v1.3

This release includes the exome depth scripts makeExomedepth.sh and genepred2exomedepth.sh. A release was not done when these two scripts were added to the repository, so this release is retrospective for these scripts, and also includes the script added at the current commit - transcript_checker.sh. The details of which bed files were made using the exome depth script before this release will be found in the QPulse audit.

• makeExomedepth.sh - Generate exomedepth targets BED from a set of known capture regions. See readme: makeExomedepth.README.md
• genepred2exomedepth.sh - This script takes a refseq file and will convert it into a format that can be used by exome depth. See readme: genepred2exomedepth.README.md
  
• transcript_checker.sh - Script for checking a bed file against an input list of transcripts (single transcript per line). Can be used for both PanXdata.bed and PanXdataSambamba.bed bed files

Correcting 5UTR function

Previously Bed files created just for 5UTRs returned errors.
Code corrected to solve this error.

Use in DNANexus. Test for transcript file header

Change the path to the code to get git tag correctly in DNANexus
Check for header in transcript input file to avoid missing genes