Add unit test for checking for range header
Add getFileHeader to AlignmentReader interface

This is to support writing of BAM/SAM. Most implementations already had a getHeader, here we renamed
Parameterize AlignmentReaders

Most of the important ones give SamAlignments, we make that explicit when possible
Update SAMWriter so we can write alignments from non-local sources

IGV-2070
Update MergedAlignmentReader to merge headers as well

Add test for exporting alignments from .bam.list file

IGV-2070
Simplify rewriting of properties file

Should also have better platform independence. Windows was having an issue with '\' in paths