This removes /gscmnt/gc13003 from test data

These files were not being diffed so we just replaced the occurances
with $GENOME_TEST_INPUTS
Use the snvs.hq.tier1.v1.annotated.top file if snvs.hq.tier1.v1.annotated.top.header doesn't exist
bed reporter needs to write .bed file for igv xml to work
Merge pull request #311 from susannasiebert/variant_reporting_igv

Bed report needs to write .bed file for igv xml to work
Updated `genome` tab completion.
Updated `gmt` tab completion.
Fix bug with somatic indels plan file
Merge pull request #310 from susannasiebert/epitope_prediction

Use alternate snvs file if snvs.hq.tier1.v1.annotated.top.header doesn't exist
Merge pull request #315 from apregier/fix_model_report_indel_plan

Fix bug with somatic indels plan file
allow multiple metrics for the same timing code
Merge pull request #312 from acoffman/allow_multiple_metrics_in_timing

Allow multiple metrics with the same timing code.
update symlink so it used current GENOME_TEST_INPUTS
Merge pull request #318 from nnutter/symlink

update symlink so it used current GENOME_TEST_INPUTS
Merge pull request #304 from davidlmorton/genome-test-inputs-transition

This removes /gscmnt/gc13003 from test data