LICENSE
README.md
setup.py
paraphase/__init__.py
paraphase/__main__.py
paraphase/genome_depth.py
paraphase/haplotype_assembler.py
paraphase/paraphase.py
paraphase/phaser.py
paraphase/prepare_bam_and_vcf.py
paraphase.egg-info/PKG-INFO
paraphase.egg-info/SOURCES.txt
paraphase.egg-info/dependency_links.txt
paraphase.egg-info/entry_points.txt
paraphase.egg-info/requires.txt
paraphase.egg-info/top_level.txt
paraphase/data/genome_region.bed
paraphase/data/cfc1/cfc1_config.yaml
paraphase/data/cfc1/homopolymer_sites.txt
paraphase/data/cfc1/ref.fa
paraphase/data/cfc1/ref.fa.fai
paraphase/data/f8/f8_config.yaml
paraphase/data/f8/homopolymer_sites.txt
paraphase/data/f8/ref.fa
paraphase/data/f8/ref.fa.fai
paraphase/data/ikbkg/homopolymer_sites.txt
paraphase/data/ikbkg/ikbkg_config.yaml
paraphase/data/ikbkg/ref.fa
paraphase/data/ikbkg/ref.fa.fai
paraphase/data/ncf1/homopolymer_sites.txt
paraphase/data/ncf1/ncf1_config.yaml
paraphase/data/ncf1/ref.fa
paraphase/data/ncf1/ref.fa.fai
paraphase/data/neb/homopolymer_sites.txt
paraphase/data/neb/neb_config.yaml
paraphase/data/neb/ref.fa
paraphase/data/neb/ref.fa.fai
paraphase/data/pms2/pms2_config.yaml
paraphase/data/pms2/pms2_homopolymer_sites.txt
paraphase/data/pms2/pms2_ref.fa
paraphase/data/pms2/pms2_ref.fa.fai
paraphase/data/rccx/cyp21_diff_sites.txt
paraphase/data/rccx/rccx_config.yaml
paraphase/data/rccx/rccx_homopolymer_sites.txt
paraphase/data/rccx/rccx_ref.fa
paraphase/data/rccx/rccx_ref.fa.fai
paraphase/data/smn1/homopolymer_sites.txt
paraphase/data/smn1/known_haplotypes.json
paraphase/data/smn1/ref.fa
paraphase/data/smn1/ref.fa.fai
paraphase/data/smn1/ref_smn2.fa
paraphase/data/smn1/ref_smn2.fa.fai
paraphase/data/smn1/smn1_config.yaml
paraphase/data/smn1/smn_matching_pos.txt
paraphase/data/strc/homopolymer_sites.txt
paraphase/data/strc/ref.fa
paraphase/data/strc/ref.fa.fai
paraphase/data/strc/strc_config.yaml
paraphase/genes/__init__.py
paraphase/genes/cfc1_phaser.py
paraphase/genes/f8_phaser.py
paraphase/genes/ikbkg_phaser.py
paraphase/genes/ncf1_phaser.py
paraphase/genes/neb_phaser.py
paraphase/genes/pms2_phaser.py
paraphase/genes/rccx_phaser.py
paraphase/genes/smn1_phaser.py
paraphase/genes/strc_phaser.py
tests/test_haplotype_assembler.py
tests/test_phaser.py
tests/test_smn1_phaser.py