Merge branch 'release/0.144' into develop
removed call to defunct Runner class
allow StepState->same_submissions_as to be unset
Revert "check vcf-annotate filter file is readable"

This reverts commit 9b904c17b1339d59bcf5a24969ce6a5029b56ed9.
Backout vcf-annotate -f param check, as this does  not need to be a file
Merge branch 'develop' of /software/vertres/git/origin/vr-pipe into develop
get_isolation_read_committed_sql() renamed get_isolation_change_sql() and takes a repeatable_read option
enabled the transaction isolation level change code so that by default try and use READ COMMITTED; 1 second hack remains for problematic edge cases though...
Merge branch 'develop' of /software/vertres/git/origin/vr-pipe into develop
added install notes for Crypt::Random
fixed run_time() call to be on the correct object
moved output file deletion log_event call to after the actual deletion, so we can report if it worked
log_event(), when it is warning, also warns the stack_trace if requested
Persistent->lock_row() gains a "no_hack" bool that disables the 1-second-minimum-transaction-time "feature", used by File->add_metadata and PipelineSetup->trigger transactions, which are called in single-process loops; renabled File metadata speed testing in PersistentProfile.t
calc rmdup_bases_mapped based upon bases_mapped_cigar
Merge branch 'develop' of /software/vertres/git/origin/vr-pipe into develop
fixed cmd() call to be on the correct object
Merge branch 'develop' of /software/vertres/git/origin/vr-pipe into develop
have a fake cmd_line when using uncompressed fastqs as well
unfinished_lsjss() now actually does what it says, returning those with no end_time; process_queue improved so it cleans up old stuff and only forks new processes when there are new jobs to run
no longer falls over if stdout/err files are /dev/null; kill_job now just deletes the row if it was pending