├── .github └── workflows │ └── cmake.yml ├── .gitignore ├── .readthedocs.yaml ├── .travis.yml ├── CMakeLists.txt ├── Dockerfile ├── LICENSE ├── README.md ├── TODO.md ├── docs ├── about.md ├── commands │ ├── cis-ase-identify.md │ ├── cis-splice-effects-associate.md │ ├── cis-splice-effects-identify.md │ ├── commands.md │ ├── junctions-annotate.md │ ├── junctions-extract.md │ └── variants-annotate.md ├── images │ ├── anchor_examples.png │ ├── csei_examples.png │ ├── junction_annotation_examples.png │ ├── plot_anchor_examples.R │ ├── plot_csei_examples.R │ ├── plot_junction_annotation_examples.R │ ├── plot_variant_annotation_examples.R │ └── variant_annotation_examples.png ├── index.md └── workflow.md ├── mkdocs.yml ├── scripts ├── README.md ├── SpliceJunctionSummary.pm ├── annotate_spliceai_gtex.py ├── compare_junctions_hist.R ├── compare_junctions_hist.py ├── compare_junctions_hist_scRNA.R ├── compare_junctions_hist_v2.R ├── create_IGVsessions.py ├── create_mutually_exclusive.py ├── filter_and_BH.R ├── run_stats_modified.py ├── run_valgrind.sh ├── stats_wrapper.py ├── variants.sh └── vep_aws_workflow.py ├── src ├── cis-ase │ ├── CMakeLists.txt │ ├── bam_plcmd_regtools.c │ ├── beta_model.h │ ├── binomial_model.h │ ├── cis_ase_identifier.cc │ ├── cis_ase_identifier.h │ └── cis_ase_main.cc ├── cis-splice-effects │ ├── CMakeLists.txt │ ├── cis_splice_effects_associator.cc │ ├── cis_splice_effects_associator.h │ ├── cis_splice_effects_identifier.cc │ ├── cis_splice_effects_identifier.h │ └── cis_splice_effects_main.cc ├── gtf │ ├── CMakeLists.txt │ ├── gtf_parser.cc │ ├── gtf_parser.h │ ├── gtf_utils.cc │ └── gtf_utils.h ├── junctions │ ├── CMakeLists.txt │ ├── junctions_annotator.cc │ ├── junctions_annotator.h │ ├── junctions_extractor.cc │ ├── junctions_extractor.h │ └── junctions_main.cc ├── regtools.cc ├── utils │ ├── bedtools │ │ ├── CMakeLists.txt │ │ ├── bedFile │ │ │ ├── Makefile │ │ │ ├── bedFile.cpp │ │ │ └── bedFile.h │ │ ├── fileType │ │ │ ├── FileRecordTypeChecker.cpp │ │ │ ├── FileRecordTypeChecker.h │ │ │ ├── Makefile │ │ │ ├── fileType.cpp │ │ │ └── fileType.h │ │ ├── gzstream │ │ │ ├── COPYING.LIB │ │ │ ├── Makefile │ │ │ ├── README │ │ │ ├── gzstream.C │ │ │ ├── gzstream.h │ │ │ └── version │ │ └── lineFileUtilities │ │ │ └── lineFileUtilities.h │ ├── common.h │ ├── gtest-1.7.0 │ │ ├── CHANGES │ │ ├── CMakeLists.txt │ │ ├── CONTRIBUTORS │ │ ├── LICENSE │ │ ├── Makefile.am │ │ ├── Makefile.in │ │ ├── README │ │ ├── aclocal.m4 │ │ ├── build-aux │ │ │ ├── config.guess │ │ │ ├── config.h.in │ │ │ ├── config.sub │ │ │ ├── depcomp │ │ │ ├── install-sh │ │ │ ├── ltmain.sh │ │ │ └── missing │ │ ├── cmake │ │ │ └── internal_utils.cmake │ │ ├── codegear │ │ │ ├── gtest.cbproj │ │ │ ├── gtest.groupproj │ │ │ ├── gtest_all.cc │ │ │ ├── gtest_link.cc │ │ │ ├── gtest_main.cbproj │ │ │ └── gtest_unittest.cbproj │ │ ├── configure │ │ ├── configure.ac │ │ ├── fused-src │ │ │ └── gtest │ │ │ │ ├── gtest-all.cc │ │ │ │ ├── gtest.h │ │ │ │ └── gtest_main.cc │ │ ├── include │ │ │ └── gtest │ │ │ │ ├── gtest-death-test.h │ │ │ │ ├── gtest-message.h │ │ │ │ ├── gtest-param-test.h │ │ │ │ ├── gtest-param-test.h.pump │ │ │ │ ├── gtest-printers.h │ │ │ │ ├── gtest-spi.h │ │ │ │ ├── gtest-test-part.h │ │ │ │ ├── gtest-typed-test.h │ │ │ │ ├── gtest.h │ │ │ │ ├── gtest_pred_impl.h │ │ │ │ ├── gtest_prod.h │ │ │ │ └── internal │ │ │ │ ├── gtest-death-test-internal.h │ │ │ │ ├── gtest-filepath.h │ │ │ │ ├── gtest-internal.h │ │ │ │ ├── gtest-linked_ptr.h │ │ │ │ ├── gtest-param-util-generated.h │ │ │ │ ├── gtest-param-util-generated.h.pump │ │ │ │ ├── gtest-param-util.h │ │ │ │ ├── gtest-port.h │ │ │ │ ├── gtest-string.h │ │ │ │ ├── gtest-tuple.h │ │ │ │ ├── gtest-tuple.h.pump │ │ │ │ ├── gtest-type-util.h │ │ │ │ └── gtest-type-util.h.pump │ │ ├── m4 │ │ │ ├── acx_pthread.m4 │ │ │ ├── gtest.m4 │ │ │ ├── libtool.m4 │ │ │ ├── ltoptions.m4 │ │ │ ├── ltsugar.m4 │ │ │ ├── ltversion.m4 │ │ │ └── lt~obsolete.m4 │ │ ├── make │ │ │ └── Makefile │ │ ├── msvc │ │ │ ├── gtest-md.sln │ │ │ ├── gtest-md.vcproj │ │ │ ├── gtest.sln │ │ │ ├── gtest.vcproj │ │ │ ├── gtest_main-md.vcproj │ │ │ ├── gtest_main.vcproj │ │ │ ├── gtest_prod_test-md.vcproj │ │ │ ├── gtest_prod_test.vcproj │ │ │ ├── gtest_unittest-md.vcproj │ │ │ └── gtest_unittest.vcproj │ │ ├── samples │ │ │ ├── prime_tables.h │ │ │ ├── sample1.cc │ │ │ ├── sample1.h │ │ │ ├── sample10_unittest.cc │ │ │ ├── sample1_unittest.cc │ │ │ ├── sample2.cc │ │ │ ├── sample2.h │ │ │ ├── sample2_unittest.cc │ │ │ ├── sample3-inl.h │ │ │ ├── sample3_unittest.cc │ │ │ ├── sample4.cc │ │ │ ├── sample4.h │ │ │ ├── sample4_unittest.cc │ │ │ ├── sample5_unittest.cc │ │ │ ├── sample6_unittest.cc │ │ │ ├── sample7_unittest.cc │ │ │ ├── sample8_unittest.cc │ │ │ └── sample9_unittest.cc │ │ ├── scripts │ │ │ ├── fuse_gtest_files.py │ │ │ ├── gen_gtest_pred_impl.py │ │ │ ├── gtest-config.in │ │ │ ├── pump.py │ │ │ └── test │ │ │ │ └── Makefile │ │ ├── src │ │ │ ├── gtest-all.cc │ │ │ ├── gtest-death-test.cc │ │ │ ├── gtest-filepath.cc │ │ │ ├── gtest-internal-inl.h │ │ │ ├── gtest-port.cc │ │ │ ├── gtest-printers.cc │ │ │ ├── gtest-test-part.cc │ │ │ ├── gtest-typed-test.cc │ │ │ ├── gtest.cc │ │ │ └── gtest_main.cc │ │ ├── test │ │ │ ├── gtest-death-test_ex_test.cc │ │ │ ├── gtest-death-test_test.cc │ │ │ ├── gtest-filepath_test.cc │ │ │ ├── gtest-linked_ptr_test.cc │ │ │ ├── gtest-listener_test.cc │ │ │ ├── gtest-message_test.cc │ │ │ ├── gtest-options_test.cc │ │ │ ├── gtest-param-test2_test.cc │ │ │ ├── gtest-param-test_test.cc │ │ │ ├── gtest-param-test_test.h │ │ │ ├── gtest-port_test.cc │ │ │ ├── gtest-printers_test.cc │ │ │ ├── gtest-test-part_test.cc │ │ │ ├── gtest-tuple_test.cc │ │ │ ├── gtest-typed-test2_test.cc │ │ │ ├── gtest-typed-test_test.cc │ │ │ ├── gtest-typed-test_test.h │ │ │ ├── gtest-unittest-api_test.cc │ │ │ ├── gtest_all_test.cc │ │ │ ├── gtest_break_on_failure_unittest.py │ │ │ ├── gtest_break_on_failure_unittest_.cc │ │ │ ├── gtest_catch_exceptions_test.py │ │ │ ├── gtest_catch_exceptions_test_.cc │ │ │ ├── gtest_color_test.py │ │ │ ├── gtest_color_test_.cc │ │ │ ├── gtest_env_var_test.py │ │ │ ├── gtest_env_var_test_.cc │ │ │ ├── gtest_environment_test.cc │ │ │ ├── gtest_filter_unittest.py │ │ │ ├── gtest_filter_unittest_.cc │ │ │ ├── gtest_help_test.py │ │ │ ├── gtest_help_test_.cc │ │ │ ├── gtest_list_tests_unittest.py │ │ │ ├── gtest_list_tests_unittest_.cc │ │ │ ├── gtest_main_unittest.cc │ │ │ ├── gtest_no_test_unittest.cc │ │ │ ├── gtest_output_test.py │ │ │ ├── gtest_output_test_.cc │ │ │ ├── gtest_output_test_golden_lin.txt │ │ │ ├── gtest_pred_impl_unittest.cc │ │ │ ├── gtest_premature_exit_test.cc │ │ │ ├── gtest_prod_test.cc │ │ │ ├── gtest_repeat_test.cc │ │ │ ├── gtest_shuffle_test.py │ │ │ ├── gtest_shuffle_test_.cc │ │ │ ├── gtest_sole_header_test.cc │ │ │ ├── gtest_stress_test.cc │ │ │ ├── gtest_test_utils.py │ │ │ ├── gtest_throw_on_failure_ex_test.cc │ │ │ ├── gtest_throw_on_failure_test.py │ │ │ ├── gtest_throw_on_failure_test_.cc │ │ │ ├── gtest_uninitialized_test.py │ │ │ ├── gtest_uninitialized_test_.cc │ │ │ ├── gtest_unittest.cc │ │ │ ├── gtest_xml_outfile1_test_.cc │ │ │ ├── gtest_xml_outfile2_test_.cc │ │ │ ├── gtest_xml_outfiles_test.py │ │ │ ├── gtest_xml_output_unittest.py │ │ │ ├── gtest_xml_output_unittest_.cc │ │ │ ├── gtest_xml_test_utils.py │ │ │ ├── production.cc │ │ │ └── production.h │ │ └── xcode │ │ │ ├── Config │ │ │ ├── DebugProject.xcconfig │ │ │ ├── FrameworkTarget.xcconfig │ │ │ ├── General.xcconfig │ │ │ ├── ReleaseProject.xcconfig │ │ │ ├── StaticLibraryTarget.xcconfig │ │ │ └── TestTarget.xcconfig │ │ │ ├── Resources │ │ │ └── Info.plist │ │ │ ├── Samples │ │ │ └── FrameworkSample │ │ │ │ ├── Info.plist │ │ │ │ ├── WidgetFramework.xcodeproj │ │ │ │ └── project.pbxproj │ │ │ │ ├── runtests.sh │ │ │ │ ├── widget.cc │ │ │ │ ├── widget.h │ │ │ │ └── widget_test.cc │ │ │ ├── Scripts │ │ │ ├── runtests.sh │ │ │ └── versiongenerate.py │ │ │ └── gtest.xcodeproj │ │ │ └── project.pbxproj │ ├── htslib │ │ ├── CMakeLists.txt │ │ ├── INSTALL │ │ ├── LICENSE │ │ ├── Makefile │ │ ├── NEWS │ │ ├── README │ │ ├── README.md │ │ ├── bgzf.c │ │ ├── bgzip.c │ │ ├── config.h │ │ ├── config.h.in │ │ ├── config.mk.in │ │ ├── configure.ac │ │ ├── cram │ │ │ ├── cram.h │ │ │ ├── cram_codecs.c │ │ │ ├── cram_codecs.h │ │ │ ├── cram_decode.c │ │ │ ├── cram_decode.h │ │ │ ├── cram_encode.c │ │ │ ├── cram_encode.h │ │ │ ├── cram_external.c │ │ │ ├── cram_index.c │ │ │ ├── cram_index.h │ │ │ ├── cram_io.c │ │ │ ├── cram_io.h │ │ │ ├── cram_samtools.c │ │ │ ├── cram_samtools.h │ │ │ ├── cram_stats.c │ │ │ ├── cram_stats.h │ │ │ ├── cram_structs.h │ │ │ ├── files.c │ │ │ ├── mFILE.c │ │ │ ├── mFILE.h │ │ │ ├── md5.c │ │ │ ├── md5.h │ │ │ ├── misc.h │ │ │ ├── open_trace_file.c │ │ │ ├── open_trace_file.h │ │ │ ├── os.h │ │ │ ├── pooled_alloc.c │ │ │ ├── pooled_alloc.h │ │ │ ├── rANS_byte.h │ │ │ ├── rANS_static.c │ │ │ ├── rANS_static.h │ │ │ ├── sam_header.c │ │ │ ├── sam_header.h │ │ │ ├── string_alloc.c │ │ │ ├── string_alloc.h │ │ │ ├── thread_pool.c │ │ │ ├── thread_pool.h │ │ │ ├── vlen.c │ │ │ ├── vlen.h │ │ │ ├── zfio.c │ │ │ └── zfio.h │ │ ├── faidx.5 │ │ ├── faidx.c │ │ ├── hfile.c │ │ ├── hfile_internal.h │ │ ├── hfile_irods.c │ │ ├── hfile_libcurl.c │ │ ├── hfile_net.c │ │ ├── hts.c │ │ ├── hts_internal.h │ │ ├── htsfile.1 │ │ ├── htsfile.c │ │ ├── htslib.mk │ │ ├── htslib.pc.in │ │ ├── htslib │ │ │ ├── bgzf.h │ │ │ ├── cram.h │ │ │ ├── faidx.h │ │ │ ├── hfile.h │ │ │ ├── hts.h │ │ │ ├── hts_defs.h │ │ │ ├── kbitset.h │ │ │ ├── kfunc.h │ │ │ ├── khash.h │ │ │ ├── khash_str2int.h │ │ │ ├── klist.h │ │ │ ├── knetfile.h │ │ │ ├── kseq.h │ │ │ ├── ksort.h │ │ │ ├── kstring.h │ │ │ ├── regidx.h │ │ │ ├── sam.h │ │ │ ├── synced_bcf_reader.h │ │ │ ├── tbx.h │ │ │ ├── vcf.h │ │ │ ├── vcf_sweep.h │ │ │ └── vcfutils.h │ │ ├── htslib_vars.mk │ │ ├── kfunc.c │ │ ├── knetfile.c │ │ ├── kstring.c │ │ ├── md5.c │ │ ├── plugin.c │ │ ├── regidx.c │ │ ├── sam.5 │ │ ├── sam.c │ │ ├── synced_bcf_reader.c │ │ ├── tabix.1 │ │ ├── tabix.c │ │ ├── tbx.c │ │ ├── vcf.5 │ │ ├── vcf.c │ │ ├── vcf_sweep.c │ │ ├── vcfutils.c │ │ └── version.h │ ├── rmath │ │ ├── CMakeLists.txt │ │ ├── Make.inc │ │ ├── Makefile │ │ ├── Rmath │ │ │ ├── R_ext │ │ │ │ ├── Arith.h │ │ │ │ ├── Boolean.h │ │ │ │ ├── Error.h │ │ │ │ ├── Print.h │ │ │ │ ├── RS.h │ │ │ │ ├── Random.h │ │ │ │ └── libextern.h │ │ │ ├── Rconfig.h │ │ │ ├── Rmath.h │ │ │ ├── Rmath.h0 │ │ │ └── config.h │ │ ├── bd0.c │ │ ├── bessel.h │ │ ├── bessel_i.c │ │ ├── bessel_j.c │ │ ├── bessel_k.c │ │ ├── bessel_y.c │ │ ├── beta.c │ │ ├── chebyshev.c │ │ ├── choose.c │ │ ├── d1mach.c │ │ ├── dbeta.c │ │ ├── dbinom.c │ │ ├── dcauchy.c │ │ ├── dchisq.c │ │ ├── dexp.c │ │ ├── df.c │ │ ├── dgamma.c │ │ ├── dgeom.c │ │ ├── dhyper.c │ │ ├── dlnorm.c │ │ ├── dlogis.c │ │ ├── dnbeta.c │ │ ├── dnbinom.c │ │ ├── dnchisq.c │ │ ├── dnf.c │ │ ├── dnorm.c │ │ ├── dnt.c │ │ ├── dpois.c │ │ ├── dpq.h │ │ ├── dt.c │ │ ├── dunif.c │ │ ├── dweibull.c │ │ ├── expm1.c │ │ ├── fmax2.c │ │ ├── fmin2.c │ │ ├── fprec.c │ │ ├── fround.c │ │ ├── fsign.c │ │ ├── ftrunc.c │ │ ├── gamma.c │ │ ├── gamma_cody.c │ │ ├── gammalims.c │ │ ├── i1mach.c │ │ ├── imax2.c │ │ ├── imin2.c │ │ ├── lbeta.c │ │ ├── lgamma.c │ │ ├── lgammacor.c │ │ ├── librandom.c │ │ ├── log1p.c │ │ ├── mlutils.c │ │ ├── nmath.h │ │ ├── pbeta.c │ │ ├── pbinom.c │ │ ├── pcauchy.c │ │ ├── pchisq.c │ │ ├── pexp.c │ │ ├── pf.c │ │ ├── pgamma.c │ │ ├── pgeom.c │ │ ├── phyper.c │ │ ├── plnorm.c │ │ ├── plogis.c │ │ ├── pnbeta.c │ │ ├── pnbinom.c │ │ ├── pnchisq.c │ │ ├── pnf.c │ │ ├── pnorm.c │ │ ├── pnt.c │ │ ├── polygamma.c │ │ ├── ppois.c │ │ ├── pt.c │ │ ├── ptukey.c │ │ ├── punif.c │ │ ├── pweibull.c │ │ ├── qbeta.c │ │ ├── qbinom.c │ │ ├── qcauchy.c │ │ ├── qchisq.c │ │ ├── qexp.c │ │ ├── qf.c │ │ ├── qgamma.c │ │ ├── qgeom.c │ │ ├── qhyper.c │ │ ├── qlnorm.c │ │ ├── qlogis.c │ │ ├── qnbeta.c │ │ ├── qnbinom.c │ │ ├── qnchisq.c │ │ ├── qnf.c │ │ ├── qnorm.c │ │ ├── qnt.c │ │ ├── qpois.c │ │ ├── qt.c │ │ ├── qtukey.c │ │ ├── qunif.c │ │ ├── qweibull.c │ │ ├── randmtzig.c │ │ ├── rbeta.c │ │ ├── rbinom.c │ │ ├── rcauchy.c │ │ ├── rchisq.c │ │ ├── rexp.c │ │ ├── rf.c │ │ ├── rgamma.c │ │ ├── rgeom.c │ │ ├── rhyper.c │ │ ├── rlnorm.c │ │ ├── rlogis.c │ │ ├── rmultinom.c │ │ ├── rnbinom.c │ │ ├── rnchisq.c │ │ ├── rnorm.c │ │ ├── rpois.c │ │ ├── rt.c │ │ ├── runif.c │ │ ├── rweibull.c │ │ ├── sexp.c │ │ ├── sign.c │ │ ├── signrank.c │ │ ├── snorm.c │ │ ├── stirlerr.c │ │ ├── sunif.c │ │ ├── toms708.c │ │ └── wilcox.c │ └── samtools │ │ ├── AUTHORS │ │ ├── CMakeLists.txt │ │ ├── ChangeLog.old │ │ ├── INSTALL │ │ ├── LICENSE │ │ ├── Makefile │ │ ├── Makefile.mingw │ │ ├── NEWS │ │ ├── README │ │ ├── README.md │ │ ├── bam.c │ │ ├── bam.h │ │ ├── bam2bcf.c │ │ ├── bam2bcf.h │ │ ├── bam2bcf_indel.c │ │ ├── bam2depth.c │ │ ├── bam_addrprg.c │ │ ├── bam_aux.c │ │ ├── bam_cat.c │ │ ├── bam_color.c │ │ ├── bam_endian.h │ │ ├── bam_flags.c │ │ ├── bam_import.c │ │ ├── bam_index.c │ │ ├── bam_lpileup.c │ │ ├── bam_lpileup.h │ │ ├── bam_mate.c │ │ ├── bam_md.c │ │ ├── bam_plbuf.c │ │ ├── bam_plbuf.h │ │ ├── bam_plcmd.c │ │ ├── bam_plcmd.h │ │ ├── bam_plcmd_regtools.c │ │ ├── bam_quickcheck.c │ │ ├── bam_reheader.c │ │ ├── bam_rmdup.c │ │ ├── bam_rmdupse.c │ │ ├── bam_sort.c │ │ ├── bam_split.c │ │ ├── bam_stat.c │ │ ├── bam_tview.c │ │ ├── bam_tview.h │ │ ├── bam_tview_curses.c │ │ ├── bam_tview_html.c │ │ ├── bamshuf.c │ │ ├── bamtk.c │ │ ├── bedcov.c │ │ ├── bedidx.c │ │ ├── config.h │ │ ├── config.h.in │ │ ├── config.mk │ │ ├── config.mk.in │ │ ├── configure.ac │ │ ├── cut_target.c │ │ ├── dict.c │ │ ├── errmod.c │ │ ├── errmod.h │ │ ├── faidx.c │ │ ├── install-sh │ │ ├── kprobaln.c │ │ ├── kprobaln.h │ │ ├── padding.c │ │ ├── phase.c │ │ ├── sam.c │ │ ├── sam.h │ │ ├── sam_header.c │ │ ├── sam_header.h │ │ ├── sam_opts.c │ │ ├── sam_opts.h │ │ ├── sam_view.c │ │ ├── sample.c │ │ ├── sample.h │ │ ├── samtools.1 │ │ ├── samtools.h │ │ ├── stats.c │ │ ├── stats_isize.c │ │ └── stats_isize.h ├── variants │ ├── CMakeLists.txt │ ├── variants_annotator.cc │ ├── variants_annotator.h │ └── variants_main.cc └── version.h.in └── tests ├── integration-test ├── CMakeLists.txt ├── data │ ├── bam │ │ ├── cis_ase_tumor_dna.bam │ │ ├── cis_ase_tumor_dna.bam.bai │ │ ├── cis_ase_tumor_rna.bam │ │ ├── cis_ase_tumor_rna.bam.bai │ │ ├── test_hcc1395.2.bam │ │ ├── test_hcc1395.2.bam.bai │ │ ├── test_hcc1395.bam │ │ └── test_hcc1395.bam.bai │ ├── bed │ │ ├── junctions.chr22.bed │ │ └── test_hcc1395_junctions.bed │ ├── cis-ase-identify │ │ ├── expected-cis-ase-identify-B.out │ │ ├── expected-cis-ase-identify-E.out │ │ └── expected-cis-ase-identify-default.out │ ├── cis-splice-effects-associate │ │ └── junctions_extract.bed │ ├── cis-splice-effects-identify │ │ ├── expected-cis-splice-effects-identify-default-annotatedjunctions.out │ │ ├── expected-cis-splice-effects-identify-default-annotatedvariants.out │ │ ├── expected-cis-splice-effects-identify-default-junctions.out │ │ ├── expected-cis-splice-effects-identify-default-stranded-annotatedjunctions.out │ │ ├── expected-cis-splice-effects-identify-default-stranded-annotatedvariants.out │ │ ├── expected-cis-splice-effects-identify-default-stranded-junctions.out │ │ └── expected-cis-splice-effects-identify-default.out │ ├── fa │ │ ├── test_chr22.fa │ │ └── test_chr22.fa.fai │ ├── gtf │ │ ├── test_ensemble_chr22.2.gtf │ │ ├── test_ensemble_chr22.3.gtf │ │ └── test_ensemble_chr22.gtf │ ├── hcc1395_igv_session.xml │ ├── junctions-annotate │ │ └── expected-annotate.out │ ├── junctions-extract │ │ ├── expected-a.out │ │ ├── expected-a30.out │ │ ├── expected-i8039-I8039.out │ │ ├── expected-r1:22405013-22405020.out │ │ ├── expected-stranded-a.out │ │ └── expected-stranded-a30.out │ ├── variants-annotate │ │ ├── expected-annotate-E-i6.out │ │ ├── expected-annotate-E.out │ │ ├── expected-annotate-I.out │ │ ├── expected-annotate-default.out │ │ ├── expected-annotate-e6-I.out │ │ └── expected-annotate-e6-i6-S.out │ └── vcf │ │ ├── test1.vcf │ │ ├── test2.vcf │ │ ├── test3.vcf │ │ ├── test4.vcf.gz │ │ └── test4.vcf.gz.tbi ├── test_cis_ase_identify.py ├── test_cis_splice_effects_associate.py ├── test_cis_splice_effects_identify.py ├── test_cis_splice_effects_main.py ├── test_junctions_annotate.py ├── test_junctions_extract.py ├── test_junctions_main.py ├── test_regtools_main.py ├── test_variants_annotate.py └── test_variants_main.py └── lib ├── CMakeLists.txt ├── cis-ase ├── CMakeLists.txt ├── test_beta_model.cc └── test_binomial_model.cc ├── cis-splice-effects ├── CMakeLists.txt └── test_cis_splice_effects_identifier.cc ├── gtf ├── CMakeLists.txt └── test_gtf_parser.cc ├── junctions ├── CMakeLists.txt ├── test_junctions_annotator.cc └── test_junctions_extractor.cc └── variants ├── CMakeLists.txt └── test_variants_annotator.cc /.github/workflows/cmake.yml: 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