Version 0.7.1
This is primarily a bugfix release. Many more unit test cases were added to the
automated test suite. Code coverage is now monitored (thanks @stevepeak) at:
https://codecov.io/github/etal/cnvkit/commits
export nexus-basic:
- New optional argument "-v"/"--vcf" extracts SNV b-allele frequencies from
the given VCF file, matches them to the bins in the .cnr file, and prints
an additional "baf" column in the output table. These allele frequencies
can then be viewed in Nexus Copy Number, similar to a SNP array.
call:
- Fixed a bug in the "threshold" method where the copy number of haploid
chromosomes was twice what it should be. The "clonal" method already
handled these chromosomes properly. (#49)
reference:
- Handle blank/empty antitarget BED and coverage (.cnn) files. This was a
regression from earlier releases in v0.7.0. (#51)
fix:
- Catch duplicated target ranges, e.g. the exact same bait labeled with two
different gene names, and report those ranges in the error message. The
"target" command's "--split" option should usually fix these, but
sometimes it's not used.
faidx:
- Catch invalid ranges that extend beyond the length of the chromosome and
raise an informative error. This would error before, too, but the message
would be baffling.