├── .gitignore ├── AUTHORS ├── COPYING ├── ChangeLog ├── Constant.h ├── Error.cpp ├── Error.h ├── INSTALL ├── LICENSE ├── Makefile.am ├── NEWS ├── PhredHelper.cpp ├── PhredHelper.h ├── README ├── README.md ├── bcf_chunked_reader.cpp ├── bcf_chunked_reader.h ├── bcf_filter_arg.h ├── bcf_filtered_reader.cpp ├── bcf_filtered_reader.h ├── bcf_ordered_reader.cpp ├── bcf_ordered_reader.h ├── bcf_variant_key.h ├── bcftools.h ├── bin ├── centos │ ├── README.md │ └── demuxlet └── macos │ ├── README.md │ └── demuxlet ├── cmd_cram_demuxlet.cpp ├── configure.ac ├── cramore.h ├── filter.cpp ├── filter.h ├── genomeChunk.cpp ├── genomeChunk.h ├── genomeLoci.h ├── genome_interval.cpp ├── genome_interval.h ├── hts_utils.cpp ├── hts_utils.h ├── interval.cpp ├── interval.h ├── interval_tree.cpp ├── interval_tree.h ├── pException.h ├── params.cpp ├── params.h ├── reference_sequence.cpp ├── reference_sequence.h ├── sam_filtered_reader.cpp ├── sam_filtered_reader.h ├── sc_drop_seq.cpp ├── sc_drop_seq.h ├── 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