LGVAR
LICENSE
MANIFEST.in
README.md
environment.yml
lgvar_cli.py
pyproject.toml
setup.sh
utils.py
./LGVAR
./environment.yml
./lgvar_cli.py
./setup.sh
./utils.py
./examples/align/align_hap1.paf
./examples/align/align_hap2.paf
./examples/data/hap1.tsv
./examples/data/hap2.tsv
./examples/genome/test.hap1.fa
./examples/genome/test.hap1.fa.fai
./examples/genome/test.hap2.fa
./examples/genome/test.hap2.fa.fai
./examples/genome/test.ref.fa
./examples/genome/test.ref.fa.fai
./examples/results/LGvarall.bed
./examples/results/LGvarhap1.bed
./examples/results/LGvarhap1.vcf
./examples/results/LGvarhap2.bed
./examples/results/LGvarhap2.vcf
./examples/results/md5sum.txt
./examples/results/sortLGvar_all.vcf
./src/pyFiles/CIGAR.py
./src/pyFiles/SDR2VCF.py
./src/pyFiles/dup_filt.py
./src/pyFiles/phenotype.py
./src/pyFiles/plotpaf.py
./src/pyFiles/restore_paf.py
./src/scripts/chaos_filt.r
./src/scripts/chrom_pair.sh
./src/scripts/denSDR.r
./src/scripts/denSDRfun.r
./src/scripts/rc_chrom.sh
./src/vcf/CIGAR2VCF.sh
./src/vcf/dup_filt.sh
./src/vcf/realign.sh
./src/vcf/splitfile.sh
./src/vcf/vcf2bedGT.sh
examples/align/align_hap1.paf
examples/align/align_hap2.paf
examples/data/hap1.tsv
examples/data/hap2.tsv
examples/genome/test.hap1.fa
examples/genome/test.hap1.fa.fai
examples/genome/test.hap2.fa
examples/genome/test.hap2.fa.fai
examples/genome/test.ref.fa
examples/genome/test.ref.fa.fai
examples/results/LGvarall.bed
examples/results/LGvarhap1.bed
examples/results/LGvarhap1.vcf
examples/results/LGvarhap2.bed
examples/results/LGvarhap2.vcf
examples/results/md5sum.txt
examples/results/sortLGvar_all.vcf
lgvar.egg-info/PKG-INFO
lgvar.egg-info/SOURCES.txt
lgvar.egg-info/dependency_links.txt
lgvar.egg-info/entry_points.txt
lgvar.egg-info/top_level.txt
src/pyFiles/CIGAR.py
src/pyFiles/SDR2VCF.py
src/pyFiles/dup_filt.py
src/pyFiles/phenotype.py
src/pyFiles/plotpaf.py
src/pyFiles/restore_paf.py
src/scripts/chaos_filt.r
src/scripts/chrom_pair.sh
src/scripts/denSDR.r
src/scripts/denSDRfun.r
src/scripts/rc_chrom.sh
src/vcf/CIGAR2VCF.sh
src/vcf/dup_filt.sh
src/vcf/realign.sh
src/vcf/splitfile.sh
src/vcf/vcf2bedGT.sh