hopefully fixed pathing/naming issue with bam_merge timing, also cgsubmit_fixed should make a different directory for each run
fixed CL and bwa_name_matcher patterns for bam header->pipeline segments
fixed (hopefully) the directory handling in the qc stats and timings reading script
fixed directory going forward using the params rather than hard coding, also fixed the commented out tmpfile clean up in cgsubmit_fixed
Merge pull request #10 from kellrott/dev_cwilks1

Dev cwilks1