dev-java/java-dep-check reports that xerces-2 and jaxp are possibly unneeded. Also build system unjars these and rebundles them to readseq.jar itself. Please check if these are really needed and drop them if not. Thanks.
The dependencies were indeed not used. I removed the xml jars and "readseq ~/Downloads/test-seq.gb -p -f 19" happily dumps xml data to stdout.