├── .circleci ├── config.yml └── setup.sh ├── .gitignore ├── LICENSE ├── README.md ├── doc ├── imgs │ ├── 4_115928726_115931880.d100.genes_reps_map.png │ ├── 4_115928726_115931880.d100.png │ ├── 4_115928726_115931880.png │ ├── X_101055330_101067156.png │ ├── cramX_101055330_101067156.png │ ├── linkedread_del.png │ ├── longread_del.png │ ├── longread_inv.png │ ├── longread_nanopore_del.png │ ├── longread_nanopore_dup.png │ ├── montage.jpg │ └── samplot_logo_v5.png └── imgs_v2 │ ├── 11_67974432_67975639_DUP_hg002.png │ ├── 11_67974432_67975639_DUP_trio.png │ ├── 12_12544868_12546613_INV_hg002.png │ ├── 12_12544868_12546613_INV_trio.png │ ├── 19_12694867_12698924_DEL_hg002.png │ ├── 19_12694867_12698924_DEL_trio.png │ ├── 1_24804398_24807302_DEL_10X.png │ ├── 1_24804398_24807302_DEL_ONT.png │ ├── 1_24804398_24807302_DEL_PacBio.png │ ├── 1_24804398_24807302_DEL_hg002.png │ ├── 1_24804398_24807302_DEL_trio.png │ ├── 1_24804398_24807302_DEL_zoom.png │ ├── 1_43059290_43059950_NA_hg002.png │ ├── 1_43059290_43059950_NA_trio.png │ ├── 4_99813787_99817098_DUP_hg002.png │ └── 4_99813787_99817098_DUP_trio.png ├── requirements.txt ├── runtests.sh ├── samplot ├── __init__.py ├── __main__.py ├── samplot.py ├── samplot_vcf.py └── templates │ └── samplot_vcf.html ├── setup.py ├── ssshtest └── test ├── README.md ├── data ├── 2_59305747-59505747_X_151018513-151218513.BND.bam ├── 2_59305747-59505747_X_151018513-151218513.BND.bam.bai ├── Alu.2_X.bed.gz ├── Alu.2_X.bed.gz.tbi ├── Alu.2_X.csionly.bed.gz ├── Alu.2_X.csionly.bed.gz.csi ├── HG002_10X.bam ├── HG002_10X.bam.bai ├── HG002_1_89475845-89478561_DEL.tenx.bam ├── HG002_1_89475845-89478561_DEL.tenx.bam.bai ├── HG002_Illumina.bam ├── HG002_Illumina.bam.bai ├── HG002_ONT.cram ├── HG002_ONT.cram.crai ├── HG002_PacBio.bam ├── HG002_PacBio.bam.bai ├── HG003_Illumina.bam ├── HG003_Illumina.bam.bai ├── HG004_Illumina.bam ├── HG004_Illumina.bam.bai ├── Homo_sapiens.GRCh37.82.sort.2_X.gff3.gz ├── Homo_sapiens.GRCh37.82.sort.2_X.gff3.gz.tbi ├── Homo_sapiens.GRCh37.csionly.2_X.gff3.gz ├── Homo_sapiens.GRCh37.csionly.2_X.gff3.gz.csi ├── NA12878_restricted.bam ├── NA12878_restricted.bam.bai ├── NA12889_restricted.bam ├── NA12889_restricted.bam.bai ├── NA12890_restricted.bam ├── NA12890_restricted.bam.bai ├── README.md ├── commands.sh ├── examples.bed ├── examples_padded.bed ├── hg19_chr1_58343117_58343622_deletion.bam ├── hg19_chr1_58343117_58343622_deletion.bam.bai ├── hg19_chr21_27373431_27375410_inversion.bam ├── hg19_chr21_27373431_27375410_inversion.bam.bai ├── nanopore-NA12878.bam ├── nanopore-NA12878.bam.bai ├── subset_alignments.sh ├── test.ped ├── test.vcf ├── test_imgs │ ├── 1_43059290_43059950.png │ ├── DEL_1_24804397_24807302.png │ ├── DUP_11_67974431_67975639.png │ ├── DUP_4_99813786_99817098.png │ ├── DUP_4_99813786_99817098_zoom.png │ ├── INV_12_12544867_12546613.png │ ├── trio_DEL_1_24804397_24807302.png │ ├── trio_DUP_11_67974431_67975639.png │ ├── trio_DUP_4_99813786_99817098.png │ └── 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