set mpileup filename to contain prefix
Merge pull request #181 from andrewjpage/snp_calling_custom_prefix

set mpileup filename to contain prefix
edited help message
Merge pull request #182 from CraigPorter/vrtrackingtool_help

edited help message
list the locus tag in a separate column
Merge pull request #183 from andrewjpage/output_locus_tag_in_rna_seq_spreadsheet

list the locus tag in a separate column
Check the annotation matches the reference filename
failing test should actually fail
Merge pull request #184 from andrewjpage/rna_seq_memory_limit_increase

Rna seq memory limit increase
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
Merge branch 'pipeline' of github.com:sanger-pathogens/vr-codebase into add_sga_step_to_pipeline