Update blacklist files

[drpatelh]

Superceeds #250

[drpatelh]

Documented commands for how we download the blacklists:

cd ..
mkdir -p v1.0
cd v1.0
wget -L https://www.encodeproject.org/files/ENCFF001TDO/@@download/ENCFF001TDO.bed.gz && gunzip ENCFF001TDO.bed.gz && mv ENCFF001TDO.bed hg19-blacklist.v1.bed

mkdir -p assets/blacklists/v2.0/
cd assets/blacklists/v2.0/
wget -L https://raw.githubusercontent.com/Boyle-Lab/Blacklist/master/lists/ce10-blacklist.v2.bed.gz && gunzip ce10-blacklist.v2.bed.gz
wget -L https://raw.githubusercontent.com/Boyle-Lab/Blacklist/master/lists/ce11-blacklist.v2.bed.gz && gunzip ce11-blacklist.v2.bed.gz
wget -L https://raw.githubusercontent.com/Boyle-Lab/Blacklist/master/lists/dm3-blacklist.v2.bed.gz && gunzip dm3-blacklist.v2.bed.gz
wget -L https://raw.githubusercontent.com/Boyle-Lab/Blacklist/master/lists/dm6-blacklist.v2.bed.gz && gunzip dm6-blacklist.v2.bed.gz
wget -L https://raw.githubusercontent.com/Boyle-Lab/Blacklist/master/lists/hg19-blacklist.v2.bed.gz && gunzip hg19-blacklist.v2.bed.gz
wget -L https://raw.githubusercontent.com/Boyle-Lab/Blacklist/master/lists/hg38-blacklist.v2.bed.gz && gunzip hg38-blacklist.v2.bed.gz
wget -L https://raw.githubusercontent.com/Boyle-Lab/Blacklist/master/lists/mm10-blacklist.v2.bed.gz && gunzip mm10-blacklist.v2.bed.gz

cd ..
mkdir -p v3.0
cd v3.0
wget -L https://www.encodeproject.org/files/ENCFF356LFX/@@download/ENCFF356LFX.bed.gz && gunzip ENCFF356LFX.bed.gz && mv ENCFF356LFX.bed hg38-blacklist.v3.bed

TODO

• v1.0 - hg19-blacklist.v1.bed -> GRCh37-blacklist.v1.bed (rename original version for GRCh37)
• v2.0 - mm10-blacklist.v2.bed -> GRCm38-blacklist.v2.bed
• v3.0 - hg38-blacklist.v3.bed -> GRCh38-blacklist.v3.bed
• Update CHANGELOG
• Update igenomes.config paths to files
• Update code to use the blacklist files
• Delete all the old and UCSC format files when approved

[drpatelh]

YAML lint will still fail here but I have pulled in the changes from the template updates so everything else should pass. Shall we merge this in @JoseEspinosa and you can add in the remaining updates in a separate PR.