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Release 1.3.0
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@tfenne tfenne released this 25 Aug 12:23
1.3.0
e172300

Important: This is the last version of fgbio that supports scala 2.12. This only affects developers who use fgbio in their projects (not end-users of the toolkit running tools). Moving forward fgbio will support scala 2.13 only.

New tools in this release:

  • AssignPrimers: takes a BAM file and a file of primer metadata and adds auxiliary tags to the BAM file to identify which primers likely generated which inserts/reads.

Updates to tools in this release:

  • UpdateGffContigNames: fix for bug that caused generation of misformatted GFFs (#591)
  • ErrorRateByReadPosition: option to not collapse substitution types (e.g. report A>C and T>G separately) (#608)
  • UpdateFastaContigNames: (i) option to sort output FASTA, and (ii) option to add in missing contigs from a second FASTA file (#590)
  • UpdateDelimitedFileContigNames: option to sort output file (#598)

Updates to APIs in this release:

  • Updated GenomicRange to handle point positions (e.g. chr1:123) and also add GenomicRange.apply() so it can be used as a command line argument
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