Update AbstractInputParser.java

Included nested exception.
File faker bug fixes.
- `ClocsFileFaker` emits too many bytes in single-record file.
- `PerTilePerCycleFileUtil` wasn't careful about cycle collisions.
Add build date to metrics definitions.
Check root html files in to github.
Reference proper source repos on the picard homepage.
Separate javadoc for picard and htsjdk.
Update release script to upload html.
Merge pull request #19 from broadinstitute/jc_update_sourceforge_website

Add build date to metrics definitions.
Create inc directory for html generated sources.
Website grammar.
Merge pull request #18 from broadinstitute/mm_bugfix_file_fakers

File faker bug fixes.
Add html upload to the build not just shtml.
Merge remote-tracking branch 'origin/master'
Merge pull request #15 from nnordborg/barcodes-dir

Add BARCODES_DIR parameter to IlluminaBasecallsToFastq and IlluminaBasecallsToSam
Merge pull request #14 from nnordborg/gc-timer-npe

FORCE_GC=false causes NPE in log
Clarify what a "non-PF read" is.
Merge pull request #17 from marcelm/master

Clarify what a "non-PF read" is.
Merge branch 'master' into lorry

Conflicts:
	build.xml