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Published June 15, 2024 | Version genozip-15.0.60

divonlan/genozip: 15.0.60

  • 1. Genozip
  • 2. University of Adelaide

Description

  • Major revamp of the --optimize option:

    Uncompression verification for files compressed with data-modifying options --optimize, --add-line-numbers and --head: Previously, if genozip modified the original data due to these options, the correctness of the uncompression was not verified in genounzip and using --test in genozip was not possible. Now, genounzip as well as genozip --test do verify that the file is reconstructed correctly, i.e. that it is identical to the data as it was after the modifications. Note that this still does not test for any errors in the modification process itself. New optimization for SAM/BAM/CRAM included in --optimize: all floating point and floating point array tags (e.g. rq:f, ZP:B:f) are rounded to 10 significant bits for BAM/CRAM (i.e. an accuracy of approximately 3 siginficant decimal digits) and 3 significant digits for SAM. New optimization for SAM/BAM/CRAM included in --optimize: tags containing base quality scores (for example, of barcodes) are binned in the same way that QUAL is binned. The tags supported are the standard tags QT:Z CY:Z BZ:Z and the 10xGenomics/STARsolo tags UY:Z sQ:Z 2Y:Z GY:Z fq:Z QX:Z. Note that OQ:Z is not binned. New optimization for VCF included in --optimize: the QUAL field and all floating-point INFO and FORMAT annotations are rounded to three significant digits New optimization for VCF included in --optimize: GQ, SPL - Phred values are capped at 60 quality scores in SAM/BAM/CRAM/FASTQ are not binned if they are already binned Command line options optimize-* --GP-to-PP --GL-to-PL are canceled - --optimize includes all the optimizations

  • SAM/BAM/CRAM: Better compression of files generated by 10xGenomics CellRanger-DNA
  • discontinued little-used optimization options for GFF/GVF/GTF
  • discontinued little-used option --match-chrom-to-reference
  • genocat --validate: change in arguments of --validate. Details: genozip.com/genocat
  • bug fixes

Files

divonlan/genozip-genozip-15.0.60.zip

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