added lefse command. added check for hard filter length. fixed bug in make.biom...

added lefse command. added check for hard filter length.  fixed bug in make.biom when multiple labels in shared file. added index file to make.contigs. fixed weird output in summary.seqs for mean values. added checks for edianness in sffinfo when oligos file is used. shhh.flows fix for reads longer than 1024. fixed bug in split.groups with count file. added several functions to linearalegra for lefse.