TODO.txt

This list tracks work items, owner (if assigned), and creator (for contact)
Items are tab-separated.

ITEM_ID	STATUS	REQUEST_TYPE	CREATOR	OWNER	DESCRIPTION
00001	working	enhancement	Kalmbach	Kalmbach	Convert echo statements to log statements at appropriate level
00002	working	enhancement	Kalmbach	Kalmbach	Examine error paths where we exit 100 and give helpful error messages
00003	open	enhancement	Kalmbach	Kalmbach	Ensure that an email is sent for every exit 100
00004	open	documentation	Kalmbach	Kalmbach	Update github README to describe installation prereqs
00005	open	documentation	Kalmbach	Kalmbach	Update internal bsiweb bior_annotate web page
00006	open	enhancement	Kalmbach	Kalmbach	Create help text for ba.merge.sh
00007	open	test	Kalmbach	Kalmbach	Test suite for validating drill_file and providing helpful errors
00008	open	test	Kalmbach	Kalmbach	Test suite for validating catalog_file and providing helpful errors
00009	open	test	Kalmbach	Kalmbach	Test suite for good path queue submission
00010	open	test	Kalmbach	Kalmbach	Add VCF verification to utility functions and test validation
00011	open	documentation	Kalmbach	Kalmbach	Update help text to describe renamed columns functionality
00012	open	documentation	Kalmbach	Kalmbach	Ensure each script has detailed help text
00013	open	enhancement	Kalmbach	Kalmbach	Ensure that error log output goes to stderr
00014	open	test	Kalmbach	Kalmbach	Add test for SNPEff
00015	open	test	Kalmbach	Kalmbach	Add test for CAVA
00016	open	refactor	Kalmbach	Kalmbach	Use consistent spacing among all files (spaces/tabs)