├── .gitignore ├── CMakeLists.txt ├── Constant.h ├── Dockerfile ├── Error.cpp ├── Error.h ├── IO.cpp ├── IO.h ├── LICENSE ├── PhredHelper.cpp ├── PhredHelper.h ├── README.md ├── allele.cpp ├── allele.h ├── bam_ordered_reader.cpp ├── bam_ordered_reader.h ├── bcf_chunked_reader.cpp ├── bcf_chunked_reader.h ├── bcf_filter_arg.h ├── bcf_filtered_reader.cpp ├── bcf_filtered_reader.h ├── bcf_variant_key.h ├── bcftools.h ├── bgzf.h ├── cmd_cram_demuxlet.cpp ├── cmd_cram_digital_pileup.cpp ├── cmd_cram_dsc_dump.cpp ├── cmd_cram_dsc_dump2pileup.cpp ├── cmd_cram_dsc_pileup.cpp ├── cmd_cram_freemux2.cpp ├── cmd_cram_freemuxlet.cpp ├── cmd_cram_gtf_util.cpp ├── cmd_cram_mux_pileup.cpp ├── cmd_cram_simuxlet.cpp ├── cmd_plp_find_mux_clust.cpp ├── cmd_plp_make_dge_matrix.cpp ├── cmd_sc_kallisto_count.cpp ├── cmd_sc_map_stamps.cpp ├── cmd_sc_multinom_em.cpp ├── cmd_sc_multinom_gibbs.cpp ├── commands.cpp ├── commands.h ├── cramore.cpp ├── cramore.h ├── discrete_log_helper.h ├── dropseq.cpp ├── dropseq.h ├── entrypoint.sh ├── filter.cpp ├── filter.h ├── genomeChunk.cpp ├── genomeChunk.h ├── genomeLoci.h ├── genome_interval.cpp ├── genome_interval.h ├── gtf.cpp ├── gtf.h ├── gtf_interval_tree.h ├── hts_utils.cpp ├── hts_utils.h ├── interval.cpp ├── interval.h ├── interval_tree.cpp ├── interval_tree.h ├── log_tool.cpp ├── log_tool.h ├── louvain.h ├── pException.h ├── params.cpp ├── params.h ├── reference_sequence.cpp ├── reference_sequence.h ├── sam_filtered_reader.cpp ├── sam_filtered_reader.h ├── sam_ordered_writer.cpp ├── sam_ordered_writer.h ├── sc_drop_seq.cpp ├── sc_drop_seq.h ├── tsv_reader.cpp ├── tsv_reader.h ├── tutorials ├── README_atac.md ├── README_vcf.md └── YeLab_scRNAseq_exome_variants.bed ├── utils.cpp ├── utils.h ├── variant.cpp ├── variant.h ├── variant_manip.cpp ├── variant_manip.h ├── vntr.cpp └── vntr.h /.gitignore: -------------------------------------------------------------------------------- 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