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.gitignore
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# general patterns
.DS_Store
*.swp
*.a
CMakeCache.txt
cmake_install.cmake
CMakeFiles
.ninja_deps
.ninja_log
build.ninja
rules.ninja
# /
/CPackConfig.cmake
/CPackSourceConfig.cmake
/Makefile
/crux_version.h
/crux_version.h.txt
# /doc
/doc/user/Makefile
/doc/user/assign-confidence.html
/doc/user/bullseye.html
/doc/user/cascade-search.html
/doc/user/cmake_install.cmake
/doc/user/comet.html
/doc/user/create-docs.html
/doc/user/default.params
/doc/user/generate-peptides.html
/doc/user/get-ms2-spectrum.html
/doc/user/hardklor.html
/doc/user/localize-modification.html
/doc/user/make-pin.html
/doc/user/param-medic.html
/doc/user/param-table.html
/doc/user/percolator.html
/doc/user/pipeline.html
/doc/user/predict-peptide-ions.html
/doc/user/print-processed-spectra.html
/doc/user/psm-convert.html
/doc/user/read-tide-index.html
/doc/user/spectral-counts.html
/doc/user/subtract-index.html
/doc/user/tide-index.html
/doc/user/tide-search.html
/doc/user/commands/assign-confidence.html
/doc/user/commands/bullseye.html
/doc/user/commands/cascade-search.html
/doc/user/commands/comet.html
/doc/user/commands/create-docs.html
/doc/user/commands/default.params
/doc/user/commands/generate-peptides.html
/doc/user/commands/get-ms2-spectrum.html
/doc/user/commands/hardklor.html
/doc/user/commands/kojak.html
/doc/user/commands/localize-modification.html
/doc/user/commands/make-pin.html
/doc/user/commands/param-medic.html
/doc/user/commands/param-table.html
/doc/user/commands/percolator.html
/doc/user/commands/pipeline.html
/doc/user/commands/predict-peptide-ions.html
/doc/user/commands/print-processed-spectra.html
/doc/user/commands/psm-convert.html
/doc/user/commands/read-tide-index.html
/doc/user/commands/sort-by-column.html
/doc/user/commands/spectral-counts.html
/doc/user/commands/stat-column.html
/doc/user/commands/subtract-index.html
/doc/user/commands/tide-index.html
/doc/user/commands/tide-search.html
# /ext
/ext/Makefile
/ext/bin/
/ext/build/
/ext/downloads/
/ext/include/
/ext/lib/
/ext/share/
# /src
/src/**/Makefile
/src/app/tide/protoobj
/src/crux
# /test
/test/performance-tests/Makefile
/test/smoke-tests/Makefile
/test/smoke-tests/crux-output/
/test/smoke-tests/small_yeast_index/
/test/smoke-tests/small_yeast_index_mc1/
/test/smoke-tests/tide_test_index/
/test/smoke-tests/good_results/*.observed
/aws-sdk/build/
# added by Yang
Release/
src/.cproject
src/.project
src/.settings/language.settings.xml
doc/user