v1.3

Added imputed MK test which estimates the proportion of weakly deleterious polymorphisms from the allele frequency data and excludes them from the total counts of the standard MK table. Also various bug fixes.

1. added recalculation of allele frequency based on ancestral allele in polarized VCF
2. fixed a bug causing pN pS undercounting
3. added imputed MKT extension
4. added imputed maf cutoff as an argument

v1.2.4

Fixed bug relating to trailing semi-colons in gff info fields (#39).

v1.2.3

Fixed bug while reading a directory of CDS files.

v1.2.2

Fixed missing return value for transcripts with no variants

v1.2.1

Adds warnings and skips sites in the VCF file where the alternate allele is longer than 1bp.

v1.2.0

This release adds a couple of options to make the MK test more flexible:

• -maf allows the user to set a cutoff for the minor allele frequency for alleles to be considered in the tests
• --no-fixed-in allows the user to tell degenotate to ignore sites where all ingroup samples are fixed for an alternate allele

v1.1.3

• Added a warning (instead of error) for transcripts with exons on differing strands (in response to
  #30).
• Added a warning for transcripts with no coding exons. These were previously silently skipped.
  In both cases, these transcripts are removed from subsequent analyses.

v1.1.2

This release fixes bugs related to missing data among samples in a VCF.

• Sites that have an alternate allele called, but that allele does not exist in any of the samples (due to sub-sampling or sample exclusion with -e) are now skipped.
• We also added a check for invariant sites to be skipped.

v1.1.1

Minor bug fixes:

• Adds warnings and skips transcripts that have 0 length
• Fixed typo on fix to trailing semicolon bug in gtf files
• Check for division by 0 when calculation dos

v1.1.0

This release fixes several minor bugs and adds the following functionality:

• The p-value and odds ratio (neutrality index) for the MK test are now directly calculated and provided in the mk.tsv output. We also calculate the direction of selection (see: https://doi.org/10.1093/molbev/msq249).
• Added options -ca and -la to write translations to amino acid sequences of all coding transcripts and the longest coding transcripts, respectively.
• Changed the behavior of -c and -l such that they now either accept a filename as input to write sequences or use a default filename if the option is provided without one. -ca and -la also behave this way.