├── .github └── workflows │ └── tests.yml ├── .gitignore ├── .gitmodules ├── .zenodo.json ├── BUILD.md ├── CMakeLists.txt ├── CONTRIBUTING.md ├── LICENSE ├── PackageInfo.cmake ├── README.md ├── cmake ├── BuildBoost.cmake ├── BuildSamtools.cmake └── CodeCoverage.cmake ├── debian ├── postinst.in └── prerm.in ├── integration-test ├── CMakeLists.txt ├── bam-readcount_test.py └── testdata.py.in ├── src ├── exe │ └── bam-readcount │ │ ├── CMakeLists.txt │ │ └── bamreadcount.cpp └── lib │ └── bamrc │ ├── BasicStat.cpp │ ├── BasicStat.hpp │ ├── CMakeLists.txt │ ├── IndelQueue.cpp │ ├── IndelQueue.hpp │ ├── IndelQueueEntry.cpp │ ├── IndelQueueEntry.hpp │ ├── ReadWarnings.hpp │ └── auxfields.hpp ├── test-data ├── cram_site_test.sh ├── expected_all_lib ├── expected_insertion_centric_all_lib ├── expected_insertion_centric_per_lib ├── expected_per_lib ├── rand1k.fa ├── rand1k.fa.fai ├── ref.fa ├── ref.fa.fai ├── site_list ├── test.bam ├── test.bam.bai ├── test_bad_rg.bam ├── test_bad_rg.bam.bai ├── twolib.sorted.cram ├── twolib.sorted.cram.crai └── twolib_site_list.txt ├── test └── lib │ └── bamrc │ ├── CMakeLists.txt │ ├── TestAuxFields.cpp │ ├── TestIndelQueue.cpp │ ├── TestIndelQueueEntry.cpp │ └── TestReadWarnings.cpp ├── tutorial ├── .gitignore ├── README.md ├── plots │ ├── vaf_vs_avg_basequality.png │ └── vaf_vs_avg_pos_as_fraction.png └── scripts │ ├── clean.sh │ ├── commands.sh │ ├── make_commands.sh │ ├── parse_brc.py │ ├── plot_vaf_vs_avg_bq.py │ └── plot_vaf_vs_avg_pos.py ├── vendor ├── Makefile.disable_curl.patch ├── README.md ├── boost-1.55-bamrc.tar.gz ├── bzip2-1.0.8.tar.gz ├── curl-7.67.0.tar.gz ├── mbedtls-2.16.4-apache.tgz ├── samtools-1.10.tar.bz2 ├── xz-5.2.4.tar.gz └── zlib-1.2.11.tar.gz └── version └── version.h.in /.github/workflows/tests.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/genome/bam-readcount/HEAD/.github/workflows/tests.yml 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