├── .github └── workflows │ └── rust.yml ├── .gitignore ├── .travis.yml ├── Cargo.toml ├── LICENSE ├── README.md ├── src ├── build_ref_cli.yaml ├── cli.yaml ├── common.rs ├── filter_cli.yaml ├── germline_cli.yaml ├── main.rs ├── microphasing.rs ├── microphasing_wholegenome.rs ├── normal_microphasing.rs ├── peptides.rs ├── somatic_cli.yaml └── wgs.yaml └── tests ├── lib.rs ├── output └── .nfs00000000020a0eba000003b7 └── resources ├── chr1.fa.fai ├── chr14.fa.fai ├── chr6.fa.fai ├── chr7.fa.fai ├── frameshift_test ├── expected_output │ ├── frameshift_test.mt.fa │ ├── frameshift_test.tsv │ └── frameshift_test.wt.fa ├── frameshift_test.bam ├── frameshift_test.gtf └── frameshift_test.vcf ├── splice_forward_test ├── INSIG1.test.bam ├── INSIG1.test.bam.bai ├── INSIG1.test.germline.vcf ├── INSIG1.test.gtf ├── INSIG1.test.vcf └── expected_output │ ├── .fuse_hidden00000bec0000006d │ ├── INSIG1.test.fa │ ├── INSIG1.test.prot.fa │ ├── INSIG1.test.tsv │ ├── splice_forward_test.fa │ ├── splice_forward_test.germline.fa │ ├── splice_forward_test.normal.fa │ └── splice_forward_test.tsv ├── splice_reverse_test ├── MMS22L.test.bam ├── MMS22L.test.bam.bai ├── MMS22L.test.gtf ├── MMS22L.test.vcf └── expected_output │ ├── MMS22L.test.fa │ ├── MMS22L.test.prot.fa │ ├── MMS22L.test.tsv │ ├── splice_reverse_test.fa │ ├── splice_reverse_test.normal.fa │ └── splice_reverse_test.tsv ├── test_build ├── expected_output │ ├── reference.binary │ └── reference_peptides.fasta └── reference.fa ├── test_empty ├── empty_test.bam ├── empty_test.bam.bai ├── empty_test.fasta ├── empty_test.fasta.fai ├── empty_test.gtf ├── empty_test.vcf └── expected_output │ ├── empty_test.fa │ ├── empty_test.fasta.out │ ├── empty_test.normal.fa │ ├── empty_test.prot.fa │ └── empty_test.tsv ├── test_filter ├── expected_output │ ├── info.filtered.tsv │ ├── normal.filtered.fa │ └── tumor.filtered.fa ├── info.tsv └── reference.binary ├── test_filter_fs ├── expected_output │ ├── info.filtered_fs.tsv │ ├── normal.filtered_fs.fa │ └── tumor.filtered_fs.fa ├── info.tsv └── reference.binary ├── test_filter_long ├── expected_output │ ├── info.filtered_long.tsv │ ├── normal.filtered_long.fa │ └── tumor.filtered_long.fa ├── info.tsv └── reference.binary ├── test_forward ├── empty_test.vcf ├── expected_output │ ├── empty_test.fasta.out │ ├── empty_test.prot.out │ ├── forward_test.csv │ ├── forward_test.fa │ ├── forward_test.fasta.out │ ├── forward_test.germline.fa │ ├── forward_test.normal.fa │ ├── forward_test.prot.out │ └── forward_test.tsv ├── forward_test.bam ├── forward_test.bam.bai ├── forward_test.germline.vcf ├── forward_test.gtf ├── forward_test.mdup.bam └── forward_test.vcf ├── test_reverse ├── expected_output │ ├── reverse_test.fa │ ├── reverse_test.fasta.out │ ├── reverse_test.germline.fa │ ├── reverse_test.normal.fa │ ├── reverse_test.prot.out │ └── reverse_test.tsv ├── reverse_test.bam ├── reverse_test.bam.bai ├── reverse_test.germline.vcf ├── reverse_test.gtf ├── reverse_test.vcf └── reverse_test_germline.gtf ├── test_unsorted_gtf ├── chr14.sorted.DHRS2_BDKRB2.gtf ├── chr14.unsorted.BDKRB2_DHRS2.gtf ├── empty.vcf ├── forward_test.bam └── forward_test.bam.bai └── three_way_splice ├── expected_output ├── three_way_splice.mt.fa ├── three_way_splice.tsv └── three_way_splice.wt.fa ├── three_way_splice.bam ├── three_way_splice.gtf └── three_way_splice.vcf /.github/workflows/rust.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/.github/workflows/rust.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/.travis.yml -------------------------------------------------------------------------------- /Cargo.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/Cargo.toml -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/README.md -------------------------------------------------------------------------------- /src/build_ref_cli.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/src/build_ref_cli.yaml -------------------------------------------------------------------------------- /src/cli.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/src/cli.yaml -------------------------------------------------------------------------------- /src/common.rs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/src/common.rs -------------------------------------------------------------------------------- /src/filter_cli.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/src/filter_cli.yaml -------------------------------------------------------------------------------- /src/germline_cli.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/src/germline_cli.yaml -------------------------------------------------------------------------------- /src/main.rs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/src/main.rs -------------------------------------------------------------------------------- /src/microphasing.rs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/src/microphasing.rs -------------------------------------------------------------------------------- /src/microphasing_wholegenome.rs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/src/microphasing_wholegenome.rs -------------------------------------------------------------------------------- /src/normal_microphasing.rs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/src/normal_microphasing.rs -------------------------------------------------------------------------------- /src/peptides.rs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/src/peptides.rs -------------------------------------------------------------------------------- /src/somatic_cli.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/src/somatic_cli.yaml -------------------------------------------------------------------------------- /src/wgs.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/src/wgs.yaml -------------------------------------------------------------------------------- /tests/lib.rs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/lib.rs -------------------------------------------------------------------------------- /tests/output/.nfs00000000020a0eba000003b7: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/output/.nfs00000000020a0eba000003b7 -------------------------------------------------------------------------------- /tests/resources/chr1.fa.fai: -------------------------------------------------------------------------------- 1 | chr1 248956422 6 50 51 2 | -------------------------------------------------------------------------------- /tests/resources/chr14.fa.fai: -------------------------------------------------------------------------------- 1 | chr14 107043718 7 50 51 2 | -------------------------------------------------------------------------------- /tests/resources/chr6.fa.fai: -------------------------------------------------------------------------------- 1 | chr6 170805979 6 50 51 2 | -------------------------------------------------------------------------------- /tests/resources/chr7.fa.fai: -------------------------------------------------------------------------------- 1 | chr7 159345973 6 50 51 2 | -------------------------------------------------------------------------------- /tests/resources/frameshift_test/expected_output/frameshift_test.mt.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/frameshift_test/expected_output/frameshift_test.mt.fa -------------------------------------------------------------------------------- /tests/resources/frameshift_test/expected_output/frameshift_test.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/frameshift_test/expected_output/frameshift_test.tsv -------------------------------------------------------------------------------- /tests/resources/frameshift_test/expected_output/frameshift_test.wt.fa: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/resources/frameshift_test/frameshift_test.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/frameshift_test/frameshift_test.bam -------------------------------------------------------------------------------- /tests/resources/frameshift_test/frameshift_test.gtf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/frameshift_test/frameshift_test.gtf -------------------------------------------------------------------------------- /tests/resources/frameshift_test/frameshift_test.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/frameshift_test/frameshift_test.vcf -------------------------------------------------------------------------------- /tests/resources/splice_forward_test/INSIG1.test.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/splice_forward_test/INSIG1.test.bam -------------------------------------------------------------------------------- /tests/resources/splice_forward_test/INSIG1.test.bam.bai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/splice_forward_test/INSIG1.test.bam.bai -------------------------------------------------------------------------------- /tests/resources/splice_forward_test/INSIG1.test.germline.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/splice_forward_test/INSIG1.test.germline.vcf -------------------------------------------------------------------------------- /tests/resources/splice_forward_test/INSIG1.test.gtf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/splice_forward_test/INSIG1.test.gtf -------------------------------------------------------------------------------- /tests/resources/splice_forward_test/INSIG1.test.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/splice_forward_test/INSIG1.test.vcf -------------------------------------------------------------------------------- /tests/resources/splice_forward_test/expected_output/.fuse_hidden00000bec0000006d: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/splice_forward_test/expected_output/.fuse_hidden00000bec0000006d -------------------------------------------------------------------------------- /tests/resources/splice_forward_test/expected_output/INSIG1.test.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/splice_forward_test/expected_output/INSIG1.test.fa -------------------------------------------------------------------------------- /tests/resources/splice_forward_test/expected_output/INSIG1.test.prot.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/splice_forward_test/expected_output/INSIG1.test.prot.fa -------------------------------------------------------------------------------- /tests/resources/splice_forward_test/expected_output/INSIG1.test.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/splice_forward_test/expected_output/INSIG1.test.tsv -------------------------------------------------------------------------------- /tests/resources/splice_forward_test/expected_output/splice_forward_test.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/splice_forward_test/expected_output/splice_forward_test.fa -------------------------------------------------------------------------------- /tests/resources/splice_forward_test/expected_output/splice_forward_test.germline.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/splice_forward_test/expected_output/splice_forward_test.germline.fa -------------------------------------------------------------------------------- /tests/resources/splice_forward_test/expected_output/splice_forward_test.normal.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/splice_forward_test/expected_output/splice_forward_test.normal.fa -------------------------------------------------------------------------------- /tests/resources/splice_forward_test/expected_output/splice_forward_test.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/splice_forward_test/expected_output/splice_forward_test.tsv -------------------------------------------------------------------------------- /tests/resources/splice_reverse_test/MMS22L.test.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/splice_reverse_test/MMS22L.test.bam -------------------------------------------------------------------------------- /tests/resources/splice_reverse_test/MMS22L.test.bam.bai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/splice_reverse_test/MMS22L.test.bam.bai -------------------------------------------------------------------------------- /tests/resources/splice_reverse_test/MMS22L.test.gtf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/splice_reverse_test/MMS22L.test.gtf -------------------------------------------------------------------------------- /tests/resources/splice_reverse_test/MMS22L.test.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/splice_reverse_test/MMS22L.test.vcf -------------------------------------------------------------------------------- /tests/resources/splice_reverse_test/expected_output/MMS22L.test.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/splice_reverse_test/expected_output/MMS22L.test.fa -------------------------------------------------------------------------------- /tests/resources/splice_reverse_test/expected_output/MMS22L.test.prot.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/splice_reverse_test/expected_output/MMS22L.test.prot.fa -------------------------------------------------------------------------------- /tests/resources/splice_reverse_test/expected_output/MMS22L.test.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/splice_reverse_test/expected_output/MMS22L.test.tsv -------------------------------------------------------------------------------- /tests/resources/splice_reverse_test/expected_output/splice_reverse_test.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/splice_reverse_test/expected_output/splice_reverse_test.fa -------------------------------------------------------------------------------- /tests/resources/splice_reverse_test/expected_output/splice_reverse_test.normal.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/splice_reverse_test/expected_output/splice_reverse_test.normal.fa -------------------------------------------------------------------------------- /tests/resources/splice_reverse_test/expected_output/splice_reverse_test.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/splice_reverse_test/expected_output/splice_reverse_test.tsv -------------------------------------------------------------------------------- /tests/resources/test_build/expected_output/reference.binary: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_build/expected_output/reference.binary -------------------------------------------------------------------------------- /tests/resources/test_build/expected_output/reference_peptides.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_build/expected_output/reference_peptides.fasta -------------------------------------------------------------------------------- /tests/resources/test_build/reference.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_build/reference.fa -------------------------------------------------------------------------------- /tests/resources/test_empty/empty_test.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_empty/empty_test.bam -------------------------------------------------------------------------------- /tests/resources/test_empty/empty_test.bam.bai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_empty/empty_test.bam.bai -------------------------------------------------------------------------------- /tests/resources/test_empty/empty_test.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_empty/empty_test.fasta -------------------------------------------------------------------------------- /tests/resources/test_empty/empty_test.fasta.fai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_empty/empty_test.fasta.fai -------------------------------------------------------------------------------- /tests/resources/test_empty/empty_test.gtf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_empty/empty_test.gtf -------------------------------------------------------------------------------- /tests/resources/test_empty/empty_test.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_empty/empty_test.vcf -------------------------------------------------------------------------------- /tests/resources/test_empty/expected_output/empty_test.fa: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/resources/test_empty/expected_output/empty_test.fasta.out: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/resources/test_empty/expected_output/empty_test.normal.fa: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/resources/test_empty/expected_output/empty_test.prot.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_empty/expected_output/empty_test.prot.fa -------------------------------------------------------------------------------- /tests/resources/test_empty/expected_output/empty_test.tsv: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/resources/test_filter/expected_output/info.filtered.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_filter/expected_output/info.filtered.tsv -------------------------------------------------------------------------------- /tests/resources/test_filter/expected_output/normal.filtered.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_filter/expected_output/normal.filtered.fa -------------------------------------------------------------------------------- /tests/resources/test_filter/expected_output/tumor.filtered.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_filter/expected_output/tumor.filtered.fa -------------------------------------------------------------------------------- /tests/resources/test_filter/info.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_filter/info.tsv -------------------------------------------------------------------------------- /tests/resources/test_filter/reference.binary: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_filter/reference.binary -------------------------------------------------------------------------------- /tests/resources/test_filter_fs/expected_output/info.filtered_fs.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_filter_fs/expected_output/info.filtered_fs.tsv -------------------------------------------------------------------------------- /tests/resources/test_filter_fs/expected_output/normal.filtered_fs.fa: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/resources/test_filter_fs/expected_output/tumor.filtered_fs.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_filter_fs/expected_output/tumor.filtered_fs.fa -------------------------------------------------------------------------------- /tests/resources/test_filter_fs/info.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_filter_fs/info.tsv -------------------------------------------------------------------------------- /tests/resources/test_filter_fs/reference.binary: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_filter_fs/reference.binary -------------------------------------------------------------------------------- /tests/resources/test_filter_long/expected_output/info.filtered_long.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_filter_long/expected_output/info.filtered_long.tsv -------------------------------------------------------------------------------- /tests/resources/test_filter_long/expected_output/normal.filtered_long.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_filter_long/expected_output/normal.filtered_long.fa -------------------------------------------------------------------------------- /tests/resources/test_filter_long/expected_output/tumor.filtered_long.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_filter_long/expected_output/tumor.filtered_long.fa -------------------------------------------------------------------------------- /tests/resources/test_filter_long/info.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_filter_long/info.tsv -------------------------------------------------------------------------------- /tests/resources/test_filter_long/reference.binary: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_filter_long/reference.binary -------------------------------------------------------------------------------- /tests/resources/test_forward/empty_test.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_forward/empty_test.vcf -------------------------------------------------------------------------------- /tests/resources/test_forward/expected_output/empty_test.fasta.out: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/resources/test_forward/expected_output/empty_test.prot.out: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_forward/expected_output/empty_test.prot.out -------------------------------------------------------------------------------- /tests/resources/test_forward/expected_output/forward_test.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_forward/expected_output/forward_test.csv -------------------------------------------------------------------------------- /tests/resources/test_forward/expected_output/forward_test.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_forward/expected_output/forward_test.fa -------------------------------------------------------------------------------- /tests/resources/test_forward/expected_output/forward_test.fasta.out: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_forward/expected_output/forward_test.fasta.out -------------------------------------------------------------------------------- /tests/resources/test_forward/expected_output/forward_test.germline.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_forward/expected_output/forward_test.germline.fa -------------------------------------------------------------------------------- /tests/resources/test_forward/expected_output/forward_test.normal.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_forward/expected_output/forward_test.normal.fa -------------------------------------------------------------------------------- /tests/resources/test_forward/expected_output/forward_test.prot.out: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_forward/expected_output/forward_test.prot.out -------------------------------------------------------------------------------- /tests/resources/test_forward/expected_output/forward_test.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_forward/expected_output/forward_test.tsv -------------------------------------------------------------------------------- /tests/resources/test_forward/forward_test.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_forward/forward_test.bam -------------------------------------------------------------------------------- /tests/resources/test_forward/forward_test.bam.bai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_forward/forward_test.bam.bai -------------------------------------------------------------------------------- /tests/resources/test_forward/forward_test.germline.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_forward/forward_test.germline.vcf -------------------------------------------------------------------------------- /tests/resources/test_forward/forward_test.gtf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_forward/forward_test.gtf -------------------------------------------------------------------------------- /tests/resources/test_forward/forward_test.mdup.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_forward/forward_test.mdup.bam -------------------------------------------------------------------------------- /tests/resources/test_forward/forward_test.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_forward/forward_test.vcf -------------------------------------------------------------------------------- /tests/resources/test_reverse/expected_output/reverse_test.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_reverse/expected_output/reverse_test.fa -------------------------------------------------------------------------------- /tests/resources/test_reverse/expected_output/reverse_test.fasta.out: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_reverse/expected_output/reverse_test.fasta.out -------------------------------------------------------------------------------- /tests/resources/test_reverse/expected_output/reverse_test.germline.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_reverse/expected_output/reverse_test.germline.fa -------------------------------------------------------------------------------- /tests/resources/test_reverse/expected_output/reverse_test.normal.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_reverse/expected_output/reverse_test.normal.fa -------------------------------------------------------------------------------- /tests/resources/test_reverse/expected_output/reverse_test.prot.out: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_reverse/expected_output/reverse_test.prot.out -------------------------------------------------------------------------------- /tests/resources/test_reverse/expected_output/reverse_test.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_reverse/expected_output/reverse_test.tsv -------------------------------------------------------------------------------- /tests/resources/test_reverse/reverse_test.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_reverse/reverse_test.bam -------------------------------------------------------------------------------- /tests/resources/test_reverse/reverse_test.bam.bai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_reverse/reverse_test.bam.bai -------------------------------------------------------------------------------- /tests/resources/test_reverse/reverse_test.germline.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_reverse/reverse_test.germline.vcf -------------------------------------------------------------------------------- /tests/resources/test_reverse/reverse_test.gtf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_reverse/reverse_test.gtf -------------------------------------------------------------------------------- /tests/resources/test_reverse/reverse_test.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_reverse/reverse_test.vcf -------------------------------------------------------------------------------- /tests/resources/test_reverse/reverse_test_germline.gtf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_reverse/reverse_test_germline.gtf -------------------------------------------------------------------------------- /tests/resources/test_unsorted_gtf/chr14.sorted.DHRS2_BDKRB2.gtf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_unsorted_gtf/chr14.sorted.DHRS2_BDKRB2.gtf -------------------------------------------------------------------------------- /tests/resources/test_unsorted_gtf/chr14.unsorted.BDKRB2_DHRS2.gtf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_unsorted_gtf/chr14.unsorted.BDKRB2_DHRS2.gtf -------------------------------------------------------------------------------- /tests/resources/test_unsorted_gtf/empty.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_unsorted_gtf/empty.vcf -------------------------------------------------------------------------------- /tests/resources/test_unsorted_gtf/forward_test.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_unsorted_gtf/forward_test.bam -------------------------------------------------------------------------------- /tests/resources/test_unsorted_gtf/forward_test.bam.bai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/test_unsorted_gtf/forward_test.bam.bai -------------------------------------------------------------------------------- /tests/resources/three_way_splice/expected_output/three_way_splice.mt.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/three_way_splice/expected_output/three_way_splice.mt.fa -------------------------------------------------------------------------------- /tests/resources/three_way_splice/expected_output/three_way_splice.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/three_way_splice/expected_output/three_way_splice.tsv -------------------------------------------------------------------------------- /tests/resources/three_way_splice/expected_output/three_way_splice.wt.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/three_way_splice/expected_output/three_way_splice.wt.fa -------------------------------------------------------------------------------- /tests/resources/three_way_splice/three_way_splice.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/three_way_splice/three_way_splice.bam -------------------------------------------------------------------------------- /tests/resources/three_way_splice/three_way_splice.gtf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/three_way_splice/three_way_splice.gtf -------------------------------------------------------------------------------- /tests/resources/three_way_splice/three_way_splice.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/koesterlab/microphaser/HEAD/tests/resources/three_way_splice/three_way_splice.vcf --------------------------------------------------------------------------------