problems about default and customized ref.fasta in variant normalisation process

[YuanfengZhang]

##Reference=hg19comment of output.vcf.gz never changes. There are two specific problems:

1. hap.py/src/python/Tools/init.py Line 132
   No matter what ref is used, b37, hg19, GRCh37d5 or GRCh38... the writeVCFHeader will always output
   ##reference=hg19

2. hap.py/src/python/Tools/init.py Line 30
   to_try = ['/opt/hap.py-data/hg19.fa']

   No ref.fa in github master branch ./example/ or ./src/data is packaged into the docker image that built by git clone + docker build ..

Considering there is already an issue about the the compatibility of the software and customized ref.fasta...

Is there any chance that you may
(1) offically provide avaliable hg19 & hg38.fasta in docker image?
(2) replace the to_try list with a dict, like to_try={'/opt/hap.py-data/hg19.fa':'hg19'}?
(3) based on (2), ask for both key and value when customized fasta file is declared? like
--reference ${ref} --reference_ver hg38 or --reference ${ref}:hg38
and make the the info string in writeVCFHeader function mutable and could be automatically modifed according to --reference_ver?

Thanks in advance
Zhang Yuanfeng

[adamnovak]

Point 1 might be related to (or the real cause of?) #59.