Handle compression with Apache commons-compress

[magicDGS]

Using Apache commons-compress will allow to write/read files compressed in several formats, including snappy and gzip. Some advantages of using it would be:

• Better gzip support. Due to some issues of java.util.zip.GZIPInputStream (unsafe use of available()), previous version of HTSJDK was broken while reading compressed trible files. Using the commons-compress version might be more robust to this.
• Read/Write compressed FASTQ files compressed with bz2 or other, not only hard-coded ones.
• Better format detection, not only based on the extension, might be possible (I did not explore this enough)
• Usage of a well-mainained interface for compression. This allows to implement bgzip IO as a compressor and support other algorithms and optimizations (e.g., GKL could implement te commons-compress interfaces).

Opinitions on this, @samtools/htsjdk-next-maintainers?