This is a bigger release with various new features and improvements. It is technically breaking, because a minor, redundant argument of genoconvert was removed.
Writing support for gzipped genotype data
After reading support for zipped data was already added in V 1.5.7.0, this release now introduces the complementary writing feature for EIGENSTRAT and PLINK files in genoconvert and forge. Both commands get a new option -z which creates gzipped output.
-z,--zip Should the resulting genotype- and snp-files be
gzipped?
Note that this feature includes a smart way of handling already available files to not overwrite them, but still consider them when updating a package's POSEIDON.yml file. -z is also usable with unpackaged genotype data (-p, --onlyGeno).
Future versions of the Poseidon package schema will formally specify this feature.
Bibliography information in list and the Web-API
The list subcommand now supports a new view (next to --packages, --groups and individuals): --bibliography allows to get a tabular overview of publications in a package repository.
$ trident list -d 2010_RasmussenNature --bibliography
...
.---------------------.--------------------------------------------------------------.-----------------------.------.---------------------------.---------------.
| BibKey | Title | Author | Year | DOI | Nr of samples |
:=====================:==============================================================:=======================:======:===========================:===============:
| AADR | The Allen Ancient DNA Resource (AADR): A curated compendium… | Swapan Mallick et al. | 2023 | 10.1101/2023.04.06.535797 | 1 |
| AADRv424 | The Allen Ancient DNA Resource (AADR): A curated compendium… | S Mallick and D Reich | 2023 | 10.7910/DVN/FFIDCW | 1 |
| RasmussenNature2010 | Ancient human genome sequence of an extinct Palaeo-Eskimo | M Rasmussen et al. | 2010 | 10.1038/nature08835 | 1 |
'---------------------'--------------------------------------------------------------'-----------------------'------'---------------------------'---------------'
Additional fields from the .bib file can be added to this table with -b|--bibField ... (just as -j|--jannoColumn ... for --individuals). --fullBib adds everything that is available (just as --fullJanno). As usual, tab-separated output can be requested with --raw for derived analyses on the command line.
Correspondingly the Web-API supports a new endpoint /bibliography to serve bibliography information via HTTP in JSON format. The optional query argument additionalJannoColumns=... allows to request extra fields here.
Remove empty .janno columns with rectify
The rectify subcommand was upgraded with a first option to manipulated .janno files in one or multiple packages: --jannoRemoveEmpty. This allows to remove empty columns from .janno files, so columns that only feature empty strings or n/a values.
--jannoRemoveEmpty Reorder the .janno file and remove empty colums.
Remember to pair this option with --checksumJanno to
also update the checksum.
With this change came a rewrite of the way trident fills empty fields with n/a when writing .janno and .ssf files. This behaviour now also affects the output of list!
Removed redundant --onlyGeno from genoconvert
We realized that --onlyGeno in genoconvert had the same effect as -o if a different output directory is chosen. We therefore decided to remove this argument and improve the documentation of -o:
-o,--outPackagePath DIR Path for the converted genotype files to be written
to. If a path is provided, only the converted
genotype files are written out, with no change of the
original package. If no path is provided, genotype
files will be converted in-place, including a change
in the POSEIDON.yml file to yield an updated valid
package (default: Nothing)
Bug fixes and technical changes
We fixed two bugs that broke the long-form genotype data input option (with --genoFile + --snpFile + ...). They were accidentally added with the recent interface changes for V 1.5.7.0. This input interface should now be fully functional again.
We finally switched to a new compiler version (GHC 9.6.6) and a new stackage resolver version (lts-22.43). This required some minor adjustments in the server code, but should not have any user-facing consequences.