VCF validation using HTSJDK

[makenzi-nzau]

Hi!
During development of my application, I encountered a broken VCF where the reserved DP was overloaded as

##FORMAT=<ID=DP,Number=1,Type=Float,Description="Average coverage of the bins">

and had correspondly rows with DP-values such as
...GT:GQ:CN:DP 1/1:200:0:374.517.

This causes a crash due to
java.lang.NumberFormatException: For input string: "374.517".
which is a valid outcome, since the VCF standard specifies that the reserved DP-field be an integer.

However, this type of a message is problematic as a feedback to an end-user.
My question is, which features of HTSJDK 3.0.3 are designed for VCF header validation and specific row value validation?
Or is there recommended way of 'reprocessing' the exception above to carry a more helpful message?

Thanks in advance,
Makenzi.

[lindenb]

it's a Locale problem.
try

LC_ALL=en_US.UTF-8 java ...