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March 2020 release
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@joachimwolff joachimwolff released this 24 Mar 10:16
· 974 commits to master since this release
3.3
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Learn about vigilant mode.

Release 3.3 adds:

  • a documentation on readthedocs: https://pygenometracks.readthedocs.io
  • progress bar for bed, gtf, bedgraph, narrowPeak, epilogos
  • all colors can be set as (r, g, b) with r, g, b values between 0 and 1.
  • all colormap can be set as an array of colors, for example [red, white, (0, 0, 0.5)]
  • the titles on the right can be align left, right or center with the argument --trackLabelHAlign
  • for the links track,
    • compact_arcs_level to be able to see both very long arcs and very small arcs.
    • ylim to be able to zoom and see small arcs.
  • a new track type: file_type = scalebar which by default is close to the UCSC scale bar.
  • for the bed tracks:
    • a new gene type: tssarrow
    • border_color and color_utr can be set to bed_rgb.
    • all_labels_inside allow to put the name of the region on the left if it ends after the plotted region.
    • labels_in_margin allow to put the name of the region in the margin if it ends after the plotted region.
  • line_width can now be set in the narrowPeak tracks.
  • colormap can now be set in bedgraphMatrix tracks.

bug fixes:

  • if a bed with no interval is provided, pgt no longer exit.
  • When an exon had both UTR start and UTR end within it, only the UTR start was considered.
  • alpha in links tracks was not used
  • qcat files with missing values are now working.
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