barclay fails to set collection arguments initialized with an immutable collection

[droazen]

If you have a barclay @Argument field of type List, barclay will fail to set the field value properly when the argument is specified if the List is initialized using an immutable Collection, such as that returned by Collections.emptyList(). Example error:

java.lang.UnsupportedOperationException
	at java.util.AbstractList.add(AbstractList.java:148)
	at java.util.AbstractList.add(AbstractList.java:108)
	at org.broadinstitute.barclay.argparser.CommandLineArgumentParser.setArgument(CommandLineArgumentParser.java:706)
	at org.broadinstitute.barclay.argparser.CommandLineArgumentParser.parseArguments(CommandLineArgumentParser.java:427)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.parseArgs(CommandLineProgram.java:220)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:194)
	at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
	at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
	at org.broadinstitute.hellbender.Main.main(Main.java:289)

Ideally, barclay should detect immutable collections and replace them with mutable ones when necessary.

[droazen]

For @cmnbroad

[magicDGS]

There's a solution here: broadinstitute/barclay#102

[magicDGS]

Also, some discussion about what to do with immutable collections in barclay is here: broadinstitute/barclay#100