removing DS_Store file
This is to commit the latest modifications to the pipeline.
The main python script "hugeseq" is restructured to upgrade the flow of the program and remove redundant
input parameters. Other additions by Cuiping are also added ot removed from the directory.
The module file is also re-written and moved to the server location.
Edited the main script to debug issues with SV options
adding to the lastest version
debugged the case where only one SV case is recalled.
testing
Debugged aln_mem

Debugged the script for the capability of processing two fastq or one
bam files with aln_mem.
Also added a function to the main script to take care of two cases
separatelt.
Debugging further

Added a new shel script to accomodate bam input files.
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).
Pre-release changes 2
Pre-release 3

Returned back all the input parameters for maximum retrocompatibility.
Pre-release notes

First version of release notes
addition of items in modulefule
pre-release debugging
pre-release debugging
daily commit
daily commit
daily commit
daily commit
daily commit