├── .gitignore ├── LICENSE ├── MANIFEST.in ├── README.md ├── calldiff ├── README.md ├── pom.xml └── src │ ├── main │ └── java │ │ └── edu │ │ └── berkeley │ │ └── cs │ │ └── amplab │ │ └── calldiff │ │ ├── ApiCallScanner.java │ │ ├── BimonotonicAStarSearcher.java │ │ ├── BronKerbosch.java │ │ ├── Call.java │ │ ├── CallScanner.java │ │ ├── CandidateCalls.java │ │ ├── CaseNormalizer.java │ │ ├── CommandLine.java │ │ ├── DiffStats.java │ │ ├── ExceptionWrapper.java │ │ ├── FastaIndex.java │ │ ├── FastaReader.java │ │ ├── HaplotypeGenerator.java │ │ ├── HashCodeAndEquals.java │ │ ├── Indexer.java │ │ ├── Main.java │ │ ├── OutputTuple.java │ │ ├── VcfCallScanner.java │ │ └── Window.java │ └── test │ ├── java │ └── edu │ │ └── berkeley │ │ └── cs │ │ └── amplab │ │ └── calldiff │ │ ├── BimonotonicAStarSearcherTest.java │ │ ├── BronKerboschTest.java │ │ ├── CandidateCallsTest.java │ │ ├── CaseNormalizerTest.java │ │ ├── CommandLineTest.java │ │ ├── FastaIndexTest.java │ │ ├── FastaReaderTest.java │ │ ├── HaplotypeGeneratorTest.java │ │ ├── IndexerTest.java │ │ ├── TestCall.java │ │ ├── TestReference.java │ │ ├── VcfCallScannerTest.java │ │ └── WindowTest.java │ └── resources │ └── edu │ └── berkeley │ └── cs │ └── amplab │ └── calldiff │ └── sample.vcf ├── scripts ├── bench_subset.sh ├── sortByRef.pl └── sortByRef.py ├── setup.cfg ├── setup.py ├── smashbenchmarking ├── __init__.py ├── bench.py ├── compare_callsets.py ├── corrupt │ ├── __init__.py │ ├── base51.py │ ├── bubble.py │ └── contaminate.py ├── normalize_vcf.py ├── parsers │ ├── __init__.py │ ├── genome.py │ ├── util.py │ └── vcfwriter.py └── vcf_eval │ ├── __init__.py │ ├── callset_helper.py │ ├── chrom_variants.py │ ├── eval_helper.py │ ├── rectify_seq.py │ └── variants.py └── test ├── chrom_stats.py ├── chrom_variants.py ├── eval_helper.py ├── normalize.py ├── pred_comments.vcf ├── ref.fasta ├── ref.fasta.fai ├── rescue.py ├── system_comments_golden_output.vcf ├── 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