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fgbio release version 0.1.1

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@nh13 nh13 released this 18 Jul 17:29

Release of fgbio that contains tools:

  1. HardMaskFasta: Converts soft-masked sequence to hard-masked in a FASTA file.
  2. TrimFastq: Trims reads in one or more line-matched fastq files to a specific read length.
  3. ExtractUmisFromBam: Extracts unique molecular indexes from reads in a BAM file into tags.
  4. FindTechnicalReads: Find reads that are from technical or synthetic sequences in a BAM file.
  5. RandomizeBam: Randomizes the order of reads in a SAM or BAM file.
  6. SetMateInformation: Adds and/or fixes mate information on paired-end reads.
  7. UpdateReadGroups: Updates one or more read groups and their identifiers.
  8. CallMolecularConsensusReads Calls consensus sequences from reads with the same unique molecular tag.
  9. GroupReadsByUmi: Groups reads together that appear to have come from the same original molecule.
  10. HapCutToVcf: Converts the output of HapCut to a VCF.