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Version 0.7.7
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@etal etal released this 25 Feb 02:19
· 1090 commits to master since this release
v0.7.7
c13f7c8

Small improvements, bugfixes, and documentation updates.

fix:

  • Removed the hard filter on RepeatMasker fraction of antitarget bins. This filter doesn't appear to improve calling on current benchmarks.
  • Drop bins that have very high coverage in the reference, in addition to the low-coverage bins already dropped (normalized log2 values outside +/- 5).
  • Ignore very-low-coverage bins when recentering (by default). For good-quality samples this doesn't make much difference, but it's safer and seems to improve the centering slightly on lower-quality samples.
  • Ensure antitarget bin weights are not set to 0 if the majority of target bins have no coverage -- this would cause segmentation to fail. (#82)
  • Don't crash if antitargets are empty (to support WGS and targeted amplicon capture), fixing a regression.

antitarget:

  • Keep untargeted contigs that appear to be "canonical" chromosomes. Prefer chromosomes with numeric names (autosomes in most mammalian reference genomes); but if none of the targeted chromosomes have numeric names, then fall back to chromosomes with names no longer than the longest-named targeted chromosome. (#37)

batch:

  • Disallow input BAMs with duplicate base filenames (#81). Now it will trigger an error instead of overwriting some output files.

segment:

  • --drop-outlier option now masks outliers according to multiples (default 10x) of the 95'ile, not 90'ile. Benchmarking looks better.

Plots scatter, heatmap:

  • With the "-c/--chromosome" option, handle unbounded ranges (e.g. "chr1:100-" or "chr5:-100000") treating the missing start/end of the range as the start/end of the specified chromosome.

heatmap:

  • A more efficient implementation. Now, plotting a heatmap of .cnr is feasible, and behavior is a bit more consistent (e.g. placement of rectangles is more accurate; plotting a selection where only some samples have data will still show all samples).
  • Don't crash if selection overlaps no segments, e.g. if the selection is a centromeric or telomeric region. Previously it would crash with an obscure error.

Misc. bugfixes:

  • batch: log # parallel processes correctly for "-p 0"
  • import-theta: fix crash; namedtuples are immutable (#77)
  • metrics: require --segments (closes #79)
  • rescale: fix crash if --purity is not specified
  • VariantArray: Fix VCF parsing if filters are not used.
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