LICENSE.rst
MANIFEST.in
README.rst
pyproject.toml
setup.cfg
setup.py
aldy/__init__.py
aldy/__main__.py
aldy/cn.py
aldy/common.py
aldy/coverage.py
aldy/diplotype.py
aldy/gene.py
aldy/genotype.py
aldy/lpinterface.py
aldy/major.py
aldy/minor.py
aldy/profile.py
aldy/query.py
aldy/sam.py
aldy/solutions.py
aldy/version.py
aldy.egg-info/PKG-INFO
aldy.egg-info/SOURCES.txt
aldy.egg-info/dependency_links.txt
aldy.egg-info/entry_points.txt
aldy.egg-info/requires.txt
aldy.egg-info/top_level.txt
aldy/indelpost/__init__.py
aldy/indelpost/alleles.py
aldy/indelpost/consensus.py
aldy/indelpost/contig.c
aldy/indelpost/contig.pxd
aldy/indelpost/contig.pyx
aldy/indelpost/gappedaln.c
aldy/indelpost/gappedaln.pyx
aldy/indelpost/local_reference.c
aldy/indelpost/local_reference.pxd
aldy/indelpost/local_reference.pyx
aldy/indelpost/localn.c
aldy/indelpost/localn.pyx
aldy/indelpost/pileup.c
aldy/indelpost/pileup.pxd
aldy/indelpost/pileup.pyx
aldy/indelpost/softclip.c
aldy/indelpost/softclip.pyx
aldy/indelpost/sse2neon.h
aldy/indelpost/ssw.c
aldy/indelpost/ssw.h
aldy/indelpost/sswpy.c
aldy/indelpost/sswpy.pyx
aldy/indelpost/utilities.c
aldy/indelpost/utilities.pxd
aldy/indelpost/utilities.pyx
aldy/indelpost/varaln.c
aldy/indelpost/varaln.pxd
aldy/indelpost/varaln.pyx
aldy/indelpost/variant.c
aldy/indelpost/variant.pxd
aldy/indelpost/variant.pyx
aldy/indelpost/version.py
aldy/resources/LICENSE.rst
aldy/resources/__init__.py
aldy/resources/genes/__init__.py
aldy/resources/genes/abcg2.yml
aldy/resources/genes/cacna1s.yml
aldy/resources/genes/cftr.yml
aldy/resources/genes/comt.yml
aldy/resources/genes/cyp1a1.yml
aldy/resources/genes/cyp1a2.yml
aldy/resources/genes/cyp2a13.yml
aldy/resources/genes/cyp2a6.yml
aldy/resources/genes/cyp2b6.yml
aldy/resources/genes/cyp2c19.yml
aldy/resources/genes/cyp2c8.yml
aldy/resources/genes/cyp2c9.yml
aldy/resources/genes/cyp2d6.yml
aldy/resources/genes/cyp2e1.yml
aldy/resources/genes/cyp2f1.yml
aldy/resources/genes/cyp2j2.yml
aldy/resources/genes/cyp2r1.yml
aldy/resources/genes/cyp2s1.yml
aldy/resources/genes/cyp2w1.yml
aldy/resources/genes/cyp3a4.yml
aldy/resources/genes/cyp3a43.yml
aldy/resources/genes/cyp3a5.yml
aldy/resources/genes/cyp3a7.yml
aldy/resources/genes/cyp4f2.yml
aldy/resources/genes/dpyd.yml
aldy/resources/genes/g6pd.yml
aldy/resources/genes/gstm1.yml
aldy/resources/genes/gstp1.yml
aldy/resources/genes/ifnl3.yml
aldy/resources/genes/mt-rnr1.yml
aldy/resources/genes/nat1.yml
aldy/resources/genes/nat2.yml
aldy/resources/genes/nudt15.yml
aldy/resources/genes/ryr1.yml
aldy/resources/genes/slco1b1.yml
aldy/resources/genes/tpmt.yml
aldy/resources/genes/ugt1a1.yml
aldy/resources/genes/ugt2b7.yml
aldy/resources/genes/vkorc1.yml
aldy/resources/profiles/10x.yml
aldy/resources/profiles/__init__.py
aldy/resources/profiles/illumina.yml
aldy/resources/profiles/pacbio-hifi-targeted-twist.yml
aldy/resources/profiles/pacbio-hifi-targeted.yml
aldy/resources/profiles/pgx1.yml
aldy/resources/profiles/pgx2.yml
aldy/resources/profiles/pgx3.yml
aldy/tests/__init__.py
aldy/tests/conftest.py
aldy/tests/test_cn_real.py
aldy/tests/test_cn_synthetic.py
aldy/tests/test_diplotype_real.py
aldy/tests/test_diplotype_synthetic.py
aldy/tests/test_full.py
aldy/tests/test_gene.py
aldy/tests/test_major_real.py
aldy/tests/test_major_synthetic.py
aldy/tests/test_minor_real.py
aldy/tests/test_minor_synthetic.py
aldy/tests/test_query.py
aldy/tests/resources/HARD.dump.tar.gz
aldy/tests/resources/HG03166.pb.bam
aldy/tests/resources/HG03166.pb.bam.bai
aldy/tests/resources/INS.dump.tar.gz
aldy/tests/resources/NA07000_SLCO1B1.vcf.gz
aldy/tests/resources/NA07000_SLCO1B1.vcf.gz.tbi
aldy/tests/resources/NA10860.bai
aldy/tests/resources/NA10860.bam
aldy/tests/resources/NA10860.out.expected
aldy/tests/resources/NA10860.profile
aldy/tests/resources/NA10860.profile.hg38
aldy/tests/resources/NA10860.vcf.expected
aldy/tests/resources/NA10860_hg38.bai
aldy/tests/resources/NA10860_hg38.bam
aldy/tests/resources/__init__.py
aldy/tests/resources/cyp2d6.test.yml
aldy/tests/resources/toy.yml