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 at Codecov (thanks @stevepeak).

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)
• When calculating GC and RepeatMasker values, catch invalid BED ranges that extend beyond the length of the chromosome and raise an informative error. This would error before, too (in ngfrills.faidx), but the message would be baffling.

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.