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Release 1.2.0
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@nh13 nh13 released this 04 Jun 08:09
1.2.0
77e79d4

Release 1.2.0 is a minor feature release.

This release adds tools to reformat FASTAs/GFFs based on alternate names (#467, #584, #585, #586)

  • CollectAlternateContigNames: Collates the alternate contig names from an NCBI assembly report.
  • UpdateFastaContigNames: Updates the sequence names in a FASTA.
  • UpdateGffContigNames: Updates the contig names in a GFF.
  • UpdateIntervalListContigNames: Updates the sequence names in an Interval List file.
  • UpdateVcfContigNames: Updates the contig names in a VCF.
  • UpdateDelimitedFileContigNames: Tool for updating contig names in a delimited data file)

The following API changes were also introduced:

  • add another date format Illumina uses in the RunInfo.xml (#555)
  • add support for Iso8610 dates in RunInfo.xml as Illumina has started using that now. (#582)
  • add the primary keyword for accessing a SamRecord's secondary flag (#560)
  • fix a bug to allow setting the primary flag on SamRecord (#562)
  • Two fixes to RefFlatSource (#564):
    • Exons were not being put into transcripts in transcription order which is required (but not verified in Transcript)
    • Gene start/end were being taken as the min of the transcript starts/ends, but for end it should be max
  • Changed the gene annotation case classes and the RefFlatSource to resolve two issues (#568):
    1. RefFlatSource would drop transcript mappings if there were mappings to > 1 chrom or > 1 strand for a given gene
    2. RefFlatSource would combine transcript mappings at wildly different locations on the same chrom/strand
  • Added a source class for parsing and reading gene annoations from an NCBI RefSeq GFF file (#573)
  • Add test to Metric for reading and writing chars (#574)
  • Remove system utility code ported to commons for the fgbio CLI (#576)
  • Migrated gzip support to commons (#575)
  • API for sequence dictionaries (#581)
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