corrected samtools sort command
removed erronoes throw from branch_job_group as we no longer allow init_branching_by_config. Added ALIGNED status check, checksum param and remove harcoded "samse" from alignment file path
removed some old methods
added some comments
changed experimental_group method to experiment method
check_file now handles checksum param better. _validate_sam_fai renamed to _validate_sam_header_fai and now actually compares entries. validate_checksum now has checksum_optional support
removed some old comments and run_controls, as this is now implicit form result_set_groups
removed some more input_set support. Added experiments_like support. better set type validation
fixed semaphore dataflow and imporved comments around that. corrected some typos. Added checksum generation and store ResultSet ALIGNMENT status. Improved alignment report handling. Now uses get_alignment_file_prefix_by_ResultSet