Release v1.1.6.0

Additional columns in .janno files (V 1.1.5.0)

This release changes the way additional columns in .janno files are treated.

So far trident fully ignored additional variables, which had the consequence that trident forge dropped them without warning. With this new release, additional variables are loaded and carried along in forge. For merging different .janno files A and B the following rules apply regarding additional columns:

• If A has an additional column which is not in B then empty cells in the rows imported from B are filled with n/a.
• If A and B share additional columns with identical column name, then they are treated as semantically identical units and merged accordingly.
• In the resulting .janno file, all additional columns from both A and B are sorted alphabetically and appended after the normal, specified variables.

The following example illustrates the described behaviour:

A.janno

Poseidon_ID	Group_Name	Genetic_Sex	AdditionalColumn1	AdditionalColumn2
XXX011	POP1	M	A	D
XXX012	POP2	F	B	E
XXX013	POP1	M	C	F

B.janno

Poseidon_ID	Group_Name	Genetic_Sex	AdditionalColumn3	AdditionalColumn2
YYY022	POP5	F	G	J
YYY023	POP5	F	H	K
YYY024	POP5	M	I	L

A.janno + B.janno

Poseidon_ID	Group_Name	Genetic_Sex	AdditionalColumn1	AdditionalColumn2	AdditionalColumn3
XXX011	POP1	M	A	D	n/a
XXX012	POP2	F	B	E	n/a
XXX013	POP1	M	C	F	n/a
YYY022	POP5	F	n/a	J	G
YYY023	POP5	F	n/a	K	H
YYY024	POP5	M	n/a	L	I

Minor changes (V 1.1.6.0)

• --verbose in trident validate was deprecated. The respective output is now logged on the DEBUG level, so can be accessed with --logMode VerboseLog
• Trailing slashes in --outPath for init, genoconvert and forge are now automatically removed. This prevents a common, confusing error, where a trailing slash would cause trident to assume the name of the resulting package is empty.