Release v1.1.10.2

This release bundles a number or minor changes, new minor command line options and some internal refactoring without immediate consequences for trident.

Changes in command line options

• By default validate only tests genotype data by parsing the first 100 SNPs. This limitation is necessary for performance reasons, but can hide issues outside of this tiny subset. We now added an option --fullGeno to validate, which forces parsing of the entire .bed/.geno file.
• The .fam file of Plink-formatted genotype data is used inconsistently across different popular aDNA software tools to store group/population name information. See more on this issue in our discussion here. We now added the (global) option --inPlinkPopName and --outPlinkPopName with the arguments asFamily (default), asPhenotype and asBoth to control the reading and writing of the population name from and to Plink .fam files.
• The --no-extract option for faster, package-wise data selection in forge was not working properly. We fixed it, renamed it to --packagewise and improved its command line help text.

Bugfixes

• As described here, our implementation of .janno file parsing struggled with some encodings of the No-Break Space unicode character. We now decided to delete these characters upon reading, following the assumption that they are generally not desired in a .janno file anyway. In this process we also decided to trim all whitespaces around .janno file fields.

Other changes

• The -j option of list, which allows to include additional .janno columns in the output with the --individuals flag now allows to access arbitrary, additional variables.
• update writes messages to the CHANGELOG file now with a prefix -, to make it proper markdown.
• The verbose debug-level (with --logMode VerboseLog) warnings about missing standard columns in the .janno file were turned off.
• The important "schema version mismatch" error message was made more verbose and clear.
• trident failes gracefully now if one or all -d/--baseDirs do not exist.
• The important "broken lines" error message in the .janno reading process now reminds users to turn on --logMode VerboseLog to get more information.