IGV-1945

Use log4j loggers instead of System.out in many places. Abstract message writer in others so we can easily use System.err (or different stream) for user info, rather than System.out
IGV-1945

Set PrintStream as a field in CommandLineStatusMonitor
IGV-1945

Remove System.out.println calls in converters and parsers where necessary
IGV-1945

Remove System.out.println calls in sorters where necessary
IGV-1945

Allow wig output of igvtools count to be directed to stdout, write test for same. Not implemented for TDF yet
IGV-1945

Allow output of igvtools sort to be directed to stdout, write test for same.
Merge pull request #47 from broadinstitute/IgvToolsStdout

Igv tools stdout