Allow for vrtrack_processed_flags to be passed into rnaseq and bam improvement pipelines
Merge pull request #185 from andrewjpage/multiple_rna_seq

Allow for vrtrack_processed_flags to be passed into rnaseq and bam impro...
provide full path to sequencing file
Merge pull request #186 from andrewjpage/rna_seq_check_bam_full_path

provide full path to sequencing file
only require done files for matching bams and annotation
Merge pull request #187 from andrewjpage/rna_seq_check_bam_full_path

only require done files for matching bams and annotation
fix rna seq lock file
Merge pull request #188 from andrewjpage/rna_seq_check_bam_full_path

fix rna seq lock file
dont include sequencing filename in jids
Merge pull request #189 from andrewjpage/rna_seq_check_bam_full_path

dont include sequencing filename in jids