├── .gitignore ├── CMakeLists.txt ├── Doxyfile ├── LICENSE ├── README ├── README.devel.org ├── express.xcodeproj ├── adarob.mode1v3 ├── adarob.pbxuser ├── project.pbxproj ├── project.xcworkspace │ ├── contents.xcworkspacedata │ └── xcuserdata │ │ └── adarob.xcuserdatad │ │ ├── UserInterfaceState.xcuserstate │ │ └── WorkspaceSettings.xcsettings └── xcuserdata │ └── adarob.xcuserdatad │ ├── xcdebugger │ └── Breakpoints.xcbkptlist │ └── xcschemes │ ├── express.xcscheme │ └── xcschememanagement.plist ├── html ├── css │ ├── googlesearch.css │ ├── mf54_content.css │ ├── mf54_grid.css │ └── mf54_reset.css ├── downloads │ ├── express-0.9.0 │ │ ├── express-0.9.0-linux_x86_64.tgz │ │ ├── express-0.9.0-macosx_x86_64.tgz │ │ └── express-0.9.0-src.tgz │ ├── express-0.9.1 │ │ ├── express-0.9.1-linux_x86_64.tgz │ │ ├── express-0.9.1-macosx_x86_64.tgz │ │ └── express-0.9.1-src.tgz │ ├── express-0.9.2 │ │ ├── express-0.9.2-linux_x86_64.tgz │ │ ├── express-0.9.2-macosx_x86_64.tgz │ │ └── express-0.9.2-src.tgz │ ├── express-0.9.3 │ │ ├── express-0.9.3-linux_x86_64.tgz │ │ ├── express-0.9.3-macosx_x86_64.tgz │ │ ├── express-0.9.3-src.tgz │ │ └── express-0.9.3-win32_x86_64.zip │ ├── express-0.9.4 │ │ ├── express-0.9.4-linux_x86_64.tgz │ │ ├── express-0.9.4-macosx_x86_64.tgz │ │ ├── express-0.9.4-src.tgz │ │ └── express-0.9.4-win32_x86_64.zip │ ├── express-0.9.5 │ │ ├── express-0.9.5-linux_x86_64.tgz │ │ ├── express-0.9.5-macosx_x86_64.tgz │ │ ├── express-0.9.5-src.tgz │ │ └── express-0.9.5-win32_x86_64.zip │ ├── express-1.0.0 │ │ ├── express-1.0.0-linux_x86_64.tgz │ │ ├── express-1.0.0-macosx_x86_64.tgz │ │ ├── express-1.0.0-src.tgz │ │ └── express-1.0.0-win32_x86_64.zip │ ├── express-1.1.0 │ │ ├── express-1.1.0-linux_x86_64.tgz │ │ ├── express-1.1.0-macosx_x86_64.tgz │ │ ├── express-1.1.0-src.tgz │ │ └── express-1.1.0-win32_x86_64.zip │ ├── express-1.1.1 │ │ ├── express-1.1.1-linux_x86_64.tgz │ │ ├── express-1.1.1-macosx_x86_64.tgz │ │ ├── express-1.1.1-src.tgz │ │ └── express-1.1.1-win32_x86_64.zip │ ├── express-1.2.0 │ │ ├── express-1.2.0-linux_x86_64.tgz │ │ ├── express-1.2.0-macosx_x86_64.tgz │ │ ├── express-1.2.0-src.tgz │ │ └── express-1.2.0-win32_x86_64.zip │ ├── express-1.2.1 │ │ ├── express-1.2.1-linux_x86_64.tgz │ │ ├── express-1.2.1-macosx_x86_64.tgz │ │ ├── express-1.2.1-src.tgz │ │ └── express-1.2.1-win32_x86_64.zip │ ├── express-1.2.2 │ │ ├── express-1.2.2-linux_x86_64.tgz │ │ ├── express-1.2.2-macosx_x86_64.tgz │ │ ├── express-1.2.2-src.tgz │ │ └── express-1.2.2-win32_x86_64.zip │ ├── express-1.3.0 │ │ ├── express-1.3.0-linux_x86_64.tgz │ │ ├── express-1.3.0-macosx_x86_64.tgz │ │ ├── express-1.3.0-src.tgz │ │ └── express-1.3.0-win32_x86_64.zip │ ├── express-1.4.0 │ │ ├── express-1.4.0-macosx_x86_64.tgz │ │ ├── express-1.4.0-src.tgz │ │ └── express-1.4.0-win32_x86_64.zip │ ├── express-1.4.1 │ │ ├── express-1.4.1-linux_x86_64.tgz │ │ ├── express-1.4.1-macosx_x86_64.tgz │ │ ├── express-1.4.1-src.tgz │ │ └── express-1.4.1-win32_x86_64.zip │ ├── express-1.5.0 │ │ ├── express-1.5.0-linux_x86_64.tgz │ │ ├── express-1.5.0-macosx_x86_64.tgz │ │ ├── express-1.5.0-src.tgz │ │ └── express-1.5.0-win32_x86_64.zip │ └── express-1.5.1 │ │ ├── express-1.5.1-linux_x86_64.tgz │ │ ├── express-1.5.1-macosx_x86_64.tgz │ │ ├── express-1.5.1-src.tgz │ │ └── express-1.5.1-win32_x86_64.zip ├── faq.html ├── img │ ├── berkeley_seal.gif │ ├── bg_bullet_arrow.gif │ ├── bg_bullet_square.gif │ ├── bg_corner_content_1col_bottom.gif │ ├── bg_corner_content_1col_top.gif │ ├── bg_corner_content_2col_bottom.gif │ ├── bg_corner_content_2col_top.gif │ ├── bg_corner_content_nosidebar_1col_bottom.gif │ ├── bg_corner_content_nosidebar_1col_top.gif │ ├── bg_corner_content_nosidebar_2col_bottom.gif │ ├── bg_corner_content_nosidebar_2col_top.gif │ ├── bg_corner_content_nosidebar_3col_bottom.gif │ ├── bg_corner_content_nosidebar_3col_top.gif │ ├── bg_corner_page_bottom.gif │ ├── bg_corner_page_top.gif │ ├── bg_corner_subcontent_bottom.gif │ ├── bg_corner_subcontent_top.gif │ ├── bg_corner_top_white.gif │ ├── image.jpg │ ├── logo.png │ ├── logo_small.png │ └── logo_yellow.png ├── index.html ├── manual.html ├── overview.html └── tutorial.html ├── linux_build └── src │ └── express ├── osx_build └── src │ └── express ├── package.sh ├── sample_data ├── reads_1.fastq ├── reads_2.fastq └── transcripts.fasta ├── src ├── CMakeLists.txt ├── alignments.proto ├── biascorrection.cpp ├── biascorrection.h ├── bundles.cpp ├── bundles.h ├── config.h.in ├── directiondetector.cpp ├── directiondetector.h ├── fragments.cpp ├── fragments.h ├── frequencymatrix.h ├── lengthdistribution.cpp ├── lengthdistribution.h ├── library.h ├── logger.h ├── main.cpp ├── main.h ├── mapparser.cpp ├── mapparser.h ├── markovmodel.cpp ├── markovmodel.h ├── mismatchmodel.cpp ├── mismatchmodel.h ├── robertsfilter.cpp ├── robertsfilter.h ├── sequence.cpp ├── sequence.h ├── targets.cpp ├── targets.h ├── targets.proto ├── threadsafety.cpp ├── threadsafety.h └── 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