added module file for v1.2
pre-release committ

Several changes in this version:
- clean_recal.sh changed to remove depricated "CountCovariates" and
replace it with "BaseRecalibrator + PrintReads".
- A new aln_mem_sam.sh and aln_mem_sam_paired.sh added to implement
"BWA's aln mem" for both pair-end libraries and BAM inputs.
- The TMP directory used to store intermediate files that was
previosly set in modulefiles as a fixed environment variable is now
defaulted to "output" directory and can be defined as input parameter.
- All indel+snp+snv variations are now computed by only SNV input
paramter
- VQSR in GATK>v2.0 are included as input parameter
- The processing can now be initiated by only BAM inputs (with or
without alignment).