---
- 2022-11-21: Create this gnm7 repository from gnm7 and comparisons to the gnm7 assembly

file_transformation: 
# Name hashes between gnm6 and gnm7:

# From the BLAST output, extract the information to be hashed into the VCF file: seqid, position, markername
  mkdir new_vcf_coords
  cat blastout_top/vigra.VC1973A.gnm6.variants_filt_1kseq.x.vigra.VC1973A.gnm7.SB53.bln_top |
    awk -v OFS="\t" '$4>=990 {printf("%s\t%d\t%s\n"), $2, $9+(($10-$9)/2), $1 }' |
    cat > new_vcf_coords/vigra.VC1973A.gnm6.div.Sandhu_Singh_2020.var_filt_posn_map.tsv
  cat blastout_top/vigra.VC1973A.gnm6.variants_main_1kseq.x.vigra.VC1973A.gnm7.SB53.bln_top |
    awk -v OFS="\t" '$4>=990 {printf("%s\t%d\t%s\n"), $2, $9+(($10-$9)/2), $1 }' |
    cat > new_vcf_coords/vigra.VC1973A.gnm6.div.Sandhu_Singh_2020.var_main_posn_map.tsv

  # looks like
  #   vigra.VC1973A.gnm7.chr4 33603402  1_16010
  #   vigra.VC1973A.gnm7.chr4 33603452  1_16060
  #   vigra.VC1973A.gnm7.chr4 33650083  1_62820

# Replace the seqid and position fields (1 and 2), based on ID in field 3.

  mkdir vigra.VC1973A.gnm7.diversity

  zcat vigra.VC1973A.gnm6.diversity/vigra.VC1973A.gnm6.div.Sandhu_Singh_2020.variants_filt.vcf.gz |
    hash_into_vcf.pl -hash new_vcf_coords/vigra.VC1973A.gnm6.div.Sandhu_Singh_2020.var_filt_posn_map.tsv \
                     -swap -out vigra.VC1973A.gnm7.diversity/vigra.VC1973A.gnm7.div.Sandhu_Singh_2020.variants_filt.vcf

  zcat vigra.VC1973A.gnm6.diversity/vigra.VC1973A.gnm6.div.Sandhu_Singh_2020.variants_main.vcf.gz |
    hash_into_vcf.pl -hash new_vcf_coords/vigra.VC1973A.gnm6.div.Sandhu_Singh_2020.var_main_posn_map.tsv \
                     -swap -out vigra.VC1973A.gnm7.diversity/vigra.VC1973A.gnm7.div.Sandhu_Singh_2020.variants_main.vcf



bcftools sort vigra.VC1973A.gnm7.div.Sandhu_Singh_2020.variants_filt.vcf_unsort > vigra.VC1973A.gnm6.div.Sandhu_Singh_2020.variants_filt.vcf &
bcftools sort vigra.VC1973A.gnm7.div.Sandhu_Singh_2020.variants_main.vcf_unsort > vigra.VC1973A.gnm6.div.Sandhu_Singh_2020.variants_main.vcf &

for file in vigra*vcf; do bgzip $file &
done

for file in vigra*vcf.gz; do tabix $file &
done



changes: 
  - 2021-09-16: Added full variants.vcf file, as vigra.VC1973A.gnm7.div.Sandhu_Singh_2020.variants_main.vcf.gz. 
                For both filtered and unfiltered vcf, added marker names, and changed contig/chrom names using 
                hash file vigra.VC1973A.gnm7.3nL8.scaff_name_hash.tsv, derived from GenBank JJMO01 contigs file.