added @RG to SAM/BAM headers
added @RG to SAM/BAM headers

- Added @RG (read-group) to SAM/BAM:
- ID is populated automatically by the name of the fastq file being mappped (or that of the PE1 read of the paired ends set).
- SM is populated automatically by the name of the fasta file being used as reference for the mapping

Alos changed BWA default algorithm from bwasw to mem

JFP-Laboratory/SNPs,PombertLab/SNPs