Release 1.9.8.4.1

[Fabien Campagne]

We pushed Goby 1.9.8.4.1:

- Improve speed of sam-to-compact when log4j is not configured properly.

- Improve alignment-to-text mode a bit. The html format now writes pair and splice flags to text. Since the sam format output was incomplete, we disabled it in this release. Goby 2 will include a fully functional SAM/BAM export. Fix problem reported by Heng Li where only the first chunk of the alignment was processed (option -e -1 was not interpreted correctly).

- Add test and fix for bug that went back to start of alignment file, even though iterate alignment was created for a slice of input. The problem only affected the IterateAlignments class because it was calling reposition(0,0) and the
method did not enforce slice limits.