.DS_Store
.dockerignore
LICENSE.txt
MANIFEST.in
Readme.md
notes.txt
release_notes.txt
setup.py
mitty/__init__.py
mitty/cli.py
mitty/version.py
mitty.egg-info/PKG-INFO
mitty.egg-info/SOURCES.txt
mitty.egg-info/dependency_links.txt
mitty.egg-info/entry_points.txt
mitty.egg-info/requires.txt
mitty.egg-info/top_level.txt
mitty/benchmarking/__init__.py
mitty/benchmarking/alignmentscore.py
mitty/benchmarking/bam_to_truth.py
mitty/benchmarking/callfate.py
mitty/benchmarking/complexity.py
mitty/benchmarking/evcfbysize.py
mitty/benchmarking/filterevalvcf.py
mitty/benchmarking/generalizedperr.py
mitty/benchmarking/god_aligner.py
mitty/benchmarking/partition_bams.py
mitty/benchmarking/subsetbam.py
mitty/benchmarking/vsizedistrib.py
mitty/benchmarking/xmv.py
mitty/benchmarking/lib/__init__.py
mitty/benchmarking/plot/__init__.py
mitty/benchmarking/plot/byvsize.py
mitty/benchmarking/plot/placeholderfigure.py
mitty/data/readmodels/1kg-pcr-free.pkl
mitty/data/readmodels/hiseq-2500-v1-pcr-free.pkl
mitty/data/readmodels/hiseq-X-v1-HLI.pkl
mitty/data/readmodels/hiseq-X-v2.5-Garvan.pkl
mitty/data/readmodels/old-Garvan.pkl
mitty/data/readmodels/test-illumina.pkl
mitty/empirical/__init__.py
mitty/empirical/bam2illumina.py
mitty/empirical/bq.py
mitty/empirical/bq_fastq.py
mitty/empirical/gc.py
mitty/empirical/gcbq_fastq.py
mitty/empirical/mabug.py
mitty/empirical/qnamestats.py
mitty/empirical/qnametruncate.py
mitty/lib/__init__.py
mitty/lib/bamfetch.py
mitty/lib/bedfile.py
mitty/lib/cigars.py
mitty/lib/evcfparse.py
mitty/lib/sanitizeseq.py
mitty/lib/vcfio.py
mitty/simulation/__init__.py
mitty/simulation/illumina.py
mitty/simulation/readcorrupt.py
mitty/simulation/readgenerate.py
mitty/simulation/rpc.py
mitty/simulation/genome/__init__.py
mitty/simulation/genome/sampledgenome.py
mitty/simulation/genome/simulatevariants.py
mitty/simulation/sequencing/__init__.py
mitty/simulation/sequencing/syntheticsequencer.py
mitty/simulation/sequencing/writefastq.py
mitty/test/__init__.py
mitty/test/benchmarking/__init__.py
mitty/test/benchmarking/test_alignmentscore.py
mitty/test/benchmarking/test_complexity.py
mitty/test/data/empty.ploidy.vcf
mitty/test/data/flawed-tiny.vcf
mitty/test/data/flawed-tiny.vcf.gz
mitty/test/data/flawed-tiny.vcf.gz.tbi
mitty/test/data/g0_s0.vcf
mitty/test/data/g0_s0.vcf.gz
mitty/test/data/g0_s0.vcf.gz.tbi
mitty/test/data/tiny.8-14.bed
mitty/test/data/tiny.complex.1.vcf
mitty/test/data/tiny.complex.1.vcf.gz
mitty/test/data/tiny.complex.1.vcf.gz.tbi
mitty/test/data/tiny.complex.vcf
mitty/test/data/tiny.complex.vcf.gz
mitty/test/data/tiny.complex.vcf.gz.tbi
mitty/test/data/tiny.fasta
mitty/test/data/tiny.haploid.vcf
mitty/test/data/tiny.vcf
mitty/test/data/tiny.vcf.gz
mitty/test/data/tiny.vcf.gz.tbi
mitty/test/data/tiny.whole.bed
mitty/test/lib/__init__.py
mitty/test/lib/test_cigars.py
mitty/test/lib/test_vcfio.py
mitty/test/simulation/__init__.py
mitty/test/simulation/test_rpc.py