BED feature#45

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isovic wants to merge 49 commits intomasterfrom

Commits on Sep 7, 2020

Added a CLI option '--bed' to specify a BED file with regions to polish.
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Now storing the start position of every window in the Window class.
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Added a operator<< to Window for debugging purposes.
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The polisher can now fill in the gap in between windows if they are far apart using the original sequence.
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Minor refactor in src/polisher.cpp - extracted the window creation code into a separate function for scoping.
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Added the suffix portion of the target sequence after the last window.
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Implemented a simple BED parser and added unit tests.
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The createPolisher function now accepts a BED file path and parses it.
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Added the interval tree library.
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Minor refactor, extracted the function transmuteId from overlap.cpp to a new file util.hpp.
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Now constructing the interval trees for the given BED records, and validating that there aren't any regions which overlap.
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Added t_begin() and t_end() to Overlap.
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Implemented overlap filtering when BED is specified, to remove overlaps outside of regions of interest.
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Now storing the intervals in the Polisher too, and sorting them right before the trees are constructed (will be useful later).
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Added the end_ coordinate to the Window class.
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Minor fix, should be squashed with previous.
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Added BED coordinate sanity check to src/bed.cpp.
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Added a verbose of the window end coordinate in src/window.cpp.
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Working on the new Polisher::create_and_populate_windows_with_bed. Right now only generating empty windows for the BED regions.
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Renamed the target_interva_s and target_trees_ to target_bed_intervals_ and target_bed_trees_, and added the trees for the windows.
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Expanded the Overlap::breaking_points_ to be a tuple and store the window ID as well.
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Added src/util.cpp and moved the IntervalTree typedefs to util.hpp. Added a placeholder for a generic function to find window breaking points base on supplied windows.
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Removed the intervaltree/interval_tree_test.cpp from vendor/meson.build because these tests hijacked my unit tests.
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Implemented a generic window splitting function generate_window_breakpoints in util.*. It breaks the alignment into supplied windows.
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Added unit tests for generate_window_breakpoints from util.* to test/util_test.cpp.
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The Overlap::find_breaking_points_from_cigar now uses the utility function generate_window_breakpoints.
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Added overloaded versions of the Overlap::find_breaking_points_from_cigar and Overlap::find_breaking_points which take a set of windows.
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Implemented the BED-selected polishing in polisher.*.
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Now writing the unpolished sequences with no BED windows.
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Updated CMakeLists.txt to compile the new code and tests.
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Added missing include to src/bed.hpp.
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Updated the initializer list in test/bed_test.cpp.
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Updated the initializer list in test/util_test.cpp.
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Updated the test initializer lists in test/bed_test.cpp.
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Updated the initializer lists in test/util_test.cpp.
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Updated the initializer lists in src/bed.cpp.
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Updated the initializer lists in src/util.cpp
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Fixed the operator<< for WindowInterval in src/util.hpp.
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Added operator<< to Overlap in src/overlap.hpp.
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Removed the legacy windowing code in src/polisher.cpp, it was buggy in the new context (the window_id was wrong). Cleanup of unused legacy code in src/polisher.hpp.
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Removed the deprecated code from ../src/overlap.hpp and ../src/overlap.cpp.
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Trying to fix an off-by-1 error.
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Reverted the off-by-1 in src/polisher.cpp.
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Fixed a bug in src/polisher.cpp window creation when BED is not used - the last window had an extra base. Interestingly, ASAN didn't complain. Also, fixed an off-by-1 error in src/util.cpp when pre…
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Minor change in logging.
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Fixed the include for the IntervalTree library in CMakeLists.txt.
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Minor bugfix with the windowing - the window start offset was still being calculated via division, while the windowing may actually begin at an arbitrary coordinate.
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Commits on Sep 8, 2020