Fix hang when USE_THREADING=true and exception reading input.
Fix hang when USE_THREADING=true and exception reading input.

nh13/picard,alecw/picard,annkupi/picard,nh13/picard,alecw/picard,broadinstitute/picard,broadinstitute/picard,annkupi/picard,alecw/picard,broadinstitute/picard,annkupi/picard,broadinstitute/picard,alecw/picard,broadinstitute/picard,nh13/picard,annkupi/picard,nh13/picard