# viewing HPRC chain files constructed by HPRC (DONE - Hiram - 2023-03-15)

mkdir /hive/data/genomes/hg38/bed/hprc/bigChains
cd /hive/data/genomes/hg38/bed/hprc/bigChains

### fetch the HPRC files:

for N in `cut -f2 /cluster/home/hiram/kent/src/hg/makeDb/doc/hprcAsmHub/assembly.hprcName.asmId.txt`
do
  printf "%s\n" "${N}"
  wget --timestamping "https://s3-us-west-2.amazonaws.com/human-pangenomics/submissions/A512ED34-9A91-4FC1-91A5-7AA162D7AFB2--Y1-BIGCHAINS/GRCh38-f1g-90-mc-aug11/aggr_bigchains/GRCh38/${N}-to-GRCh38.bigChain.bb"
  wget --timestamping "https://s3-us-west-2.amazonaws.com/human-pangenomics/submissions/A512ED34-9A91-4FC1-91A5-7AA162D7AFB2--Y1-BIGCHAINS/GRCh38-f1g-90-mc-aug11/aggr_bigchains/GRCh38/${N}-to-GRCh38.bigLink.bb"
done


### symlink those files into gbdb for use in a composite track:
### (DONE - Hiram - 2023-03-15)

egrep -v "NA19240.1|NA19240.2|HG005.1|HG005.2|HG002.1|HG002.2" /cluster/home/hiram/kent/src/hg/makeDb/doc/hprcAsmHub/assembly.hprcName.asmId.txt | while read L
do
  gbdb="/gbdb/hg38/chainNet"
  TOP="/hive/data/genomes/hg38/bed/hprc/bigChains"
  accession=`echo ${L} | cut -d' ' -f1`
  hprc=`echo ${L} | cut -d' ' -f2`
  asmId=`echo ${L} | cut -d' ' -f3`
  chainFile="${hprc}-to-GRCh38.bigChain.bb"
  linkFile="${hprc}-to-GRCh38.bigLink.bb"
  destChain="hg38.chainHprc${accession}.bb"
  destLink="hg38.chainHprc${accession}Link.bb"
  if [ ! -s "${linkFile}" ]; then
    printf "# missing: %s\n" "${linkFile}" 1>&2
    exit 255
  fi
  if [ ! -s "${chainFile}" ]; then
    printf "# missing: %s\n" "${chainFile}" 1>&2
  else
    printf "ln -s %s %s\n" "$TOP/$chainFile" "$gbdb/${destChain}"
    printf "ln -s %s %s\n" "$TOP/$linkFile" "$gbdb/${destLink}"
    ln -s "$TOP/$chainFile" "$gbdb/${destChain}"
    ln -s "$TOP/$linkFile" "$gbdb/${destLink}"
  fi
done