├── .gitignore ├── LICENSE.txt ├── README.FastGT.md ├── README.GenomeTester4.md ├── README.KATK.md ├── README.md ├── scripts ├── MakeIntersection.pl ├── MakeUnion.pl ├── generate_vcf.pl ├── katk2vcf.pl └── repeats │ ├── _filter_collated.pl │ ├── _filter_final.pl │ ├── _unique.pl │ ├── collate_repeats.pl │ └── find_regions.pl └── src ├── .depend ├── Makefile ├── Makefile.gmer ├── az ├── active-object.c ├── active-object.h ├── array-of.c ├── array-of.h ├── base.h ├── class.c ├── class.h ├── collection.c ├── collection.h ├── field.c ├── field.h ├── function-object.c ├── function-object.h ├── function.c ├── function.h ├── interface.c ├── interface.h ├── list.c ├── list.h ├── object-list.c ├── object-list.h ├── object.c ├── object.h ├── primitives.c ├── primitives.h ├── reference-of.c ├── reference-of.h ├── reference.c ├── reference.h ├── serialization.c ├── serialization.h ├── string.c ├── string.h ├── types.c ├── types.h ├── value-array.c ├── value-array.h ├── value.c └── value.h ├── binomial.c ├── binomial.h ├── bloom.c ├── bloom.h ├── buffer.c ├── buffer.h ├── common.c ├── common.h ├── database.c ├── database.h ├── distro.c ├── fasta.c ├── fasta.h ├── file-array.c ├── file-array.h ├── gassembler.c ├── gdistribution.c ├── genotypes.c ├── genotypes.h ├── glistcompare.c ├── glistmaker.c ├── glistmaker2.c ├── glistquery.c ├── gmasker.c ├── gmer_caller.c ├── gmer_counter.c ├── index-map.c ├── index-map.h ├── index.c ├── index.h ├── interfaces.txt ├── iotest.c ├── kmer-predictor.c ├── libarikkei ├── arikkei-cache.c ├── arikkei-cache.h ├── arikkei-dict.c ├── arikkei-dict.h ├── arikkei-iolib.c ├── arikkei-iolib.h ├── arikkei-strlib.c ├── arikkei-strlib.h ├── arikkei-token.c ├── arikkei-token.h ├── arikkei-url.c ├── arikkei-url.h ├── arikkei-utils.c └── arikkei-utils.h ├── listmaker-queue.c ├── listmaker-queue.h ├── matrix.c ├── matrix.h ├── queue.c ├── queue.h ├── sequence-block.c ├── sequence-block.h ├── sequence-collection.c ├── sequence-collection.h ├── sequence-file.c ├── sequence-file.h ├── sequence-source.c ├── sequence-source.h ├── sequence-stream.c ├── sequence-stream.h ├── sequence-zstream.c ├── sequence-zstream.h ├── sequence.c ├── sequence.h ├── set-operations.c ├── set-operations.h ├── simplex.c ├── simplex.h ├── thread-pool.c ├── thread-pool.h ├── trie.c ├── trie.h ├── utils.c ├── utils.h ├── version.h ├── word-array-sorted.c ├── word-array-sorted.h ├── word-dict.c ├── word-dict.h ├── word-index.c ├── word-index.h ├── word-list-sorted.c ├── word-list-sorted.h ├── word-list-stream.c ├── word-list-stream.h ├── word-list.c ├── word-list.h ├── word-map.c ├── word-map.h ├── word-table.c └── word-table.h /.gitignore: -------------------------------------------------------------------------------- 1 | .DS_Store 2 | -------------------------------------------------------------------------------- /LICENSE.txt: -------------------------------------------------------------------------------- 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