Version 0.7.7
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 (#79)
- rescale: fix crash if --purity is not specified
- VariantArray: Fix VCF parsing if filters are not used.