LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.py
prismalign/__init__.py
prismalign/cli.py
prismalign/colorops.py
prismalign/em.py
prismalign/engine.py
prismalign/pe_rescore.py
prismalign/schemes.py
prismalign/seqops.c
prismalign.egg-info/PKG-INFO
prismalign.egg-info/SOURCES.txt
prismalign.egg-info/dependency_links.txt
prismalign.egg-info/entry_points.txt
prismalign.egg-info/requires.txt
prismalign.egg-info/top_level.txt
prismalign/adapters/__init__.py
prismalign/adapters/base.py
prismalign/adapters/bridge.py
prismalign/adapters/registry.py
prismalign/adapters/bowtie2/__init__.py
prismalign/adapters/bwa/__init__.py
prismalign/adapters/bwa_mem2/__init__.py
prismalign/adapters/hisat2/__init__.py
prismalign/adapters/minimap2/__init__.py
prismalign/adapters/sam/__init__.py
prismalign/adapters/strobealign/__init__.py
prismalign/backends/__init__.py
prismalign/backends/base.py
prismalign/backends/registry.py
prismalign/backends/bwamem/__init__.py
prismalign/backends/bwamem2/__init__.py
prismalign/backends/mappy/__init__.py
prismalign/backends/minibwa/__init__.py
prismalign/backends/wfa2/__init__.py
prismalign/backends/wfa2/wrap.c
prismalign/backends/wfa2/wfa2lib/LICENSE.wfa2
prismalign/backends/wfa2/wfa2lib/alignment/affine2p_penalties.c
prismalign/backends/wfa2/wfa2lib/alignment/affine2p_penalties.h
prismalign/backends/wfa2/wfa2lib/alignment/affine_penalties.c
prismalign/backends/wfa2/wfa2lib/alignment/affine_penalties.h
prismalign/backends/wfa2/wfa2lib/alignment/cigar.c
prismalign/backends/wfa2/wfa2lib/alignment/cigar.h
prismalign/backends/wfa2/wfa2lib/alignment/cigar_utils.c
prismalign/backends/wfa2/wfa2lib/alignment/cigar_utils.h
prismalign/backends/wfa2/wfa2lib/alignment/linear_penalties.h
prismalign/backends/wfa2/wfa2lib/alignment/score_matrix.c
prismalign/backends/wfa2/wfa2lib/alignment/score_matrix.h
prismalign/backends/wfa2/wfa2lib/system/mm_allocator.c
prismalign/backends/wfa2/wfa2lib/system/mm_allocator.h
prismalign/backends/wfa2/wfa2lib/system/mm_stack.c
prismalign/backends/wfa2/wfa2lib/system/mm_stack.h
prismalign/backends/wfa2/wfa2lib/system/profiler_counter.c
prismalign/backends/wfa2/wfa2lib/system/profiler_counter.h
prismalign/backends/wfa2/wfa2lib/system/profiler_timer.c
prismalign/backends/wfa2/wfa2lib/system/profiler_timer.h
prismalign/backends/wfa2/wfa2lib/utils/bitmap.c
prismalign/backends/wfa2/wfa2lib/utils/bitmap.h
prismalign/backends/wfa2/wfa2lib/utils/commons.c
prismalign/backends/wfa2/wfa2lib/utils/commons.h
prismalign/backends/wfa2/wfa2lib/utils/dna_text.c
prismalign/backends/wfa2/wfa2lib/utils/dna_text.h
prismalign/backends/wfa2/wfa2lib/utils/heatmap.c
prismalign/backends/wfa2/wfa2lib/utils/heatmap.h
prismalign/backends/wfa2/wfa2lib/utils/sequence_buffer.c
prismalign/backends/wfa2/wfa2lib/utils/sequence_buffer.h
prismalign/backends/wfa2/wfa2lib/utils/vector.c
prismalign/backends/wfa2/wfa2lib/utils/vector.h
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront.c
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront.h
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_align.c
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_align.h
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_aligner.c
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_aligner.h
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_attributes.c
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_attributes.h
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_backtrace.c
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_backtrace.h
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_backtrace_buffer.c
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_backtrace_buffer.h
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_backtrace_offload.c
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_backtrace_offload.h
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_bialign.c
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_bialign.h
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_bialigner.c
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_bialigner.h
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_components.c
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_components.h
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_compute.c
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_compute.h
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_compute_affine.c
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_compute_affine.h
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_compute_affine2p.c
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_compute_affine2p.h
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_compute_edit.c
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_compute_edit.h
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_compute_linear.c
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_compute_linear.h
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_debug.c
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_debug.h
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_display.c
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_display.h
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_extend.c
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_extend.h
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_extend_kernels.c
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_extend_kernels.h
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_extend_kernels_avx.h
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_heuristic.c
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_heuristic.h
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_offset.h
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_pcigar.c
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_pcigar.h
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_penalties.c
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_penalties.h
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_plot.c
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_plot.h
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_sequences.c
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_sequences.h
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_slab.c
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_slab.h
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_termination.c
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_termination.h
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_unialign.c
prismalign/backends/wfa2/wfa2lib/wavefront/wavefront_unialign.h
prismalign/backends/wfa2/wfa2lib/wavefront/wfa.h
tests/test_adapters.py
tests/test_backends.py
tests/test_backends_matrix.py
tests/test_batch_backend.py
tests/test_colorops.py
tests/test_em.py
tests/test_engine.py
tests/test_hierarchy.py
tests/test_parity.py
tests/test_pe_minibwa.py
tests/test_sam_backend.py
tests/test_wfa2_backend.py