converted pipe to use uncompressed bam insted of sam.
added archive support
 updated merge_bam call to use sam_ref_fai intead of header
added immediate archive of unfiltered bam file. Updated merge_bams call to use sam_ref_fai instead of header
Squashed control/signal TR suffix bug. Added analysis name to set prefix
Added debug output to validate_sam_header. Optimized merge_bams piping and now takes fai file. Added no exit mode for run_backtick_cmd and tweaked output of _handle_exit_status
added ALIGNED AND ALIGNING_CONTROL states
Added _InitEnv and also STARTUP_CMD support
Updated _InitPipelineEnv to use bash test operators, CheckGlobalVariables and now returns 1 instead of exits when init fails.
Fixed control experiment handling. Fixed set naming for single rep IDR ftype sets which need to be processed as merged
update is_idr_feature_type to is_idr_FeatureType and added assert_ref. Changed checksum param in get_alignment_files_by_ResultSet_formats to under, this activates checksum generation/validation. Fixed ALIGNED_CONTROL status to use experiment. Change _set_out_db to use disconnect_if_idle instead of disconnect_when_inactive
added disconnect_if_idle default
fixed ALIGNED_CONTROL to use experiment. added write_checksum to merge_bams params. Added disconnect_if_idle default
added a debug statment to define_ResultSet