta for consistency. #397

  • Updated generateIndex to reduce the size of genomic annotation data and the memory usage when loaded. #395

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