├── .gitignore ├── .gitmodules ├── LICENSE ├── README.md ├── dataset ├── query.fa ├── ref.fa └── sequences.fa ├── hardware ├── README.md ├── TALCO-WFAA │ ├── hdl │ │ ├── BRAM.sv │ │ ├── TALCO_WFAA.sv │ │ ├── WFAReduce.sv │ │ ├── compute_conv.sv │ │ ├── tb.sv │ │ ├── thresholdCalc.sv │ │ └── traceback.sv │ ├── host │ │ └── main.cpp │ └── openroad │ │ ├── Makefile │ │ └── config │ │ ├── config.mk │ │ └── constraint.sdc ├── TALCO-XDrop │ ├── hdl │ │ ├── BRAM.sv │ │ ├── DPBram.sv │ │ ├── PE.sv │ │ ├── PE_Array.sv │ │ ├── TALCO_XDrop.sv │ │ ├── ascii2nt.sv │ │ ├── nt2param.sv │ │ ├── reduction_tree.sv │ │ ├── tb.sv │ │ ├── top.v │ │ └── traceback.sv │ ├── host │ │ └── main.cpp │ └── openroad │ │ ├── Makefile │ │ ├── config │ │ ├── config.mk │ │ └── constraint.sdc │ │ └── rtl │ │ ├── gcd.sv │ │ └── gcd.v └── scripts │ ├── ASIC_analysis.sh │ ├── DRAM_analysis.sh │ ├── SRAM_analysis.sh │ ├── build.cfg │ ├── install_dependecies.sh │ ├── openram.sh │ ├── params.tcl │ └── run.sh ├── images ├── TALCO_image.png ├── gif.gif └── talco.gif ├── paper └── TALCO.pdf └── software ├── .gitignore ├── README.md ├── TALCO-WFAA ├── CMakeLists.txt ├── LICENSE ├── Makefile ├── README.md ├── VERSION ├── alignment │ ├── Makefile │ ├── affine2p_penalties.c │ ├── affine2p_penalties.h │ ├── affine_penalties.c │ ├── affine_penalties.h │ ├── cigar.c │ ├── cigar.h │ ├── linear_penalties.h │ ├── score_matrix.c │ └── score_matrix.h ├── bindings │ ├── cpp │ │ ├── Makefile │ │ ├── WFAligner.cpp │ │ └── WFAligner.hpp │ └── rust │ │ ├── build.rs │ │ └── example.rs ├── build │ └── TALCO-WFAA ├── examples │ ├── Makefile │ ├── README.md │ ├── wfa_adapt.c │ ├── wfa_basic.c │ ├── wfa_bindings.cpp │ ├── wfa_lambda.cpp │ └── wfa_repeated.c ├── guix.scm ├── img │ ├── heuristics.aband.10.10.png │ ├── heuristics.aband.50.50.png │ ├── heuristics.band.10.10.png │ ├── heuristics.band.10.150.png │ ├── heuristics.drop.none.png │ ├── heuristics.none.png │ ├── heuristics.wfadap.10.50.1.png │ ├── heuristics.wfadap.10.50.10.png │ ├── heuristics.xdrop.200.png │ ├── heuristics.zdrop.200.png │ └── wfa.vs.swg.png ├── scripts │ ├── fasta2seq.sh │ ├── seq2fasta.sh │ ├── wfa.alg.cmp.py │ ├── wfa.alg.cmp.score.sh │ ├── wfa.alg.rescore.py │ └── wfa.plot.py ├── system │ ├── Makefile │ ├── mm_allocator.c │ ├── mm_allocator.h │ ├── mm_stack.c │ ├── mm_stack.h │ ├── profiler_counter.c │ ├── profiler_counter.h │ ├── profiler_timer.c │ └── profiler_timer.h ├── tests │ ├── wfa.utest.check │ │ ├── test.affine.alg │ │ ├── test.affine.p0.alg │ │ ├── test.affine.p1.alg │ │ ├── test.affine.p2.alg │ │ ├── test.affine.p3.alg │ │ ├── test.affine.p4.alg │ │ ├── test.affine.p5.alg │ │ ├── test.affine.wfapt0.alg │ │ ├── test.affine.wfapt1.alg │ │ ├── test.affine2p.alg │ │ ├── test.biwfa.affine.alg │ │ ├── test.biwfa.affine.p0.alg │ │ ├── test.biwfa.affine.p1.alg │ │ ├── test.biwfa.affine.p2.alg │ │ ├── test.biwfa.affine.p3.alg │ │ ├── test.biwfa.affine.p4.alg │ │ ├── test.biwfa.affine.p5.alg │ │ ├── test.biwfa.affine.wfapt0.alg │ │ ├── test.biwfa.affine.wfapt1.alg │ │ ├── test.biwfa.affine2p.alg │ │ ├── test.biwfa.edit.alg │ │ ├── test.biwfa.indel.alg │ │ ├── test.biwfa.score.affine.alg │ │ ├── test.biwfa.score.affine.p0.alg │ │ ├── test.biwfa.score.affine.p1.alg │ │ ├── test.biwfa.score.affine.p2.alg │ │ ├── test.biwfa.score.affine.p3.alg │ │ ├── test.biwfa.score.affine.p4.alg │ │ ├── test.biwfa.score.affine.p5.alg │ │ ├── test.biwfa.score.affine.wfapt0.alg │ │ ├── test.biwfa.score.affine.wfapt1.alg │ │ ├── test.biwfa.score.affine2p.alg │ │ ├── test.biwfa.score.edit.alg │ │ ├── test.biwfa.score.indel.alg │ │ ├── test.edit.alg │ │ ├── test.indel.alg │ │ ├── test.pb.affine.alg │ │ ├── test.pb.affine.p0.alg │ │ ├── test.pb.affine.p1.alg │ │ ├── test.pb.affine.p2.alg │ │ ├── test.pb.affine.p3.alg │ │ ├── test.pb.affine.p4.alg │ │ ├── test.pb.affine.p5.alg │ │ ├── test.pb.affine.wfapt0.alg │ │ ├── test.pb.affine.wfapt1.alg │ │ ├── test.pb.affine2p.alg │ │ ├── test.pb.edit.alg │ │ ├── test.pb.indel.alg │ │ ├── test.score.affine.alg │ │ ├── test.score.affine.p0.alg │ │ ├── test.score.affine.p1.alg │ │ ├── test.score.affine.p2.alg │ │ ├── test.score.affine.p3.alg │ │ ├── test.score.affine.p4.alg │ │ ├── test.score.affine.p5.alg │ │ ├── test.score.affine.wfapt0.alg │ │ ├── test.score.affine.wfapt1.alg │ │ ├── test.score.affine2p.alg │ │ ├── test.score.edit.alg │ │ ├── test.score.indel.alg │ │ ├── wfa.utest.log │ │ ├── wfa.utest.log.mem │ │ └── wfa.utest.log.time │ ├── wfa.utest.cmp.sh │ ├── wfa.utest.log │ ├── wfa.utest.log.correct │ ├── wfa.utest.log.mem │ ├── wfa.utest.log.time │ ├── wfa.utest.performance.cmp.sh │ ├── wfa.utest.performance.sh │ ├── wfa.utest.seq │ ├── wfa.utest.sh │ └── wfa.utest.valgrind.sh ├── tiling_test │ ├── debug_main.cpp │ ├── err_stats.cpp │ ├── err_stats.hpp │ ├── main.cpp │ ├── nanosim_input.cpp │ ├── nanosim_input.hpp │ └── tbb_main.cpp ├── tools │ ├── README.md │ ├── align_benchmark │ │ ├── Makefile │ │ ├── align_benchmark.c │ │ ├── align_benchmark_params.c │ │ ├── align_benchmark_params.h │ │ ├── benchmark │ │ │ ├── Makefile │ │ │ ├── benchmark_check.c │ │ │ ├── benchmark_check.h │ │ │ ├── benchmark_edit.c │ │ │ ├── benchmark_edit.h │ │ │ ├── benchmark_gap_affine.c │ │ │ ├── benchmark_gap_affine.h │ │ │ ├── benchmark_gap_affine2p.c │ │ │ ├── benchmark_gap_affine2p.h │ │ │ ├── benchmark_gap_linear.c │ │ │ ├── benchmark_gap_linear.h │ │ │ ├── benchmark_indel.c │ │ │ ├── benchmark_indel.h │ │ │ ├── benchmark_utils.c │ │ │ └── benchmark_utils.h │ │ ├── edit │ │ │ ├── Makefile │ │ │ ├── edit_bpm.c │ │ │ ├── edit_bpm.h │ │ │ ├── edit_dp.c │ │ │ └── edit_dp.h │ │ ├── gap_affine │ │ │ ├── Makefile │ │ │ ├── affine_matrix.c │ │ │ ├── affine_matrix.h │ │ │ ├── swg.c │ │ │ └── swg.h │ │ ├── gap_affine2p │ │ │ ├── Makefile │ │ │ ├── affine2p_dp.c │ │ │ ├── affine2p_dp.h │ │ │ ├── affine2p_matrix.c │ │ │ └── affine2p_matrix.h │ │ ├── gap_linear │ │ │ ├── Makefile │ │ │ ├── nw.c │ │ │ └── nw.h │ │ └── indel │ │ │ ├── Makefile │ │ │ ├── indel_dp.c │ │ │ └── indel_dp.h │ └── generate_dataset │ │ ├── Makefile │ │ └── generate_dataset.c ├── utils │ ├── Makefile │ ├── bitmap.c │ ├── bitmap.h │ ├── commons.c │ ├── commons.h │ ├── dna_text.c │ ├── dna_text.h │ ├── heatmap.c │ ├── heatmap.h │ ├── sequence_buffer.c │ ├── sequence_buffer.h │ ├── string_padded.c │ ├── string_padded.h │ ├── vector.c │ └── vector.h └── wavefront │ ├── Makefile │ ├── wavefront.c │ ├── wavefront.h │ ├── wavefront_align.c │ ├── wavefront_align.h │ ├── wavefront_aligner.c │ ├── wavefront_aligner.h │ ├── wavefront_attributes.c │ ├── wavefront_attributes.h │ ├── wavefront_backtrace.c │ ├── wavefront_backtrace.h │ ├── wavefront_backtrace_buffer.c │ ├── wavefront_backtrace_buffer.h │ ├── wavefront_backtrace_offload.c │ ├── wavefront_backtrace_offload.h │ ├── wavefront_bialign.c │ ├── wavefront_bialign.h │ ├── wavefront_bialigner.c │ ├── wavefront_bialigner.h │ ├── wavefront_components.c │ ├── wavefront_components.h │ ├── wavefront_compute.c │ ├── wavefront_compute.h │ ├── wavefront_compute_affine.c │ ├── wavefront_compute_affine.h │ ├── wavefront_compute_affine2p.c │ ├── wavefront_compute_affine2p.h │ ├── wavefront_compute_edit.c │ ├── wavefront_compute_edit.h │ ├── wavefront_compute_linear.c │ ├── wavefront_compute_linear.h │ ├── wavefront_debug.c │ ├── wavefront_debug.h │ ├── wavefront_display.c │ ├── wavefront_display.h │ ├── wavefront_extend.c │ ├── wavefront_extend.h │ ├── wavefront_heuristic.c │ ├── wavefront_heuristic.h │ ├── wavefront_offset.h │ ├── wavefront_pcigar.c │ ├── wavefront_pcigar.h │ ├── wavefront_penalties.c │ ├── wavefront_penalties.h │ ├── wavefront_plot.c │ ├── wavefront_plot.h │ ├── wavefront_slab.c │ ├── wavefront_slab.h │ ├── wavefront_unialign.c │ ├── wavefront_unialign.h │ ├── wfa.h │ └── wfa.hpp ├── TALCO-XDrop ├── .gitignore ├── CMakeLists.txt ├── README.md ├── build │ └── TALCO-XDrop └── src │ ├── TALCO-XDrop.cpp │ ├── TALCO-XDrop.hpp │ ├── kseq.h │ ├── main.cpp │ └── timer.hpp ├── baselines 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