minimap2 0.2.24.6 → 0.2.25.0
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- checksums.yaml +4 -4
- data/ext/minimap2.patch +3 -3
- data/lib/minimap2/aligner.rb +4 -0
- data/lib/minimap2/ffi/constants.rb +90 -88
- data/lib/minimap2/version.rb +2 -2
- metadata +1 -97
- data/ext/minimap2/lib/simde/CONTRIBUTING.md +0 -114
- data/ext/minimap2/lib/simde/COPYING +0 -20
- data/ext/minimap2/lib/simde/README.md +0 -333
- data/ext/minimap2/lib/simde/amalgamate.py +0 -58
- data/ext/minimap2/lib/simde/meson.build +0 -33
- data/ext/minimap2/lib/simde/netlify.toml +0 -20
- data/ext/minimap2/lib/simde/simde/arm/neon/float32x2.h +0 -140
- data/ext/minimap2/lib/simde/simde/arm/neon/float32x4.h +0 -137
- data/ext/minimap2/lib/simde/simde/arm/neon/float64x1.h +0 -142
- data/ext/minimap2/lib/simde/simde/arm/neon/float64x2.h +0 -145
- data/ext/minimap2/lib/simde/simde/arm/neon/int16x4.h +0 -140
- data/ext/minimap2/lib/simde/simde/arm/neon/int16x8.h +0 -145
- data/ext/minimap2/lib/simde/simde/arm/neon/int32x2.h +0 -140
- data/ext/minimap2/lib/simde/simde/arm/neon/int32x4.h +0 -143
- data/ext/minimap2/lib/simde/simde/arm/neon/int64x1.h +0 -137
- data/ext/minimap2/lib/simde/simde/arm/neon/int64x2.h +0 -141
- data/ext/minimap2/lib/simde/simde/arm/neon/int8x16.h +0 -147
- data/ext/minimap2/lib/simde/simde/arm/neon/int8x8.h +0 -141
- data/ext/minimap2/lib/simde/simde/arm/neon/uint16x4.h +0 -134
- data/ext/minimap2/lib/simde/simde/arm/neon/uint16x8.h +0 -138
- data/ext/minimap2/lib/simde/simde/arm/neon/uint32x2.h +0 -134
- data/ext/minimap2/lib/simde/simde/arm/neon/uint32x4.h +0 -137
- data/ext/minimap2/lib/simde/simde/arm/neon/uint64x1.h +0 -131
- data/ext/minimap2/lib/simde/simde/arm/neon/uint64x2.h +0 -135
- data/ext/minimap2/lib/simde/simde/arm/neon/uint8x16.h +0 -141
- data/ext/minimap2/lib/simde/simde/arm/neon/uint8x8.h +0 -135
- data/ext/minimap2/lib/simde/simde/arm/neon.h +0 -97
- data/ext/minimap2/lib/simde/simde/check.h +0 -267
- data/ext/minimap2/lib/simde/simde/debug-trap.h +0 -83
- data/ext/minimap2/lib/simde/simde/hedley.h +0 -1899
- data/ext/minimap2/lib/simde/simde/simde-arch.h +0 -445
- data/ext/minimap2/lib/simde/simde/simde-common.h +0 -697
- data/ext/minimap2/lib/simde/simde/x86/avx.h +0 -5385
- data/ext/minimap2/lib/simde/simde/x86/avx2.h +0 -2402
- data/ext/minimap2/lib/simde/simde/x86/avx512bw.h +0 -391
- data/ext/minimap2/lib/simde/simde/x86/avx512f.h +0 -3389
- data/ext/minimap2/lib/simde/simde/x86/avx512vl.h +0 -112
- data/ext/minimap2/lib/simde/simde/x86/fma.h +0 -659
- data/ext/minimap2/lib/simde/simde/x86/mmx.h +0 -2210
- data/ext/minimap2/lib/simde/simde/x86/sse.h +0 -3696
- data/ext/minimap2/lib/simde/simde/x86/sse2.h +0 -5991
- data/ext/minimap2/lib/simde/simde/x86/sse3.h +0 -343
- data/ext/minimap2/lib/simde/simde/x86/sse4.1.h +0 -1783
- data/ext/minimap2/lib/simde/simde/x86/sse4.2.h +0 -105
- data/ext/minimap2/lib/simde/simde/x86/ssse3.h +0 -1053
- data/ext/minimap2/lib/simde/simde/x86/svml.h +0 -543
- data/ext/minimap2/lib/simde/test/CMakeLists.txt +0 -166
- data/ext/minimap2/lib/simde/test/arm/meson.build +0 -4
- data/ext/minimap2/lib/simde/test/arm/neon/meson.build +0 -23
- data/ext/minimap2/lib/simde/test/arm/neon/skel.c +0 -871
- data/ext/minimap2/lib/simde/test/arm/neon/test-neon-internal.h +0 -134
- data/ext/minimap2/lib/simde/test/arm/neon/test-neon.c +0 -39
- data/ext/minimap2/lib/simde/test/arm/neon/test-neon.h +0 -10
- data/ext/minimap2/lib/simde/test/arm/neon/vadd.c +0 -1260
- data/ext/minimap2/lib/simde/test/arm/neon/vdup_n.c +0 -873
- data/ext/minimap2/lib/simde/test/arm/neon/vmul.c +0 -1084
- data/ext/minimap2/lib/simde/test/arm/neon/vsub.c +0 -1260
- data/ext/minimap2/lib/simde/test/arm/test-arm-internal.h +0 -18
- data/ext/minimap2/lib/simde/test/arm/test-arm.c +0 -20
- data/ext/minimap2/lib/simde/test/arm/test-arm.h +0 -8
- data/ext/minimap2/lib/simde/test/cmake/AddCompilerFlags.cmake +0 -171
- data/ext/minimap2/lib/simde/test/cmake/ExtraWarningFlags.cmake +0 -68
- data/ext/minimap2/lib/simde/test/meson.build +0 -64
- data/ext/minimap2/lib/simde/test/munit/COPYING +0 -21
- data/ext/minimap2/lib/simde/test/munit/Makefile +0 -55
- data/ext/minimap2/lib/simde/test/munit/README.md +0 -54
- data/ext/minimap2/lib/simde/test/munit/example.c +0 -351
- data/ext/minimap2/lib/simde/test/munit/meson.build +0 -37
- data/ext/minimap2/lib/simde/test/munit/munit.c +0 -2055
- data/ext/minimap2/lib/simde/test/munit/munit.h +0 -535
- data/ext/minimap2/lib/simde/test/run-tests.c +0 -20
- data/ext/minimap2/lib/simde/test/run-tests.h +0 -260
- data/ext/minimap2/lib/simde/test/x86/avx.c +0 -13752
- data/ext/minimap2/lib/simde/test/x86/avx2.c +0 -9977
- data/ext/minimap2/lib/simde/test/x86/avx512bw.c +0 -2664
- data/ext/minimap2/lib/simde/test/x86/avx512f.c +0 -10416
- data/ext/minimap2/lib/simde/test/x86/avx512vl.c +0 -210
- data/ext/minimap2/lib/simde/test/x86/fma.c +0 -2557
- data/ext/minimap2/lib/simde/test/x86/meson.build +0 -33
- data/ext/minimap2/lib/simde/test/x86/mmx.c +0 -2878
- data/ext/minimap2/lib/simde/test/x86/skel.c +0 -2984
- data/ext/minimap2/lib/simde/test/x86/sse.c +0 -5121
- data/ext/minimap2/lib/simde/test/x86/sse2.c +0 -9860
- data/ext/minimap2/lib/simde/test/x86/sse3.c +0 -486
- data/ext/minimap2/lib/simde/test/x86/sse4.1.c +0 -3446
- data/ext/minimap2/lib/simde/test/x86/sse4.2.c +0 -101
- data/ext/minimap2/lib/simde/test/x86/ssse3.c +0 -2084
- data/ext/minimap2/lib/simde/test/x86/svml.c +0 -1545
- data/ext/minimap2/lib/simde/test/x86/test-avx.h +0 -16
- data/ext/minimap2/lib/simde/test/x86/test-avx512.h +0 -25
- data/ext/minimap2/lib/simde/test/x86/test-mmx.h +0 -13
- data/ext/minimap2/lib/simde/test/x86/test-sse.h +0 -13
- data/ext/minimap2/lib/simde/test/x86/test-sse2.h +0 -13
- data/ext/minimap2/lib/simde/test/x86/test-x86-internal.h +0 -196
- data/ext/minimap2/lib/simde/test/x86/test-x86.c +0 -48
- data/ext/minimap2/lib/simde/test/x86/test-x86.h +0 -8
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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---
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SHA256:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 3c31d89fb8741da359e9fe0002b19af7b02a21aff94d9b5a03d7a112cb98f771
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data.tar.gz: c5fbb3f83361bd5b76f0742c5ab592aecd13b8ef0decfbdab6d536ee191351b9
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 4d25538bbf117a6ece697f28660e58caaac1ea57a09fb33d9017b683655ee08a776a061d95c327d15cbb8868672ab3ee383ac503263804529ec67a3bf255159b
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data.tar.gz: 70462c3229d0335ae5d1542a359c074d139d6ca4953de5cc3e7032115ac92d8eef0a93409256e85a689476bb55177bed16d3877c052a58e738a4ab876f32aa3f
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data/ext/minimap2.patch
CHANGED
@@ -1,5 +1,5 @@
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-
--- Makefile
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+++ Makefile
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--- a/Makefile
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+++ b/Makefile
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@@ -1,9 +1,9 @@
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-CFLAGS= -g -Wall -O2 -Wc++-compat #-Wextra
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+CFLAGS= -g -Wall -O2 -Wc++-compat -fPIC #-Wextra
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@@ -12,7 +12,7 @@
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PROG= minimap2
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PROG_EXTRA= sdust minimap2-lite
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LIBS= -lm -lz -lpthread
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-
@@ -
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@@ -134,3 +134,4 @@ sdust.o: kalloc.h kdq.h kvec.h sdust.h
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seed.o: mmpriv.h minimap.h bseq.h kseq.h kalloc.h ksort.h
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sketch.o: kvec.h kalloc.h mmpriv.h minimap.h bseq.h kseq.h
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splitidx.o: mmpriv.h minimap.h bseq.h kseq.h
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data/lib/minimap2/aligner.rb
CHANGED
@@ -139,6 +139,7 @@ module Minimap2
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)
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return if index.null?
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return if (map_opt[:flag] & 4).zero? && (index[:flag] & 2).zero?
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map_opt[:max_frag_len] = max_frag_len if max_frag_len
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map_opt[:flag] |= extra_flags if extra_flags
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@@ -201,6 +202,9 @@ module Minimap2
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# @param stop
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def seq(name, start = 0, stop = 0x7fffffff)
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return if index.null?
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return if (map_opt[:flag] & 4).zero? && (index[:flag] & 2).zero?
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+
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lp = ::FFI::MemoryPointer.new(:int)
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s = FFI.mappy_fetch_seq(index, name, start, stop, lp)
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l = lp.read_int
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@@ -34,10 +34,12 @@ module Minimap2
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NO_END_FLT = 0x10000000
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HARD_MLEVEL = 0x20000000
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SAM_HIT_ONLY = 0x40000000
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-
RMQ = 0x80000000
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QSTRAND = 0x100000000
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NO_INV = 0x200000000
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NO_HASH_NAME = 0x400000000
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RMQ = 0x80000000
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QSTRAND = 0x100000000
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NO_INV = 0x200000000
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NO_HASH_NAME = 0x400000000
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SPLICE_OLD = 0x800000000
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SECONDARY_SEQ = 0x1000000000 # output SEQ field for seqondary alignments using hard clipping
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HPC = 0x1
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NO_SEQ = 0x2
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@@ -74,79 +76,6 @@ module Minimap2
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:a, MM128.ptr
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end
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-
# indexing option
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class IdxOpt < ::FFI::Struct
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layout \
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:k, :short,
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:w, :short,
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:flag, :short,
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:bucket_bits, :short,
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:mini_batch_size, :int64_t,
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:batch_size, :uint64_t
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end
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-
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# mapping option
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class MapOpt < ::FFI::Struct
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layout \
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:flag, :int64_t, # see MM_F_* macros
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:seed, :int,
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-
:sdust_thres, :int, # score threshold for SDUST; 0 to disable
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-
:max_qlen, :int, # max query length
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:bw, :int, # bandwidth
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-
:bw_long, :int,
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-
:max_gap, :int, # break a chain if there are no minimizers in a max_gap window
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-
:max_gap_ref, :int,
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-
:max_frag_len, :int,
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:max_chain_skip, :int,
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:max_chain_iter, :int,
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:min_cnt, :int, # min number of minimizers on each chain
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:min_chain_score, :int, # min chaining score
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:chain_gap_scale, :float,
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:chain_skip_scale, :float,
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:rmq_size_cap, :int,
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:rmq_inner_dist, :int,
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:rmq_rescue_size, :int,
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:rmq_rescue_ratio, :float,
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:mask_level, :float,
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:mask_len, :int,
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:pri_ratio, :float,
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:best_n, :int, # top best_n chains are subjected to DP alignment
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:alt_drop, :float,
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:a, :int, # matching score
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:b, :int, # mismatch
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:q, :int, # gap-open
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:e, :int, # gap-ext
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:q2, :int, # gap-open
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:e2, :int, # gap-ext
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:sc_ambi, :int, # score when one or both bases are "N"
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:noncan, :int, # cost of non-canonical splicing sites
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:junc_bonus, :int,
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:zdrop, :int, # break alignment if alignment score drops too fast along the diagonal
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:zdrop_inv, :int,
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:end_bonus, :int,
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:min_dp_max, :int, # drop an alignment if the score of the max scoring segment is below this threshold
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:min_ksw_len, :int,
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:anchor_ext_len, :int,
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:anchor_ext_shift, :int,
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:max_clip_ratio, :float, # drop an alignment if BOTH ends are clipped above this ratio
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:rank_min_len, :int,
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:rank_frac, :float,
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:pe_ori, :int,
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:pe_bonus, :int,
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:mid_occ_frac, :float, # only used by mm_mapopt_update(); see below
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:q_occ_frac, :float,
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:min_mid_occ, :int32,
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:max_mid_occ, :int32,
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:mid_occ, :int32, # ignore seeds with occurrences above this threshold
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:max_occ, :int32,
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:max_max_occ, :int32,
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:occ_dist, :int32,
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:mini_batch_size, :int64_t, # size of a batch of query bases to process in parallel
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:max_sw_mat, :int64_t,
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:cap_kalloc, :int64_t,
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:split_prefix, :string
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-
end
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-
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79
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# minimap2 index
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class IdxSeq < ::FFI::Struct
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layout \
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@@ -173,17 +102,6 @@ module Minimap2
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:h, :pointer
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end
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# index reader
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class IdxReader < ::FFI::Struct
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layout \
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:is_idx, :int,
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:n_parts, :int,
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:idx_size, :int64_t,
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:opt, IdxOpt,
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:fp_out, :pointer, # FILE
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:seq_or_idx, :pointer # FIXME: Union mm_bseq_files or FILE
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-
end
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-
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105
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# minimap2 alignment
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106
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class Extra < ::FFI::BitStruct
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107
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layout \
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@@ -242,6 +160,90 @@ module Minimap2
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:dummy, 5
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end
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# indexing option
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class IdxOpt < ::FFI::Struct
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layout \
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:k, :short,
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:w, :short,
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:flag, :short,
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:bucket_bits, :short,
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:mini_batch_size, :int64_t,
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:batch_size, :uint64_t
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+
end
|
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+
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# mapping option
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+
class MapOpt < ::FFI::Struct
|
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+
layout \
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+
:flag, :int64_t, # see MM_F_* macros
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+
:seed, :int,
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179
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+
:sdust_thres, :int, # score threshold for SDUST; 0 to disable
|
180
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+
:max_qlen, :int, # max query length
|
181
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+
:bw, :int, # bandwidth
|
182
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+
:bw_long, :int,
|
183
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+
:max_gap, :int, # break a chain if there are no minimizers in a max_gap window
|
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+
:max_gap_ref, :int,
|
185
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+
:max_frag_len, :int,
|
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+
:max_chain_skip, :int,
|
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+
:max_chain_iter, :int,
|
188
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+
:min_cnt, :int, # min number of minimizers on each chain
|
189
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+
:min_chain_score, :int, # min chaining score
|
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+
:chain_gap_scale, :float,
|
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+
:chain_skip_scale, :float,
|
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+
:rmq_size_cap, :int,
|
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+
:rmq_inner_dist, :int,
|
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+
:rmq_rescue_size, :int,
|
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+
:rmq_rescue_ratio, :float,
|
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:mask_level, :float,
|
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+
:mask_len, :int,
|
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:pri_ratio, :float,
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|
+
:best_n, :int, # top best_n chains are subjected to DP alignment
|
200
|
+
:alt_drop, :float,
|
201
|
+
:a, :int, # matching score
|
202
|
+
:b, :int, # mismatch
|
203
|
+
:q, :int, # gap-open
|
204
|
+
:e, :int, # gap-ext
|
205
|
+
:q2, :int, # gap-open
|
206
|
+
:e2, :int, # gap-ext
|
207
|
+
:sc_ambi, :int, # score when one or both bases are "N"
|
208
|
+
:noncan, :int, # cost of non-canonical splicing sites
|
209
|
+
:junc_bonus, :int,
|
210
|
+
:zdrop, :int, # break alignment if alignment score drops too fast along the diagonal
|
211
|
+
:zdrop_inv, :int,
|
212
|
+
:end_bonus, :int,
|
213
|
+
:min_dp_max, :int, # drop an alignment if the score of the max scoring segment is below this threshold
|
214
|
+
:min_ksw_len, :int,
|
215
|
+
:anchor_ext_len, :int,
|
216
|
+
:anchor_ext_shift, :int,
|
217
|
+
:max_clip_ratio, :float, # drop an alignment if BOTH ends are clipped above this ratio
|
218
|
+
:rank_min_len, :int,
|
219
|
+
:rank_frac, :float,
|
220
|
+
:pe_ori, :int,
|
221
|
+
:pe_bonus, :int,
|
222
|
+
:mid_occ_frac, :float, # only used by mm_mapopt_update(); see below
|
223
|
+
:q_occ_frac, :float,
|
224
|
+
:min_mid_occ, :int32,
|
225
|
+
:max_mid_occ, :int32,
|
226
|
+
:mid_occ, :int32, # ignore seeds with occurrences above this threshold
|
227
|
+
:max_occ, :int32,
|
228
|
+
:max_max_occ, :int32,
|
229
|
+
:occ_dist, :int32,
|
230
|
+
:mini_batch_size, :int64_t, # size of a batch of query bases to process in parallel
|
231
|
+
:max_sw_mat, :int64_t,
|
232
|
+
:cap_kalloc, :int64_t,
|
233
|
+
:split_prefix, :string
|
234
|
+
end
|
235
|
+
|
236
|
+
# index reader
|
237
|
+
class IdxReader < ::FFI::Struct
|
238
|
+
layout \
|
239
|
+
:is_idx, :int,
|
240
|
+
:n_parts, :int,
|
241
|
+
:idx_size, :int64_t,
|
242
|
+
:opt, IdxOpt,
|
243
|
+
:fp_out, :pointer, # FILE
|
244
|
+
:seq_or_idx, :pointer # FIXME: Union mm_bseq_files or FILE
|
245
|
+
end
|
246
|
+
|
245
247
|
# memory buffer for thread-local storage during mapping
|
246
248
|
class TBuf < ::FFI::Struct
|
247
249
|
layout \
|
data/lib/minimap2/version.rb
CHANGED
metadata
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: minimap2
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.2.
|
4
|
+
version: 0.2.25.0
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- kojix2
|
@@ -87,102 +87,6 @@ files:
|
|
87
87
|
- ext/minimap2/kthread.h
|
88
88
|
- ext/minimap2/kvec.h
|
89
89
|
- ext/minimap2/lchain.c
|
90
|
-
- ext/minimap2/lib/simde/CONTRIBUTING.md
|
91
|
-
- ext/minimap2/lib/simde/COPYING
|
92
|
-
- ext/minimap2/lib/simde/README.md
|
93
|
-
- ext/minimap2/lib/simde/amalgamate.py
|
94
|
-
- ext/minimap2/lib/simde/meson.build
|
95
|
-
- ext/minimap2/lib/simde/netlify.toml
|
96
|
-
- ext/minimap2/lib/simde/simde/arm/neon.h
|
97
|
-
- ext/minimap2/lib/simde/simde/arm/neon/float32x2.h
|
98
|
-
- ext/minimap2/lib/simde/simde/arm/neon/float32x4.h
|
99
|
-
- ext/minimap2/lib/simde/simde/arm/neon/float64x1.h
|
100
|
-
- ext/minimap2/lib/simde/simde/arm/neon/float64x2.h
|
101
|
-
- ext/minimap2/lib/simde/simde/arm/neon/int16x4.h
|
102
|
-
- ext/minimap2/lib/simde/simde/arm/neon/int16x8.h
|
103
|
-
- ext/minimap2/lib/simde/simde/arm/neon/int32x2.h
|
104
|
-
- ext/minimap2/lib/simde/simde/arm/neon/int32x4.h
|
105
|
-
- ext/minimap2/lib/simde/simde/arm/neon/int64x1.h
|
106
|
-
- ext/minimap2/lib/simde/simde/arm/neon/int64x2.h
|
107
|
-
- ext/minimap2/lib/simde/simde/arm/neon/int8x16.h
|
108
|
-
- ext/minimap2/lib/simde/simde/arm/neon/int8x8.h
|
109
|
-
- ext/minimap2/lib/simde/simde/arm/neon/uint16x4.h
|
110
|
-
- ext/minimap2/lib/simde/simde/arm/neon/uint16x8.h
|
111
|
-
- ext/minimap2/lib/simde/simde/arm/neon/uint32x2.h
|
112
|
-
- ext/minimap2/lib/simde/simde/arm/neon/uint32x4.h
|
113
|
-
- ext/minimap2/lib/simde/simde/arm/neon/uint64x1.h
|
114
|
-
- ext/minimap2/lib/simde/simde/arm/neon/uint64x2.h
|
115
|
-
- ext/minimap2/lib/simde/simde/arm/neon/uint8x16.h
|
116
|
-
- ext/minimap2/lib/simde/simde/arm/neon/uint8x8.h
|
117
|
-
- ext/minimap2/lib/simde/simde/check.h
|
118
|
-
- ext/minimap2/lib/simde/simde/debug-trap.h
|
119
|
-
- ext/minimap2/lib/simde/simde/hedley.h
|
120
|
-
- ext/minimap2/lib/simde/simde/simde-arch.h
|
121
|
-
- ext/minimap2/lib/simde/simde/simde-common.h
|
122
|
-
- ext/minimap2/lib/simde/simde/x86/avx.h
|
123
|
-
- ext/minimap2/lib/simde/simde/x86/avx2.h
|
124
|
-
- ext/minimap2/lib/simde/simde/x86/avx512bw.h
|
125
|
-
- ext/minimap2/lib/simde/simde/x86/avx512f.h
|
126
|
-
- ext/minimap2/lib/simde/simde/x86/avx512vl.h
|
127
|
-
- ext/minimap2/lib/simde/simde/x86/fma.h
|
128
|
-
- ext/minimap2/lib/simde/simde/x86/mmx.h
|
129
|
-
- ext/minimap2/lib/simde/simde/x86/sse.h
|
130
|
-
- ext/minimap2/lib/simde/simde/x86/sse2.h
|
131
|
-
- ext/minimap2/lib/simde/simde/x86/sse3.h
|
132
|
-
- ext/minimap2/lib/simde/simde/x86/sse4.1.h
|
133
|
-
- ext/minimap2/lib/simde/simde/x86/sse4.2.h
|
134
|
-
- ext/minimap2/lib/simde/simde/x86/ssse3.h
|
135
|
-
- ext/minimap2/lib/simde/simde/x86/svml.h
|
136
|
-
- ext/minimap2/lib/simde/test/CMakeLists.txt
|
137
|
-
- ext/minimap2/lib/simde/test/arm/meson.build
|
138
|
-
- ext/minimap2/lib/simde/test/arm/neon/meson.build
|
139
|
-
- ext/minimap2/lib/simde/test/arm/neon/skel.c
|
140
|
-
- ext/minimap2/lib/simde/test/arm/neon/test-neon-internal.h
|
141
|
-
- ext/minimap2/lib/simde/test/arm/neon/test-neon.c
|
142
|
-
- ext/minimap2/lib/simde/test/arm/neon/test-neon.h
|
143
|
-
- ext/minimap2/lib/simde/test/arm/neon/vadd.c
|
144
|
-
- ext/minimap2/lib/simde/test/arm/neon/vdup_n.c
|
145
|
-
- ext/minimap2/lib/simde/test/arm/neon/vmul.c
|
146
|
-
- ext/minimap2/lib/simde/test/arm/neon/vsub.c
|
147
|
-
- ext/minimap2/lib/simde/test/arm/test-arm-internal.h
|
148
|
-
- ext/minimap2/lib/simde/test/arm/test-arm.c
|
149
|
-
- ext/minimap2/lib/simde/test/arm/test-arm.h
|
150
|
-
- ext/minimap2/lib/simde/test/cmake/AddCompilerFlags.cmake
|
151
|
-
- ext/minimap2/lib/simde/test/cmake/ExtraWarningFlags.cmake
|
152
|
-
- ext/minimap2/lib/simde/test/meson.build
|
153
|
-
- ext/minimap2/lib/simde/test/munit/COPYING
|
154
|
-
- ext/minimap2/lib/simde/test/munit/Makefile
|
155
|
-
- ext/minimap2/lib/simde/test/munit/README.md
|
156
|
-
- ext/minimap2/lib/simde/test/munit/example.c
|
157
|
-
- ext/minimap2/lib/simde/test/munit/meson.build
|
158
|
-
- ext/minimap2/lib/simde/test/munit/munit.c
|
159
|
-
- ext/minimap2/lib/simde/test/munit/munit.h
|
160
|
-
- ext/minimap2/lib/simde/test/run-tests.c
|
161
|
-
- ext/minimap2/lib/simde/test/run-tests.h
|
162
|
-
- ext/minimap2/lib/simde/test/x86/avx.c
|
163
|
-
- ext/minimap2/lib/simde/test/x86/avx2.c
|
164
|
-
- ext/minimap2/lib/simde/test/x86/avx512bw.c
|
165
|
-
- ext/minimap2/lib/simde/test/x86/avx512f.c
|
166
|
-
- ext/minimap2/lib/simde/test/x86/avx512vl.c
|
167
|
-
- ext/minimap2/lib/simde/test/x86/fma.c
|
168
|
-
- ext/minimap2/lib/simde/test/x86/meson.build
|
169
|
-
- ext/minimap2/lib/simde/test/x86/mmx.c
|
170
|
-
- ext/minimap2/lib/simde/test/x86/skel.c
|
171
|
-
- ext/minimap2/lib/simde/test/x86/sse.c
|
172
|
-
- ext/minimap2/lib/simde/test/x86/sse2.c
|
173
|
-
- ext/minimap2/lib/simde/test/x86/sse3.c
|
174
|
-
- ext/minimap2/lib/simde/test/x86/sse4.1.c
|
175
|
-
- ext/minimap2/lib/simde/test/x86/sse4.2.c
|
176
|
-
- ext/minimap2/lib/simde/test/x86/ssse3.c
|
177
|
-
- ext/minimap2/lib/simde/test/x86/svml.c
|
178
|
-
- ext/minimap2/lib/simde/test/x86/test-avx.h
|
179
|
-
- ext/minimap2/lib/simde/test/x86/test-avx512.h
|
180
|
-
- ext/minimap2/lib/simde/test/x86/test-mmx.h
|
181
|
-
- ext/minimap2/lib/simde/test/x86/test-sse.h
|
182
|
-
- ext/minimap2/lib/simde/test/x86/test-sse2.h
|
183
|
-
- ext/minimap2/lib/simde/test/x86/test-x86-internal.h
|
184
|
-
- ext/minimap2/lib/simde/test/x86/test-x86.c
|
185
|
-
- ext/minimap2/lib/simde/test/x86/test-x86.h
|
186
90
|
- ext/minimap2/main.c
|
187
91
|
- ext/minimap2/map.c
|
188
92
|
- ext/minimap2/minimap.h
|
@@ -1,114 +0,0 @@
|
|
1
|
-
# Contributing to SIMDe
|
2
|
-
|
3
|
-
First off, if you're even reading this, thank you! There is a lot of
|
4
|
-
work to do, and any help is appreciated.
|
5
|
-
|
6
|
-
If you haven't already, please read the
|
7
|
-
[README](https://github.com/nemequ/simde/blob/master/README.md). The
|
8
|
-
[wiki](https://github.com/nemequ/simde/wiki) also has some good
|
9
|
-
information, especially the
|
10
|
-
[FAQ](https://github.com/nemequ/simde/wiki/FAQ) and a guide on how to
|
11
|
-
[implement a new
|
12
|
-
function](https://github.com/nemequ/simde/wiki/Implementing-a-New-Function).
|
13
|
-
|
14
|
-
For information on developing for architectures you don't have access
|
15
|
-
to, please see the [Development
|
16
|
-
Environment](https://github.com/nemequ/simde/wiki/Development-Environment)
|
17
|
-
page on the wiki.
|
18
|
-
|
19
|
-
If you still have questions, or if anything below doesn't make sense
|
20
|
-
to you, please feel free to use the [issue
|
21
|
-
tracker](https://github.com/nemequ/simde/issues) or the [mailing
|
22
|
-
list](https://groups.google.com/forum/#!forum/simde) to ask. I know
|
23
|
-
the SIMDe documentation needs a lot of improvement, and asking
|
24
|
-
questions will help us understand what is missing, so please don't be
|
25
|
-
shy!
|
26
|
-
|
27
|
-
## Building the Tests
|
28
|
-
|
29
|
-
SIMDe contains an extensive test suite used for development. Most
|
30
|
-
users will never need to build the suite, but if you're contributing
|
31
|
-
code to SIMDe you'll need to build them.
|
32
|
-
|
33
|
-
Here is the basic procedure for compiling the tests:
|
34
|
-
|
35
|
-
```bash
|
36
|
-
mkdir test/build
|
37
|
-
cd test/build
|
38
|
-
CFLAGS="-march=native" CXXFLAGS="-march=native" cmake ..
|
39
|
-
make -j
|
40
|
-
./run-tests
|
41
|
-
```
|
42
|
-
|
43
|
-
Note that `-march=native` may not be the right flag for your compiler.
|
44
|
-
That should work for most compilers on x86/x86_64, though MSVC is an
|
45
|
-
exception (try `/arch:AVX2` instead of `-march=native`). On other
|
46
|
-
architectures please consult your compiler documentation to find out
|
47
|
-
what flags you should use to enable the SIMD extension for your target
|
48
|
-
platform. Here are a few to try:
|
49
|
-
|
50
|
-
* ARM:
|
51
|
-
* `-march=armv8-a+simd` (for ARMv8)
|
52
|
-
* `-march=armv7-a -mfpu=neon` (for ARMv7)
|
53
|
-
* POWER
|
54
|
-
* `-mcpu=native`
|
55
|
-
|
56
|
-
If you need a flag not listed above, please let us know so we can add
|
57
|
-
it to the list.
|
58
|
-
|
59
|
-
## Coding Style
|
60
|
-
|
61
|
-
SIMDe uses two spaces for indentation. Please adjust your editor
|
62
|
-
accordingly.
|
63
|
-
|
64
|
-
The coding style for preprocessor macros is a bit mixed since I made
|
65
|
-
some changes mid-project. For new code, please indent the
|
66
|
-
preprocessor conditions before the hash to the same level as the
|
67
|
-
normal code would be, and indent the code inside of preprocessor
|
68
|
-
conditions as if the conditions were normal code. For example:
|
69
|
-
|
70
|
-
```c
|
71
|
-
int
|
72
|
-
foo(void) {
|
73
|
-
#if 1
|
74
|
-
bar();
|
75
|
-
#else
|
76
|
-
baz();
|
77
|
-
#endif
|
78
|
-
}
|
79
|
-
```
|
80
|
-
|
81
|
-
Other than that, please just try to follow the existing style. We'll
|
82
|
-
add new rules here as the need arises.
|
83
|
-
|
84
|
-
## Commit Messages
|
85
|
-
|
86
|
-
Git commit messages should contain lines no longer than 72 characters.
|
87
|
-
The first line should always be a one-line summary of the commit, with
|
88
|
-
the relevant component followed by a colon and a space (if
|
89
|
-
applicable), then the summary.
|
90
|
-
|
91
|
-
If the one-line summary is insufficient to fully describe the changes
|
92
|
-
further descriptive paragraphs should be added, separated by blank
|
93
|
-
lines.
|
94
|
-
|
95
|
-
For example:
|
96
|
-
|
97
|
-
```
|
98
|
-
sse: add magical code to make everything go fast
|
99
|
-
|
100
|
-
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Curabitur
|
101
|
-
interdum scelerisque risus non ultricies. Vivamus id tristique mauris.
|
102
|
-
Mauris et augue vel urna aliquam posuere. Morbi in sem nec ante
|
103
|
-
ullamcorper ultrices in quis nibh. In felis velit, semper a mauris sed,
|
104
|
-
congue ullamcorper enim. Vestibulum ante ipsum primis in faucibus orci
|
105
|
-
luctus et ultrices posuere cubilia Curae; Nulla facilisi. Donec
|
106
|
-
scelerisque elit dui, et aliquet magna tincidunt eu.
|
107
|
-
|
108
|
-
Curabitur rhoncus lacus ac elit pulvinar, quis posuere ante ultrices.
|
109
|
-
Suspendisse at mauris vitae justo pretium tempor et in mauris. Nunc
|
110
|
-
facilisis nulla a ante tincidunt, imperdiet rhoncus metus interdum.
|
111
|
-
Vivamus sed nunc vel tellus porta consequat. Donec quis porttitor elit,
|
112
|
-
et cursus urna. Donec et sapien lorem. In imperdiet magna at aliquet
|
113
|
-
hendrerit.
|
114
|
-
```
|
@@ -1,20 +0,0 @@
|
|
1
|
-
Copyright (c) 2017 Evan Nemerson <evan@nemerson.com>
|
2
|
-
|
3
|
-
Permission is hereby granted, free of charge, to any person obtaining
|
4
|
-
a copy of this software and associated documentation files (the
|
5
|
-
"Software"), to deal in the Software without restriction, including
|
6
|
-
without limitation the rights to use, copy, modify, merge, publish,
|
7
|
-
distribute, sublicense, and/or sell copies of the Software, and to
|
8
|
-
permit persons to whom the Software is furnished to do so, subject to
|
9
|
-
the following conditions:
|
10
|
-
|
11
|
-
The above copyright notice and this permission notice shall be
|
12
|
-
included in all copies or substantial portions of the Software.
|
13
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-
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14
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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15
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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16
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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17
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NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
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18
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LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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19
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OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
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20
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WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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